[devel] I: итоги NMU по добавлению BR: texinfo

[devel] I: итоги NMU по добавлению BR: texinfo

[Igor Vlasenko]

Уважаемые коллеги,
по итогам транзакции по добавлению BR: texinfo
1) из 64 пакетов которым нужно было добавить BR: texinfo
и на которые у меня не было acl, осталось 49 пакетов.

из них большинство принадлежит Дмитрию или же ldv входит в acl.
остались следующие 15 пакетов:
cat makeinfocurrent.txt \
| altlinux-acl-filter-list-by-access -n -u viy | \
| altlinux-acl-filter-list-by-access -n -u ldv | \
altlinux-acl-filter-list-append-acl

avrdude week sin
cgdb    legion
ddd     oddity
emacspeak       msp
freehdl mithraen
gengetopt       aris
isight-firmware-tools   icesik
libisoburn      amike sem boyarsh mike
libmicrohttpd   sbolshakov
make-initrd     legion
ne      legion
ocrad   oddity
speech-dispatcher       msp manowar
uucp    sbolshakov
which   george

далее, 31 пакет, которые тоже нуждаются в NMU
но сломаны и я их сходу не смог починить:

a2ps	george @everybody
aalib	ldv @everybody
bashdb	lav legion @qa
cilk	real @everybody
emacs-chess	@emacs
emacs-mode-auctex	partizan kirill @emacs
fbgetty	force @everybody
fftw	@nobody
geda-gaf	lav @everybody
gforth	george @everybody
glib	ldv @everybody
gri	real @qa @everybody
gsasl	alexsid @qa @everybody
guile18	inger voins @qa @everybody
libassuan0	zerg @everybody
libccrtp	sbolshakov lav @qa zerg
libnetcdff5-mpi	real @everybody
libnetcdff5-seq	real @everybody
libretto	real @everybody
mydns	valintinr @everybody
nasm	force @everybody
octave	manowar @everybody
R-base	kirill ldv @everybody
sawfish	vsu @everybody
serveez	@nobody
slepc4py-real	real sin @python @qa @everybody
tamu_anova	real @everybody
ucblogo	george @everybody
ulog-acctd	enp @qa
xboard	inger @qa @everybody
zsh	george @qa



-- 

I V

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Michael Shigorin]

On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:
> avrdude week sin

Видимо, add @qa

> libisoburn      amike sem boyarsh mike

Сделал (NB: xorriso стоит обновлять аккуратно и с проверками).

> make-initrd     legion

Там недостаточно добавить BR: texinfo (не makeinfo, т.к. бранчи):

---
make-initrd.texi:275: warning: @anchor should not appear in @unnumberedsubsec
make-initrd.texi:123: raising the section level of @unnumberedsubsec which is too low
make-initrd.texi:269: raising the section level of @unnumberedsubsec which is too low
make-initrd.texi:100: warning: node next `Configuration' in menu `Index' and in sectioning `Variables' differ
make-initrd.texi:283: warning: node prev `Index' in menu `Configuration' and in sectioning `Goals' differ
make: *** [make-initrd.info] Error 1
---

> xboard	inger @qa @everybody

Последнее время им тоже занимался...

-- 
 ---- WBR, Michael Shigorin / http://altlinux.org
  ------ http://opennet.ru / http://anna-news.info

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Sergey V Turchin]

On Wednesday 09 December 2015 19:43:25 MSK Igor Vlasenko wrote:

[...]
> libassuan0	zerg @everybody
Более не нужен. Удяляю.

[...]

-- 
Regards, Sergey.       ALT Linux, http://www.altlinux.ru/

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Kirill Maslinsky]

On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:
> Уважаемые коллеги,
> по итогам транзакции по добавлению BR: texinfo
> 1) из 64 пакетов которым нужно было добавить BR: texinfo
> и на которые у меня не было acl, осталось 49 пакетов.

[...]

> далее, 31 пакет, которые тоже нуждаются в NMU
> но сломаны и я их сходу не смог починить:
> 
> R-base	kirill ldv @everybody

А что именно в нем сломано? Я могу его обновить и попробовать починить,
но пока не понимаю суть проблемы.

-- 
KM

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Gleb Fotengauer-Malinovskiy]

On Fri, Dec 11, 2015 at 02:45:09PM +0300, Kirill Maslinsky wrote:
> On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:
> > Уважаемые коллеги,
> > по итогам транзакции по добавлению BR: texinfo
> > 1) из 64 пакетов которым нужно было добавить BR: texinfo
> > и на которые у меня не было acl, осталось 49 пакетов.
> 
> [...]
> 
> > далее, 31 пакет, которые тоже нуждаются в NMU
> > но сломаны и я их сходу не смог починить:
> > 
> > R-base	kirill ldv @everybody
> 
> А что именно в нем сломано? Я могу его обновить и попробовать починить,
> но пока не понимаю суть проблемы.

/beehive/logs/Sisyphus-x86_64/latest/error/R-base-3.1.2-alt1:
> 'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
> file R-lang.html will be missing

Добавить зависимость на makeinfo.

-- 
glebfm

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Dmitry V. Levin]

[-- Attachment #1: Type: text/plain, Size: 1309 bytes --]

On Fri, Dec 11, 2015 at 03:33:56PM +0300, Gleb Fotengauer-Malinovskiy wrote:
> On Fri, Dec 11, 2015 at 02:45:09PM +0300, Kirill Maslinsky wrote:
> > On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:
> > > Уважаемые коллеги,
> > > по итогам транзакции по добавлению BR: texinfo
> > > 1) из 64 пакетов которым нужно было добавить BR: texinfo
> > > и на которые у меня не было acl, осталось 49 пакетов.
> > 
> > [...]
> > 
> > > далее, 31 пакет, которые тоже нуждаются в NMU
> > > но сломаны и я их сходу не смог починить:
> > > 
> > > R-base	kirill ldv @everybody
> > 
> > А что именно в нем сломано? Я могу его обновить и попробовать починить,
> > но пока не понимаю суть проблемы.
> 
> /beehive/logs/Sisyphus-x86_64/latest/error/R-base-3.1.2-alt1:
> > 'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
> > file R-lang.html will be missing
> 
> Добавить зависимость на makeinfo.

Добавить зависимость на makeinfo И texi2dvi И починить сборку
документации.  После добавления makeinfo и texi2dvi в сборочную среду
возникают ошибки вида

ERROR: 'makeinfo' v4.7 or later needed but missing on your system.
make[2]: *** [R-FAQ.info] Error 1
File not found by glob: /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/*.html


-- 
ldv

[-- Attachment #2: Type: application/pgp-signature, Size: 819 bytes --]

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Igor Vlasenko]

[-- Attachment #1: Type: text/plain, Size: 1056 bytes --]

прикладываю лог неудавшейся сборки
(в спеке добавлено BR: texinfo)

2015-12-11 13:45 GMT+02:00 Kirill Maslinsky <kirill@altlinux.org>:
> On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:
>> Уважаемые коллеги,
>> по итогам транзакции по добавлению BR: texinfo
>> 1) из 64 пакетов которым нужно было добавить BR: texinfo
>> и на которые у меня не было acl, осталось 49 пакетов.
>
> [...]
>
>> далее, 31 пакет, которые тоже нуждаются в NMU
>> но сломаны и я их сходу не смог починить:
>>
>> R-base        kirill ldv @everybody
>
> А что именно в нем сломано? Я могу его обновить и попробовать починить,
> но пока не понимаю суть проблемы.
>
> --
> KM



-- 
С уважением,
Игорь Власенко.

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: R-base.log --]
[-- Type: text/x-log; charset=US-ASCII; name="R-base.log", Size: 2529583 bytes --]

~/src/repo/foreign/MAKEINFONMU/OUT.gits/R-base.git ~/src/repo/foreign/MAKEINFONMU
gear --hasher -- hsh --apt-config=/etc/apt/apt.conf.SS --with-stuff --mountpoints=/proc --packager=Igor Vlasenko <viy@altlinux.ru> --number 2 /tmp/.private/igor/hasher2
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
debug:hsh-mkchroot:gid1=517 517:517=ugid1
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
<86>Dec 11 12:22:04 userdel[17466]: delete user 'rooter'
<86>Dec 11 12:22:04 userdel[17466]: removed group 'rooter' owned by 'rooter'
<86>Dec 11 12:22:04 userdel[17466]: removed shadow group 'rooter' owned by 'rooter'
<86>Dec 11 12:22:04 groupadd[17471]: group added to /etc/group: name=rooter, GID=517
<86>Dec 11 12:22:04 groupadd[17471]: group added to /etc/gshadow: name=rooter
<86>Dec 11 12:22:04 groupadd[17471]: new group: name=rooter, GID=517
<86>Dec 11 12:22:04 useradd[17475]: new user: name=rooter, UID=517, GID=517, home=/root, shell=/bin/bash
<86>Dec 11 12:22:04 userdel[17481]: delete user 'builder'
<86>Dec 11 12:22:04 userdel[17481]: removed group 'builder' owned by 'builder'
<86>Dec 11 12:22:04 userdel[17481]: removed shadow group 'builder' owned by 'builder'
<86>Dec 11 12:22:04 groupadd[17486]: group added to /etc/group: name=builder, GID=518
<86>Dec 11 12:22:04 groupadd[17486]: group added to /etc/gshadow: name=builder
<86>Dec 11 12:22:04 groupadd[17486]: new group: name=builder, GID=518
<86>Dec 11 12:22:04 useradd[17490]: new user: name=builder, UID=518, GID=518, home=/usr/src, shell=/bin/bash
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
warning: Macro %add_tcl_lib_path not found
deduce_number_from_directory: dir=/tmp/.private/igor/hasher2/chroot gid=517
<13>Dec 11 12:22:14 rpmi: tex-common-0.2-alt4 1244804096 installed
<13>Dec 11 12:22:14 rpmi: texlive-common-0.1-alt3 1244804816 installed
<13>Dec 11 12:22:14 rpmi: xorg-xproto-devel-7.0.28-alt1 1448272470 installed
<13>Dec 11 12:22:14 rpmi: libjpeg-2:1.3.1-alt0.1 1388074033 installed
<13>Dec 11 12:22:14 rpmi: perl-Encode-2.78-alt1.1 1448469971 installed
<13>Dec 11 12:22:14 rpmi: libpng15-1.5.25-alt1 1449329557 installed
<13>Dec 11 12:22:14 rpmi: libtiff5-4.0.3-alt1 1348347498 installed
<13>Dec 11 12:22:14 rpmi: libpng12-1.2.50-alt2 1347753407 installed
<13>Dec 11 12:22:14 rpmi: libexpat-2.1.0-alt1 1347469765 installed
<13>Dec 11 12:22:14 rpmi: libICE-1.0.9-alt1 1409902719 installed
<13>Dec 11 12:22:14 rpmi: libSM-1.2.2-alt1 1391072686 installed
<13>Dec 11 12:22:14 rpmi: perl-Term-ANSIColor-4.04-alt1 1449507765 installed
<13>Dec 11 12:22:14 rpmi: rpm-macros-info-install-6.0-alt2 1449157524 installed
<13>Dec 11 12:22:14 rpmi: libtcl-8.5.9-alt2 1351878901 installed
<13>Dec 11 12:22:14 rpmi: tcl-8.5.9-alt2 1351878901 installed
<13>Dec 11 12:22:14 rpmi: liblcms2-2.7-alt1 1428681013 installed
<13>Dec 11 12:22:14 rpmi: libopenblas-0.2.14-alt1.git20150324 1433158855 installed
<13>Dec 11 12:22:14 rpmi: zlib-devel-1.2.8-alt1 1371079009 installed
<13>Dec 11 12:22:14 rpmi: libwayland-client-1.9.0-alt1 1442913481 installed
<13>Dec 11 12:22:14 rpmi: libXau-1.0.8-alt1 1369565807 installed
<13>Dec 11 12:22:14 rpmi: libnspr-1:4.10.10-alt1 1447166548 installed
<13>Dec 11 12:22:14 rpmi: libkpathsea-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:14 rpmi: libquadmath0-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:14 rpmi: libgfortran3-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:14 rpmi: libgdbm-1.8.3-alt9 1297723357 installed
<13>Dec 11 12:22:15 rpmi: ca-certificates-2015.08.04-alt1 1441020102 installed
<13>Dec 11 12:22:15 rpmi: libcrypto10-1.0.1k-alt4 1436449862 installed
<13>Dec 11 12:22:15 rpmi: libssh2-1.4.3-alt2 1448445217 installed
<13>Dec 11 12:22:15 rpmi: perl-DBM-1:5.22.0-alt2 1448833096 installed
<13>Dec 11 12:22:15 rpmi: libquadmath5-devel-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:15 rpmi: libXau-devel-1.0.8-alt1 1369565807 installed
<13>Dec 11 12:22:15 rpmi: libpng-devel-1.5.25-alt1 1449329557 installed
<13>Dec 11 12:22:15 rpmi: libopenblas-devel-0.2.14-alt1.git20150324 1433158855 installed
<13>Dec 11 12:22:15 rpmi: texi2dvi-6.0-alt2 1449157524 installed
<13>Dec 11 12:22:15 rpmi: libICE-devel-1.0.9-alt1 1409902719 installed
<13>Dec 11 12:22:15 rpmi: libSM-devel-1.2.2-alt1 1391072686 installed
<13>Dec 11 12:22:15 rpmi: perl-libintl-1.24-alt1.1 1448485129 installed
<13>Dec 11 12:22:15 rpmi: libjasper-1.900.1-alt3 1391718482 installed
<13>Dec 11 12:22:15 rpmi: fonts-type1-tipa-tex-1.3-alt4 1246545601 installed
<13>Dec 11 12:22:15 rpmi: texlive-doc-base-2008.0-alt0.10 1238420746 installed
<13>Dec 11 12:22:15 rpmi: texmf-tex4ht-1.0.2009_06_11_1038-alt1 1328304130 installed
<13>Dec 11 12:22:15 rpmi: tcsh-6.18.01-alt2 1442313244 installed
<13>Dec 11 12:22:15 rpmi: t1lib-5.1.2-alt5 1326979643 installed
<13>Dec 11 12:22:15 rpmi: rpm-build-tcl-0.4-alt2 1445508295 installed
<13>Dec 11 12:22:15 rpmi: tcl-devel-8.5.9-alt2 1351878901 installed
<13>Dec 11 12:22:15 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed
<13>Dec 11 12:22:15 rpmi: perl-Unicode-EastAsianWidth-1.33-alt1 1383358357 installed
<13>Dec 11 12:22:15 rpmi: perl-Text-Unidecode-1.27-alt1 1445859908 installed
<13>Dec 11 12:22:15 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed
<13>Dec 11 12:22:15 rpmi: perl-Pod-Simple-3.32-alt1 1447205413 installed
<13>Dec 11 12:22:15 rpmi: libruby-2.0.0-alt10 1404231146 installed
<13>Dec 11 12:22:15 rpmi: ruby-2.0.0-alt10 1404231146 installed
<13>Dec 11 12:22:16 rpmi: poppler-data-0.4.7-alt1 1415971818 installed
<13>Dec 11 12:22:16 rpmi: libpcre16-8.38-alt1 1448366677 installed
<13>Dec 11 12:22:16 rpmi: pcretest-8.38-alt1 1448366677 installed
<13>Dec 11 12:22:16 rpmi: libopenjpeg-1.3-alt1.3 1349374484 installed
<13>Dec 11 12:22:16 rpmi: libxblas-1.0.248-alt1 1322010716 installed
<13>Dec 11 12:22:16 rpmi: liblapack-1:3.5.0-alt1 1401382194 installed
<13>Dec 11 12:22:16 rpmi: libdatrie-0.2.8-alt1_5 1410185969 installed
<13>Dec 11 12:22:16 rpmi: libthai-0.1.21-alt1_1 1410187251 installed
<13>Dec 11 12:22:16 rpmi: libidn-1.28-alt1 1374528190 installed
<13>Dec 11 12:22:16 rpmi: libpixman-3:0.32.8-alt1 1447610691 installed
<13>Dec 11 12:22:16 rpmi: xorg-renderproto-devel-0.11.1-alt3 1303465056 installed
<13>Dec 11 12:22:16 rpmi: xorg-xextproto-devel-2:7.3.0-alt1 1389258977 installed
<13>Dec 11 12:22:16 rpmi: xorg-kbproto-devel-1.0.6-alt1 1332531883 installed
<13>Dec 11 12:22:16 rpmi: libwayland-server-1.9.0-alt1 1442913481 installed
<13>Dec 11 12:22:16 rpmi: libxshmfence-1.2-alt1 1420972191 installed
<13>Dec 11 12:22:16 rpmi: libpciaccess-1:0.13.4-alt1 1431681688 installed
<13>Dec 11 12:22:16 rpmi: libdrm-1:2.4.63-alt1 1439650113 installed
<13>Dec 11 12:22:16 rpmi: libgbm-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:16 rpmi: libX11-locales-3:1.6.3-alt1 1431956885 installed
<13>Dec 11 12:22:16 rpmi: libXdmcp-1.1.1-alt1 1334617699 installed
<13>Dec 11 12:22:16 rpmi: libxcb-1.11-alt1 1409047934 installed
<13>Dec 11 12:22:16 rpmi: libX11-3:1.6.3-alt1 1431956911 installed
<13>Dec 11 12:22:16 rpmi: libXext-1.3.3-alt1 1409902932 installed
<13>Dec 11 12:22:16 rpmi: libXt-1.1.4-alt1 1369984716 installed
<13>Dec 11 12:22:16 rpmi: libXrender-0.9.8-alt1 1371312110 installed
<13>Dec 11 12:22:16 rpmi: libXmu-1.1.2-alt1 1391072528 installed
<13>Dec 11 12:22:16 rpmi: libXpm-3.5.11-alt1 1391072398 installed
<13>Dec 11 12:22:17 rpmi: libxcb-devel-1.11-alt1 1409047934 installed
<13>Dec 11 12:22:17 rpmi: libX11-devel-3:1.6.3-alt1 1431956911 installed
<13>Dec 11 12:22:17 rpmi: libXrender-devel-0.9.8-alt1 1371312110 installed
<13>Dec 11 12:22:17 rpmi: libXext-devel-1.3.3-alt1 1409902932 installed
<13>Dec 11 12:22:17 rpmi: libXt-devel-1.1.4-alt1 1369984716 installed
<13>Dec 11 12:22:17 rpmi: libXaw-1.0.12-alt1 1391072621 installed
<13>Dec 11 12:22:17 rpmi: libXxf86vm-1.1.3-alt1 1369984824 installed
<13>Dec 11 12:22:17 rpmi: libXdamage-1.1.3-alt4 1297162596 installed
<13>Dec 11 12:22:17 rpmi: libXfixes-5.0.1-alt1 1369809606 installed
<13>Dec 11 12:22:17 rpmi: libGL-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:17 rpmi: libEGL-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:17 rpmi: libEGL-devel-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:17 rpmi: libGL-devel-4:11.0.6-alt1 1448452293 installed
<13>Dec 11 12:22:17 rpmi: mailx-8.1.2-alt7 1366314831 installed
<13>Dec 11 12:22:17 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed
<13>Dec 11 12:22:17 rpmi: libsqlite3-3.8.10.2-alt1 1432747242 installed
<13>Dec 11 12:22:17 rpmi: libnss-3.20.1-alt1 1447166823 installed
<13>Dec 11 12:22:17 rpmi: nss-utils-3.20.1-alt1 1447166823 installed
<13>Dec 11 12:22:17 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed
<13>Dec 11 12:22:17 rpmi: libjbig-2.1-alt1 1401380921 installed
<13>Dec 11 12:22:17 rpmi: xorg-rgb-1.0.4-alt1.qa1 1366268675 installed
<13>Dec 11 12:22:17 rpmi: libnetpbm-10.35.97-alt1 1447854203 installed
<13>Dec 11 12:22:17 rpmi: netpbm-10.35.97-alt1 1447854203 installed
<13>Dec 11 12:22:18 rpmi: libicu50-1:5.1.1-alt3 1368393235 installed
<13>Dec 11 12:22:18 rpmi: icu-utils-1:5.1.1-alt3 1368393235 installed
<13>Dec 11 12:22:18 rpmi: xml-utils-1:2.9.3-alt1 1448028556 installed
<13>Dec 11 12:22:18 rpmi: rpm-build-gir-0.7.2-alt2 1390711550 installed
<13>Dec 11 12:22:18 rpmi: libpaper-1.1.24-alt4 1315383473 installed
<13>Dec 11 12:22:18 rpmi: liblz4-r131-alt1 1447866717 installed
<13>Dec 11 12:22:18 rpmi: libgpg-error-1.20-alt1.1 1449204243 installed
<13>Dec 11 12:22:18 rpmi: libgcrypt20-1.6.4-alt1.1 1449202893 installed
<13>Dec 11 12:22:18 rpmi: libsystemd-1:228-alt2 1449588193 installed
<13>Dec 11 12:22:18 rpmi: libdbus-1.10.6-alt1 1449475477 installed
<13>Dec 11 12:22:18 rpmi: libavahi-0.6.31-alt6 1447371819 installed
<13>Dec 11 12:22:18 rpmi: gcc-fortran-common-1.4.20-alt1 1432315196 installed
<13>Dec 11 12:22:18 rpmi: libgfortran5-devel-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:18 rpmi: gcc-c++-common-1.4.20-alt1 1432315196 installed
<13>Dec 11 12:22:18 rpmi: libstdc++5-devel-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:18 rpmi: libgraphite2-1.2.4-alt1 1393325247 installed
<13>Dec 11 12:22:18 rpmi: libtinfo-devel-5.9-alt7 1442415999 installed
<13>Dec 11 12:22:18 rpmi: libncurses-devel-5.9-alt7 1442415999 installed
<13>Dec 11 12:22:18 rpmi: python-modules-curses-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:18 rpmi: libverto-0.2.6-alt1_5 1442994337 installed
<13>Dec 11 12:22:18 rpmi: libkeyutils-1.5.9-alt1 1398435624 installed
<13>Dec 11 12:22:18 rpmi: libcom_err-1.42.13-alt2 1449075846 installed
<13>Dec 11 12:22:19 rpmi: gcc5-c++-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:19 rpmi: gcc5-fortran-5.2.1-alt1 1440730975 installed
<13>Dec 11 12:22:19 rpmi: libicu-devel-1:5.1.1-alt3 1368393235 installed
<13>Dec 11 12:22:19 rpmi: libXmu-devel-1.1.2-alt1 1391072528 installed
<13>Dec 11 12:22:19 rpmi: liblapack-devel-1:3.5.0-alt1 1401382194 installed
<13>Dec 11 12:22:19 rpmi: libpcre-devel-8.38-alt1 1448366677 installed
<13>Dec 11 12:22:19 rpmi: libtiff-devel-4.0.3-alt1 1348347498 installed
<13>Dec 11 12:22:19 rpmi: libjpeg-devel-2:1.3.1-alt0.1 1388074033 installed
<13>Dec 11 12:22:19 rpmi: libreadline-devel-6.3.8-alt1 1418911064 installed
<13>Dec 11 12:22:19 rpmi: bzlib-devel-1:1.0.6-alt4 1449156902 installed
<13>Dec 11 12:22:19 rpmi: liblzma-devel-5.0.7-alt1 1416090478 installed
<13>Dec 11 12:22:20 rpmi: texlive-base-bin-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:21 rpmi: texlive-base-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:22 rpmi: texlive-latex-base-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:22 rpmi: texlive-font-utils-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:22 rpmi: perl-Pod-Usage-1.67-alt2 1445108310 installed
<13>Dec 11 12:22:23 rpmi: libssl10-1.0.1k-alt4 1436449862 installed
<13>Dec 11 12:22:23 rpmi: perl-Unicode-Normalize-1:5.22.0-alt2 1448833096 installed
<13>Dec 11 12:22:23 rpmi: libharfbuzz-1.1.1-alt1 1448577010 installed
<13>Dec 11 12:22:23 rpmi: libfreetype-2.6-alt1 1433953073 installed
<13>Dec 11 12:22:23 rpmi: fontconfig-2.11.1-alt4 1447161344 installed
Updating fonts cache: <29>Dec 11 12:22:24 fontconfig: Updating fonts cache: succeeded
[ DONE ]
<13>Dec 11 12:22:24 rpmi: libXft-2.3.2-alt1 1409902650 installed
<13>Dec 11 12:22:24 rpmi: libfreetype-devel-2.6-alt1 1433953073 installed
<13>Dec 11 12:22:24 rpmi: fontconfig-devel-2.11.1-alt4 1447161344 installed
<13>Dec 11 12:22:24 rpmi: libcairo-1:1.14.4-alt1 1447005495 installed
<13>Dec 11 12:22:24 rpmi: libkrb5-1.13.2-alt2 1447670694 installed
<13>Dec 11 12:22:24 rpmi: libcups-2.1.0-alt1 1447854832 installed
<13>Dec 11 12:22:24 rpmi: libgs-9.16-alt1 1444660003 installed
<13>Dec 11 12:22:24 rpmi: libcairo-devel-1:1.14.4-alt1 1447005495 installed
<13>Dec 11 12:22:24 rpmi: libpango-1.38.1-alt1 1444685285 installed
<13>Dec 11 12:22:24 rpmi: libXft-devel-2.3.2-alt1 1409902650 installed
<13>Dec 11 12:22:24 rpmi: libtk-8.5.9-alt3 1308047279 installed
<13>Dec 11 12:22:24 rpmi: tk-8.5.9-alt3 1308047279 installed
<13>Dec 11 12:22:24 rpmi: perl-Tk-804.033-alt1.1 1448484960 installed
<13>Dec 11 12:22:24 rpmi: fonts-type1-urw-3:1.0.7pre44-alt2 1419342366 installed
<13>Dec 11 12:22:25 rpmi: makeinfo-6.0-alt2 1449157524 installed
<13>Dec 11 12:22:25 rpmi: libcurl-7.46.0-alt1 1449521272 installed
<13>Dec 11 12:22:25 rpmi: libpoppler57-0.38.0-alt1 1449158942 installed
<13>Dec 11 12:22:25 rpmi: poppler-0.38.0-alt1 1449158942 installed
<13>Dec 11 12:22:25 rpmi: texlive-latex3-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:25 rpmi: texlive-lang-tibetan-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:25 rpmi: texlive-lang-polish-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:25 rpmi: texmf-latex-tipa-1.3-alt4 1246545601 installed
<13>Dec 11 12:22:25 rpmi: texlive-generic-extra-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:25 rpmi: perl-podlators-4.03-alt1 1449507577 installed
<13>Dec 11 12:22:25 rpmi: perl-unicore-1:5.22.0-alt2 1448833189 installed
<13>Dec 11 12:22:25 rpmi: texinfo-6.0-alt2 1449157516 installed
<13>Dec 11 12:22:25 rpmi: tk-devel-8.5.9-alt3 1308047279 installed
<13>Dec 11 12:22:25 rpmi: python-modules-compiler-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: ghostscript-common-9.16-alt1 1444660041 installed
<13>Dec 11 12:22:26 rpmi: ghostscript-classic-9.16-alt1 1444660003 installed
<13>Dec 11 12:22:26 rpmi: latex2html-2008-alt1 1244296992 installed
<13>Dec 11 12:22:26 rpmi: python-modules-email-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-unittest-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-xml-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-encodings-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-hotshot-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-bsddb-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-ctypes-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-multiprocessing-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-modules-logging-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: python-dev-2.7.10-alt1 1447441053 installed
<13>Dec 11 12:22:26 rpmi: glib2-devel-2.46.2-alt1 1446853786 installed
<13>Dec 11 12:22:26 rpmi: libpango-devel-1.38.1-alt1 1444685285 installed
<13>Dec 11 12:22:29 rpmi: texlive-fonts-recommended-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:36 rpmi: texlive-latex-recommended-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:36 rpmi: texlive-generic-recommended-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:36 rpmi: texlive-math-extra-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:36 rpmi: texlive-lang-french-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:37 rpmi: texlive-extra-utils-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:37 rpmi: texlive-lang-german-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:37 rpmi: texlive-lang-cyrillic-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:37 rpmi: texmf-latex-xcolor-2.06-alt3 1244802289 installed
<13>Dec 11 12:22:38 rpmi: texmf-pgf-3.0.1-alt1 1439012888 installed
<13>Dec 11 12:22:43 rpmi: texlive-fonts-extra-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:50 rpmi: texlive-pstricks-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:50 rpmi: texlive-games-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:50 rpmi: texmf-latex-obsolete-0.1-alt1 1244748792 installed
<13>Dec 11 12:22:51 rpmi: texlive-lang-arab-2008.0-alt0.14 1248958512 installed
<13>Dec 11 12:22:51 rpmi: texlive-xetex-2008.0-alt0.15.6 1449446882 installed
<13>Dec 11 12:22:51 rpmi: texmf-latex-beamer-3.36-alt3 1445751824 installed
<13>Dec 11 12:22:53 rpmi: texlive-publishers-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:53 rpmi: texlive-pictures-2008.0-alt0.15 1300007455 installed
<13>Dec 11 12:22:54 rpmi: texlive-science-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:22:54 rpmi: texlive-humanities-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:23:00 rpmi: texlive-latex-extra-2008.0-alt0.16 1300008623 installed
<13>Dec 11 12:23:01 rpmi: texlive-bibtex-extra-2008.0-alt0.16 1300008623 installed
Building target platforms: x86_64
Building for target x86_64
Wrote: /usr/src/in/srpm/R-base-3.1.2-alt1.1.src.rpm
Installing R-base-3.1.2-alt1.1.src.rpm
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.13082
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ rm -rf R-3.1.2
+ echo 'Source #0 (R-3.1.2.tar):'
Source #0 (R-3.1.2.tar):
+ /bin/tar -xf /usr/src/RPM/SOURCES/R-3.1.2.tar
+ cd R-3.1.2
+ /bin/chmod -c -Rf u+rwX,go-w .
+ echo 'Patch #0 (R-3.1.2-alt1.1.patch):'
Patch #0 (R-3.1.2-alt1.1.patch):
+ /usr/bin/patch -p1
patching file .gear/rules
patching file .gear/tags/15fa18936deccebb8baa76357c7a902b06205ce0
patching file .gear/tags/a3506a8419eb2903e6d3ce37c465295a254fd1d5
patching file .gear/tags/c7dc0028771e7098f72fe8ac9e9575451d4fb020
patching file .gear/tags/list
patching file R-base.spec
patching file src/extra/blas/Makefile.in
patching file src/extra/bzip2/Makefile.in
patching file src/extra/pcre/Makefile.in
patching file src/extra/xdr/Makefile.in
patching file src/extra/zlib/Makefile.in
+ rm src/extra/zlib/adler32.c src/extra/zlib/compress.c src/extra/zlib/crc32.c src/extra/zlib/crc32.h src/extra/zlib/deflate.c src/extra/zlib/deflate.h src/extra/zlib/infback.c src/extra/zlib/inffast.c src/extra/zlib/inffast.h src/extra/zlib/inffixed.h src/extra/zlib/inflate.c src/extra/zlib/inflate.h src/extra/zlib/inftrees.c src/extra/zlib/inftrees.h src/extra/zlib/trees.c src/extra/zlib/trees.h src/extra/zlib/uncompr.c src/extra/zlib/zconf.h src/extra/zlib/zlib.h src/extra/zlib/zutil.c src/extra/zlib/zutil.h src/extra/bzip2/blocksort.c src/extra/bzip2/bzcompress.c src/extra/bzip2/bzlib.c src/extra/bzip2/bzlib.h src/extra/bzip2/bzlib_private.h src/extra/bzip2/crctable.c src/extra/bzip2/decompress.c src/extra/bzip2/huffman.c src/extra/bzip2/randtable.c src/extra/pcre/pcre.h src/extra/pcre/pcre_chartables.c src/extra/pcre/pcre_compile.c src/extra/pcre/pcre_config.c src/extra/pcre/pcre_exec.c src/extra/pcre/pcre_fullinfo.c src/extra/pcre/pcre_get.c src/extra/pcre/pcre_globals.c src/extra/pcre/pcre_internal.h src/extra/pcre/pcre_jit_compile.c src/extra/pcre/pcre_maketables.c src/extra/pcre/pcre_newline.c src/extra/pcre/pcre_ord2utf8.c src/extra/pcre/pcre_refcount.c src/extra/pcre/pcre_study.c src/extra/pcre/pcre_tables.c src/extra/pcre/pcre_ucd.c src/extra/pcre/pcre_valid_utf8.c src/extra/pcre/pcre_version.c src/extra/pcre/pcre_xclass.c src/extra/pcre/ucp.h
+ rm src/extra/xz/api/lzma.h src/extra/xz/check/check.c src/extra/xz/check/check.h src/extra/xz/check/crc32_fast.c src/extra/xz/check/crc32_small.c src/extra/xz/check/crc32_table.c src/extra/xz/check/crc32_table_be.h src/extra/xz/check/crc32_table_le.h src/extra/xz/check/crc32_tablegen.c src/extra/xz/check/crc64_fast.c src/extra/xz/check/crc64_small.c src/extra/xz/check/crc64_table.c src/extra/xz/check/crc64_table_be.h src/extra/xz/check/crc64_table_le.h src/extra/xz/check/crc64_tablegen.c src/extra/xz/check/crc_macros.h src/extra/xz/check/sha256.c src/extra/xz/common/alone_decoder.c src/extra/xz/common/alone_decoder.h src/extra/xz/common/alone_encoder.c src/extra/xz/common/auto_decoder.c src/extra/xz/common/block_buffer_decoder.c src/extra/xz/common/block_buffer_encoder.c src/extra/xz/common/block_decoder.c src/extra/xz/common/block_decoder.h src/extra/xz/common/block_encoder.c src/extra/xz/common/block_encoder.h src/extra/xz/common/block_header_decoder.c src/extra/xz/common/block_header_encoder.c src/extra/xz/common/block_util.c src/extra/xz/common/bsr.h src/extra/xz/common/bswap.h src/extra/xz/common/common.c src/extra/xz/common/common.h src/extra/xz/common/easy_buffer_encoder.c src/extra/xz/common/easy_decoder_memusage.c src/extra/xz/common/easy_encoder.c src/extra/xz/common/easy_encoder_memusage.c src/extra/xz/common/easy_preset.c src/extra/xz/common/easy_preset.h src/extra/xz/common/filter_buffer_decoder.c src/extra/xz/common/filter_buffer_encoder.c src/extra/xz/common/filter_common.c src/extra/xz/common/filter_common.h src/extra/xz/common/filter_decoder.c src/extra/xz/common/filter_decoder.h src/extra/xz/common/filter_encoder.c src/extra/xz/common/filter_encoder.h src/extra/xz/common/filter_flags_decoder.c src/extra/xz/common/filter_flags_encoder.c src/extra/xz/common/index.c src/extra/xz/common/index.h src/extra/xz/common/index_decoder.c src/extra/xz/common/index_encoder.c src/extra/xz/common/index_encoder.h src/extra/xz/common/index_hash.c src/extra/xz/common/local.h src/extra/xz/common/mythread.h src/extra/xz/common/stream_buffer_decoder.c src/extra/xz/common/stream_buffer_encoder.c src/extra/xz/common/stream_decoder.c src/extra/xz/common/stream_decoder.h src/extra/xz/common/stream_encoder.c src/extra/xz/common/stream_encoder.h src/extra/xz/common/stream_flags_common.c src/extra/xz/common/stream_flags_common.h src/extra/xz/common/stream_flags_decoder.c src/extra/xz/common/stream_flags_encoder.c src/extra/xz/common/sysdefs.h src/extra/xz/common/tuklib_common.h src/extra/xz/common/tuklib_config.h src/extra/xz/common/tuklib_integer.h src/extra/xz/common/vli_decoder.c src/extra/xz/common/vli_encoder.c src/extra/xz/common/vli_size.c src/extra/xz/delta/delta_common.c src/extra/xz/delta/delta_common.h src/extra/xz/delta/delta_decoder.c src/extra/xz/delta/delta_decoder.h src/extra/xz/delta/delta_encoder.c src/extra/xz/delta/delta_encoder.h src/extra/xz/delta/delta_private.h src/extra/xz/lz/lz_decoder.c src/extra/xz/lz/lz_decoder.h src/extra/xz/lz/lz_encoder.c src/extra/xz/lz/lz_encoder.h src/extra/xz/lz/lz_encoder_hash.h src/extra/xz/lz/lz_encoder_hash_table.h src/extra/xz/lz/lz_encoder_mf.c src/extra/xz/lzma/fastpos.h src/extra/xz/lzma/fastpos_table.c src/extra/xz/lzma/fastpos_tablegen.c src/extra/xz/lzma/lzma2_decoder.c src/extra/xz/lzma/lzma2_decoder.h src/extra/xz/lzma/lzma2_encoder.c src/extra/xz/lzma/lzma2_encoder.h src/extra/xz/lzma/lzma_common.h src/extra/xz/lzma/lzma_decoder.c src/extra/xz/lzma/lzma_decoder.h src/extra/xz/lzma/lzma_encoder.c src/extra/xz/lzma/lzma_encoder.h src/extra/xz/lzma/lzma_encoder_optimum_fast.c src/extra/xz/lzma/lzma_encoder_optimum_normal.c src/extra/xz/lzma/lzma_encoder_presets.c src/extra/xz/lzma/lzma_encoder_private.h src/extra/xz/rangecoder/price.h src/extra/xz/rangecoder/price_table.c src/extra/xz/rangecoder/price_tablegen.c src/extra/xz/rangecoder/range_common.h src/extra/xz/rangecoder/range_decoder.h src/extra/xz/rangecoder/range_encoder.h src/extra/xz/simple/arm.c src/extra/xz/simple/armthumb.c src/extra/xz/simple/ia64.c src/extra/xz/simple/powerpc.c src/extra/xz/simple/simple_coder.c src/extra/xz/simple/simple_coder.h src/extra/xz/simple/simple_decoder.c src/extra/xz/simple/simple_decoder.h src/extra/xz/simple/simple_encoder.c src/extra/xz/simple/simple_encoder.h src/extra/xz/simple/simple_private.h src/extra/xz/simple/sparc.c src/extra/xz/simple/x86.c
+ rm src/extra/blas/blas.f src/extra/blas/cmplxblas.f src/modules/lapack/cmplx.f src/modules/lapack/dlamch.f src/modules/lapack/dlapack.f src/modules/lapack/vecLibg95f.f
+ exit 0
Executing(%build): /bin/sh -e /usr/src/tmp/rpm-tmp.13082
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.1.2
+ export lt_cv_prog_cc_static_works=no ac_cv_path_R_ZIPCMD=zip ac_cv_path_R_UNZIPCMD=unzip ac_cv_path_R_BROWSER=firefox ac_cv_path_R_PDFVIEWER=evince 'ac_cv_path_PAGER=less -isR' ac_cv_prog_R_PRINTCMD=lpr
+ lt_cv_prog_cc_static_works=no
+ ac_cv_path_R_ZIPCMD=zip
+ ac_cv_path_R_UNZIPCMD=unzip
+ ac_cv_path_R_BROWSER=firefox
+ ac_cv_path_R_PDFVIEWER=evince
+ ac_cv_path_PAGER='less -isR'
+ ac_cv_prog_R_PRINTCMD=lpr
+ CFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing'
+ export CFLAGS
+ CXXFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing'
+ export CXXFLAGS
+ FFLAGS='-pipe -Wall -g -O2 -fno-strict-aliasing'
+ export FFLAGS
+ '[' -n '' ']'
++ printf %s '-pipe -Wall -g -O2 -fno-strict-aliasing'
++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g'
+ ASFLAGS=
+ export ASFLAGS
+ export lt_cv_deplibs_check_method=pass_all
+ lt_cv_deplibs_check_method=pass_all
+ readlink -e -- ./configure
+ xargs -ri dirname -- '{}'
+ xargs -ri find '{}' -type f '(' -name config.sub -or -name config.guess ')' -printf '%h/\n'
+ xargs -rn1 install -pm755 -- /usr/share/gnu-config/config.sub /usr/share/gnu-config/config.guess
+ sort -u
+ ./configure --build=x86_64-alt-linux --host=x86_64-alt-linux --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/lib --localstatedir=/var/lib --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-dependency-tracking --without-included-gettext --enable-prebuilt-html --enable-R-shlib --with-x --with-system-zlib --with-system-bzlib --with-system-pcre --with-system-xz --with-blas=openblas --with-lapack=lapack --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh '--libdir=${prefix}/lib64' 'rincludedir=${prefix}/include/R' 'rdocdir=${prefix}/share/doc/R-3.1'
configure: WARNING: unrecognized options: --disable-dependency-tracking
checking build system type... x86_64-alt-linux-gnu
checking host system type... x86_64-alt-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking for gawk... gawk
checking whether ln -s works... yes
checking for bison... bison -y
checking for ar... ar
checking for a BSD-compatible install... /bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... (cached) less -isR
checking for gtar... /usr/bin/gtar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for makeinfo... /usr/bin/makeinfo
checking whether makeinfo version is at least 4.7... no
checking for ginstall-info... no
checking for install-info... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... missing
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
checking for unzip... (cached) unzip
checking for zip... (cached) zip
checking for gzip... /bin/gzip
checking for bzip2... /bin/bzip2
checking for firefox... (cached) firefox
using default browser ... firefox
checking for acroread... (cached) evince
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-alt-linux-gcc accepts -g... yes
checking for x86_64-alt-linux-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether x86_64-alt-linux-gcc needs -traditional... no
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
checking for f95... f95
checking for x86_64-alt-linux-g77... (cached) f95
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether f95 accepts -g... yes
checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-alt-linux-g++ accepts -g... yes
checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether x86_64-alt-linux-gcc accepts -fvisibility... yes
checking whether f95 accepts -fvisibility... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether we are using the GNU Objective C compiler... no
checking whether x86_64-alt-linux-gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether x86_64-alt-linux-g++ can compile ObjC++... no
no working ObjC++ compiler found
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for x86_64-alt-linux-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... (cached) pass_all
checking for x86_64-alt-linux-ar... (cached) ar
checking for x86_64-alt-linux-strip... no
checking for strip... strip
checking for x86_64-alt-linux-ranlib... no
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from x86_64-alt-linux-gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether x86_64-alt-linux-g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E
checking for x86_64-alt-linux-g77... (cached) f95
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether f95 accepts -g... (cached) yes
checking for objdir... .libs
checking if x86_64-alt-linux-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-alt-linux-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-alt-linux-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-alt-linux-gcc static flag -static works... no
checking if x86_64-alt-linux-gcc supports -c -o file.o... yes
checking if x86_64-alt-linux-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by x86_64-alt-linux-g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for x86_64-alt-linux-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-alt-linux-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-alt-linux-g++ static flag -static works... no
checking if x86_64-alt-linux-g++ supports -c -o file.o... yes
checking if x86_64-alt-linux-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f95 option to produce PIC... -fPIC
checking if f95 PIC flag -fPIC works... yes
checking if f95 static flag -static works... no
checking if f95 supports -c -o file.o... yes
checking if f95 supports -c -o file.o... (cached) yes
checking whether the f95 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking whether rl_completion_matches exists and is declared... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking dl.h usability... no
checking dl.h presence... no
checking for dl.h... no
checking for dlfcn.h... (cached) yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking fpu_control.h usability... yes
checking fpu_control.h presence... yes
checking for fpu_control.h... yes
checking glob.h usability... yes
checking glob.h presence... yes
checking for glob.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for strings.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for x86_64-alt-linux-gcc option to accept ISO C99... none needed
checking for x86_64-alt-linux-gcc option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether x86_64-alt-linux-gcc supports -c -o FILE.lo... yes
checking for x86_64-alt-linux-gcc option to support OpenMP... unsupported
checking how to get verbose linking output from f95... -v
checking for Fortran 77 libraries of f95...  -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../.. -lgfortran -lm -lquadmath
checking how to get verbose linking output from x86_64-alt-linux-gcc... -v
checking for C libraries of x86_64-alt-linux-gcc...  -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/5/../../.. -lgcc_s
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking whether f95 appends underscores to external names... yes
checking whether f95 appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether f95 and x86_64-alt-linux-gcc agree on int and double... yes
checking whether f95 and x86_64-alt-linux-gcc agree on double complex... yes
checking for f95 option to support OpenMP... unsupported
checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes
checking for x86_64-alt-linux-g++ option to support OpenMP... unsupported
checking whether we can compute ObjC Make dependencies... no
checking for ObjC runtime library... 
checking whether x86_64-alt-linux-gcc accepts -fobjc-exceptions... no
checking whether C runtime needs -D__NO_MATH_INLINES... no
checking for xmkmf... no
checking whether x86_64-alt-linux-g++  supports C++11 features by default... no
checking whether x86_64-alt-linux-g++  supports C++11 features with -std=c++11... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log1pl exists and is declared... yes
checking whether log2 exists and is declared... yes
checking whether log10 exists and is declared... yes
checking whether nearbyint exists and is declared... yes
checking whether nearbyintl exists and is declared... yes
checking whether powl exists and is declared... yes
checking whether rint exists and is declared... yes
checking whether rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
checking sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking for cospi in -lsunmath... no
checking for atanpi... no
checking for atan2pi... no
checking for cospi... no
checking for exp10... yes
checking for pown... no
checking for sinpi... no
checking for tanpi... no
checking for fseeko... yes
checking for ftello... yes
checking for matherr... yes
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
checking whether gmtime_r exists and is declared... yes
checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... yes
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... yes
checking for realpath... yes
checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for __setfpucw... no
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... yes
checking whether mktime works correctly outside 1902-2037... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for cblas_cdotu_sub in Accelerate framework... no
checking for dgemm_ in -lopenblas... yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
checking for dpstrf_... no
checking for dpstrf_ in -llapack... yes
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking for iconvlist... no
checking for iconv... yes
checking for iconv declaration... 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... yes
checking wctype.h presence... yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether iswblank exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking X11/Xmu/Atoms.h usability... yes
checking X11/Xmu/Atoms.h presence... yes
checking for X11/Xmu/Atoms.h... yes
checking for XmuInternAtom in -lXmu... yes
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for /usr/lib64/tclConfig.sh... /usr/lib64/tclConfig.sh
checking for /usr/lib64/tkConfig.sh... /usr/lib64/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking for main in -lz... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support needs to be compiled... no
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support needs to be compiled... no
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
checking for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... no
checking pcre.h presence... no
checking for pcre.h... no
checking pcre/pcre.h usability... yes
checking pcre/pcre.h presence... yes
checking for pcre/pcre.h... yes
checking if PCRE version >= 8.10... yes
checking whether PCRE support needs to be compiled... no
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for sys/time.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
checking for lpr... (cached) lpr
checking for paperconf... /usr/bin/paperconf
checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether x86_64-alt-linux-gfortran accepts -g... yes
checking for x86_64-alt-linux-gfortran... (cached) x86_64-alt-linux-gfortran
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether x86_64-alt-linux-gfortran accepts -g... (cached) yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for x86_64-alt-linux-gfortran option to produce PIC... -fPIC
checking if x86_64-alt-linux-gfortran PIC flag -fPIC works... yes
checking if x86_64-alt-linux-gfortran static flag -static works... no
checking if x86_64-alt-linux-gfortran supports -c -o file.o... yes
checking if x86_64-alt-linux-gfortran supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-gfortran linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for x86_64-alt-linux-gfortran option to support OpenMP... unsupported
checking for recommended packages... yes
checking whether NLS is requested... yes

Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for x86_64-alt-linux-ranlib... ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking argz.h usability... yes
checking argz.h presence... yes
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached) 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... bison
checking version of bison... 3.0.4.0.14.8, ok
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for shared library run path origin... done
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... yes
checking whether to use NLS... yes
checking where the gettext function comes from... libc
Finished configuring src/extra/intl directory

using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
config.status: creating Makeconf
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/manual/Makefile
config.status: creating etc/Makefile
config.status: creating etc/Makeconf
config.status: creating etc/Renviron
config.status: creating etc/javaconf
config.status: creating etc/ldpaths
config.status: creating m4/Makefile
config.status: creating po/Makefile
config.status: creating share/Makefile
config.status: creating src/Makefile
config.status: creating src/appl/Makefile
config.status: creating src/extra/Makefile
config.status: creating src/extra/blas/Makefile
config.status: creating src/extra/bzip2/Makefile
config.status: creating src/extra/intl/Makefile
config.status: creating src/extra/pcre/Makefile
config.status: creating src/extra/tre/Makefile
config.status: creating src/extra/tzone/Makefile
config.status: creating src/extra/xdr/Makefile
config.status: creating src/extra/xz/Makefile
config.status: creating src/extra/zlib/Makefile
config.status: creating src/include/Makefile
config.status: creating src/include/Rmath.h0
config.status: creating src/include/R_ext/Makefile
config.status: creating src/library/Recommended/Makefile
config.status: creating src/library/Makefile
config.status: creating src/library/base/DESCRIPTION
config.status: creating src/library/base/Makefile
config.status: creating src/library/compiler/DESCRIPTION
config.status: creating src/library/compiler/Makefile
config.status: creating src/library/datasets/DESCRIPTION
config.status: creating src/library/datasets/Makefile
config.status: creating src/library/graphics/DESCRIPTION
config.status: creating src/library/graphics/Makefile
config.status: creating src/library/graphics/src/Makefile
config.status: creating src/library/grDevices/DESCRIPTION
config.status: creating src/library/grDevices/Makefile
config.status: creating src/library/grDevices/src/Makefile
config.status: creating src/library/grDevices/src/cairo/Makefile
config.status: creating src/library/grid/DESCRIPTION
config.status: creating src/library/grid/Makefile
config.status: creating src/library/grid/src/Makefile
config.status: creating src/library/methods/DESCRIPTION
config.status: creating src/library/methods/Makefile
config.status: creating src/library/methods/src/Makefile
config.status: creating src/library/parallel/DESCRIPTION
config.status: creating src/library/parallel/Makefile
config.status: creating src/library/parallel/src/Makefile
config.status: creating src/library/profile/Makefile
config.status: creating src/library/stats/DESCRIPTION
config.status: creating src/library/stats/Makefile
config.status: creating src/library/stats/src/Makefile
config.status: creating src/library/stats4/DESCRIPTION
config.status: creating src/library/stats4/Makefile
config.status: creating src/library/splines/DESCRIPTION
config.status: creating src/library/splines/Makefile
config.status: creating src/library/splines/src/Makefile
config.status: creating src/library/tcltk/DESCRIPTION
config.status: creating src/library/tcltk/Makefile
config.status: creating src/library/tcltk/src/Makefile
config.status: creating src/library/tools/DESCRIPTION
config.status: creating src/library/tools/Makefile
config.status: creating src/library/tools/src/Makefile
config.status: creating src/library/translations/DESCRIPTION
config.status: creating src/library/translations/Makefile
config.status: creating src/library/utils/DESCRIPTION
config.status: creating src/library/utils/Makefile
config.status: creating src/library/utils/src/Makefile
config.status: creating src/main/Makefile
config.status: creating src/modules/Makefile
config.status: creating src/modules/X11/Makefile
config.status: creating src/modules/internet/Makefile
config.status: creating src/modules/lapack/Makefile
config.status: creating src/modules/vfonts/Makefile
config.status: creating src/nmath/Makefile
config.status: creating src/nmath/standalone/Makefile
config.status: creating src/scripts/Makefile
config.status: creating src/scripts/R.sh
config.status: creating src/scripts/Rcmd
config.status: creating src/scripts/f77_f2c
config.status: creating src/scripts/javareconf
config.status: creating src/scripts/mkinstalldirs
config.status: creating src/scripts/pager
config.status: creating src/scripts/rtags
config.status: creating src/unix/Makefile
config.status: creating tests/Makefile
config.status: creating tests/Embedding/Makefile
config.status: creating tests/Examples/Makefile
config.status: creating tools/Makefile
config.status: creating src/include/config.h
config.status: executing libtool commands
config.status: executing stamp-h commands
configure: WARNING: unrecognized options: --disable-dependency-tracking

R is now configured for x86_64-alt-linux-gnu

  Source directory:          .
  Installation directory:    /usr

  C compiler:                x86_64-alt-linux-gcc  -pipe -Wall -g -O2 -fno-strict-aliasing
  Fortran 77 compiler:       f95  -pipe -Wall -g -O2 -fno-strict-aliasing

  C++ compiler:              x86_64-alt-linux-g++  -pipe -Wall -g -O2 -fno-strict-aliasing
  C++ 11 compiler:           x86_64-alt-linux-g++  -std=c++11 -pipe -Wall -g -O2 -fno-strict-aliasing
  Fortran 90/95 compiler:    x86_64-alt-linux-gfortran -g -O2
  Obj-C compiler:	     x86_64-alt-linux-gcc 

  Interfaces supported:      X11, tcltk
  External libraries:        readline, BLAS(OpenBLAS), LAPACK(generic), lzma
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:           shared R library, R profiling, static HTML

  Capabilities skipped:      
  Options not enabled:       shared BLAS, memory profiling

  Recommended packages:      yes

configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
+ '[' -n '' ']'
+ NPROCS=4
+ make -j4
make: Entering directory `/usr/src/RPM/BUILD/R-3.1.2'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/m4'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/m4'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tools'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tools'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[2]: Nothing to be done for `R'.
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/etc'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/etc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/share'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/share'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/include'
mkdir -p -- ../../include
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/include/R_ext'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/include'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
making regcomp.d from regcomp.c
making regerror.d from regerror.c
making regexec.d from regexec.c
making tre-ast.d from tre-ast.c
making tre-compile.d from tre-compile.c
making tre-match-approx.d from tre-match-approx.c
making tre-match-backtrack.d from tre-match-backtrack.c
making tre-match-parallel.d from tre-match-parallel.c
making tre-mem.d from tre-mem.c
making tre-stack.d from tre-stack.c
making tre-parse.d from tre-parse.c
making xmalloc.d from xmalloc.c
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c regcomp.c -o regcomp.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c regerror.c -o regerror.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c regexec.c -o regexec.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-ast.c -o tre-ast.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-compile.c -o tre-compile.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-mem.c -o tre-mem.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-parse.c -o tre-parse.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-stack.c -o tre-stack.o
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c xmalloc.c -o xmalloc.o
rm -f libtre.a
ar cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o
ranlib libtre.a
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
making integrate.d from integrate.c
making interv.d from interv.c
making maxcol.d from maxcol.c
making optim.d from optim.c
making pretty.d from pretty.c
making uncmin.d from uncmin.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c integrate.c -o integrate.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c interv.c -o interv.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c maxcol.c -o maxcol.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c optim.c -o optim.o
In file included from /usr/include/math.h:26:0,
                 from ../../src/include/R_ext/Arith.h:37,
                 from maxcol.c:33:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pretty.c -o pretty.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c uncmin.c -o uncmin.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dchdc.f -o dchdc.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dpbfa.f -o dpbfa.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dpbsl.f -o dpbsl.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dpoco.f -o dpoco.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dpodi.f -o dpodi.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dpofa.f -o dpofa.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dposl.f -o dposl.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dqrdc.f -o dqrdc.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dqrdc2.f -o dqrdc2.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dqrls.f -o dqrls.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dqrsl.f -o dqrsl.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dqrutl.f -o dqrutl.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dsvdc.f -o dsvdc.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dtrco.f -o dtrco.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dtrsl.f -o dtrsl.o
rm -f libappl.a
ar cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o 
ranlib libappl.a
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making ftrunc.d from ftrunc.c
making fround.d from fround.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making expm1.d from expm1.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making bessel_k.d from bessel_k.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making plnorm.d from plnorm.c
making dlnorm.d from dlnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making rcauchy.d from rcauchy.c
making qcauchy.d from qcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c mlutils.c -o mlutils.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c d1mach.c -o d1mach.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c i1mach.c -o i1mach.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fmax2.c -o fmax2.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fmin2.c -o fmin2.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fprec.c -o fprec.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fround.c -o fround.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ftrunc.c -o ftrunc.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sign.c -o sign.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fsign.c -o fsign.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c imax2.c -o imax2.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c imin2.c -o imin2.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chebyshev.c -o chebyshev.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c log1p.c -o log1p.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c expm1.c -o expm1.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lgammacor.c -o lgammacor.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gammalims.c -o gammalims.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c stirlerr.c -o stirlerr.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bd0.c -o bd0.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gamma.c -o gamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lgamma.c -o lgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gamma_cody.c -o gamma_cody.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c beta.c -o beta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lbeta.c -o lbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c polygamma.c -o polygamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cospi.c -o cospi.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bessel_i.c -o bessel_i.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bessel_j.c -o bessel_j.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bessel_k.c -o bessel_k.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bessel_y.c -o bessel_y.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c choose.c -o choose.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c snorm.c -o snorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sexp.c -o sexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dgamma.c -o dgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pgamma.c -o pgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qgamma.c -o qgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rgamma.c -o rgamma.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dbeta.c -o dbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pbeta.c -o pbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qbeta.c -o qbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rbeta.c -o rbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dunif.c -o dunif.o
qbeta.c: In function 'Rf_qbeta':
qbeta.c:58:14: warning: variable 'warned' set but not used [-Wunused-but-set-variable]
     Rboolean warned = FALSE;
              ^
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c punif.c -o punif.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qunif.c -o qunif.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c runif.c -o runif.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dnorm.c -o dnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pnorm.c -o pnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qnorm.c -o qnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rnorm.c -o rnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dlnorm.c -o dlnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c plnorm.c -o plnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qlnorm.c -o qlnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rlnorm.c -o rlnorm.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c df.c -o df.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pf.c -o pf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qf.c -o qf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rf.c -o rf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dnf.c -o dnf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dt.c -o dt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pt.c -o pt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qt.c -o qt.o
dt.c: In function 'Rf_dt':
dt.c:80:44: warning: 'ax' may be used uninitialized in this function [-Wmaybe-uninitialized]
     double I_sqrt_ = (lrg_x2n ? sqrt(n)/ax : exp(-l_x2n));
                                            ^
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rt.c -o rt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dnt.c -o dnt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dchisq.c -o dchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pchisq.c -o pchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qchisq.c -o qchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rchisq.c -o rchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rnchisq.c -o rnchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dbinom.c -o dbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pbinom.c -o pbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qbinom.c -o qbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rbinom.c -o rbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rmultinom.c -o rmultinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dcauchy.c -o dcauchy.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pcauchy.c -o pcauchy.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qcauchy.c -o qcauchy.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rcauchy.c -o rcauchy.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dexp.c -o dexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pexp.c -o pexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qexp.c -o qexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rexp.c -o rexp.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dgeom.c -o dgeom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pgeom.c -o pgeom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qgeom.c -o qgeom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rgeom.c -o rgeom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dhyper.c -o dhyper.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c phyper.c -o phyper.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qhyper.c -o qhyper.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rhyper.c -o rhyper.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dnbinom.c -o dnbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pnbinom.c -o pnbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qnbinom.c -o qnbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rnbinom.c -o rnbinom.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dpois.c -o dpois.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ppois.c -o ppois.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qpois.c -o qpois.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rpois.c -o rpois.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dweibull.c -o dweibull.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pweibull.c -o pweibull.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qweibull.c -o qweibull.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rweibull.c -o rweibull.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dlogis.c -o dlogis.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c plogis.c -o plogis.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qlogis.c -o qlogis.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rlogis.c -o rlogis.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dnchisq.c -o dnchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pnchisq.c -o pnchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qnchisq.c -o qnchisq.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dnbeta.c -o dnbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pnbeta.c -o pnbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qnbeta.c -o qnbeta.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pnf.c -o pnf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pnt.c -o pnt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qnf.c -o qnf.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qnt.c -o qnt.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ptukey.c -o ptukey.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qtukey.c -o qtukey.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c toms708.c -o toms708.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c wilcox.c -o wilcox.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c signrank.c -o signrank.o
rm -rf libnmath.a
ar cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
config.status: creating src/unix/Makefile
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
making Rembedded.d from Rembedded.c
making dynload.d from dynload.c
making system.d from system.c
making sys-unix.d from sys-unix.c
making sys-std.d from sys-std.c
making X11.d from X11.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Rembedded.c -o Rembedded.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dynload.c -o dynload.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c system.c -o system.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sys-unix.c -o sys-unix.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sys-std.c -o sys-std.o
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c X11.c -o X11.o
rm -rf libunix.a
ar cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o
ranlib libunix.a
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-3.1.2"' \
  -o Rscript ./Rscript.c
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
config.status: creating src/main/Makefile
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
making CommandLineArgs.d from CommandLineArgs.c
making Rdynload.d from Rdynload.c
making Renviron.d from Renviron.c
making RNG.d from RNG.c
making agrep.d from agrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making vfonts.d from vfonts.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c CommandLineArgs.c -o CommandLineArgs.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Rdynload.c -o Rdynload.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Renviron.c -o Renviron.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c RNG.c -o RNG.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agrep.c -o agrep.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c apply.c -o apply.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c arithmetic.c -o arithmetic.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c array.c -o array.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c attrib.c -o attrib.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bind.c -o bind.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c builtin.c -o builtin.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c character.c -o character.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coerce.c -o coerce.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c colors.c -o colors.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c complex.c -o complex.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c connections.c -o connections.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c context.c -o context.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cum.c -o cum.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dcf.c -o dcf.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c datetime.c -o datetime.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c debug.c -o debug.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c deparse.c -o deparse.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c devices.c -o devices.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dotcode.c -o dotcode.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dounzip.c -o dounzip.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dstruct.c -o dstruct.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c duplicate.c -o duplicate.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c edit.c -o edit.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c engine.c -o engine.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c envir.c -o envir.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c errors.c -o errors.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c eval.c -o eval.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c format.c -o format.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gevents.c -o gevents.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gram.c -o gram.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gram-ex.c -o gram-ex.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c graphics.c -o graphics.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c grep.c -o grep.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c identical.c -o identical.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c inlined.c -o inlined.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c inspect.c -o inspect.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c internet.c -o internet.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c iosupport.c -o iosupport.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lapack.c -o lapack.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c list.c -o list.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c localecharset.c -o localecharset.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c logic.c -o logic.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c main.c -o main.o
main.c: In function 'dummy_ii':
main.c:1594:12: warning: function returns address of local variable [-Wreturn-local-addr]
     return (uintptr_t) &ii;
            ^
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c mapply.c -o mapply.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c match.c -o match.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c memory.c -o memory.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c names.c -o names.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c objects.c -o objects.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c options.c -o options.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c paste.c -o paste.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c platform.c -o platform.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c plot.c -o plot.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c plot3d.c -o plot3d.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c plotmath.c -o plotmath.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c print.c -o print.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c printarray.c -o printarray.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c printvector.c -o printvector.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c printutils.c -o printutils.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qsort.c -o qsort.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c random.c -o random.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c raw.c -o raw.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c registration.c -o registration.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c relop.c -o relop.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rlocale.c -o rlocale.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c saveload.c -o saveload.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c scan.c -o scan.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c seq.c -o seq.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c serialize.c -o serialize.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sort.c -o sort.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c source.c -o source.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c split.c -o split.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sprintf.c -o sprintf.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c startup.c -o startup.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c subassign.c -o subassign.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c subscript.c -o subscript.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c subset.c -o subset.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c summary.c -o summary.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sysutils.c -o sysutils.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c times.c -o times.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c unique.c -o unique.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c util.c -o util.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c version.c -o version.o
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c vfonts.c -o vfonts.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c xxxpr.f -o xxxpr.o
x86_64-alt-linux-gcc -shared -L/usr/local/lib64  -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o vfonts.o xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o`    ../extra/tre/libtre.a     -lopenblas -lgfortran -lm -lquadmath   -lreadline  -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
mkdir -p -- /usr/src/RPM/BUILD/R-3.1.2/bin/exec
mkdir -p -- /usr/src/RPM/BUILD/R-3.1.2/lib
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
x86_64-alt-linux-gcc    -I../../src/extra   -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Rmain.c -o Rmain.o
x86_64-alt-linux-gcc -Wl,--export-dynamic  -L../../lib -L/usr/local/lib64 -o R.bin Rmain.o  -lR 
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
making g_alab_her.d from g_alab_her.c
making Lapack.d from Lapack.c
making Rhttpd.d from Rhttpd.c
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
making devX11.d from devX11.c
making Rsock.d from Rsock.c
making g_cntrlify.d from g_cntrlify.c
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Lapack.c -o Lapack.o
making g_fontdb.d from g_fontdb.c
making rotated.d from rotated.c
making internet.d from internet.c
making rbitmap.d from rbitmap.c
making g_her_glyph.d from g_her_glyph.c
making nanoftp.d from nanoftp.c
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c g_alab_her.c -o g_alab_her.o
making nanohttp.d from nanohttp.c
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c devX11.c -o devX11.o
making sock.d from sock.c
making sockconn.d from sockconn.c
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c g_cntrlify.c -o g_cntrlify.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c g_fontdb.c -o g_fontdb.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c g_her_glyph.c -o g_her_glyph.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c Rsock.c -o Rsock.o
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o vfonts.so g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o -lR -lm 
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
mkdir -p -- /usr/src/RPM/BUILD/R-3.1.2/modules
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c internet.c -o internet.o
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o lapack.so  Lapack.o  -lR  -llapack -lopenblas -lgfortran -lm -lquadmath
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c nanoftp.c -o nanoftp.o
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c nanohttp.c -o nanohttp.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c sock.c -o sock.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c sockconn.c -o sockconn.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rotated.c -o rotated.o
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rbitmap.c -o rbitmap.o
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o sockconn.o -lR  
x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dataentry.c -o dataentry.o
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o R_X11.so devX11.o rotated.o rbitmap.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext   -lX11 -lXt -lXmu  -ltiff -ljpeg -lpng -lz -lR -lm 
x86_64-alt-linux-gcc -shared -L../../../lib -L/usr/local/lib64 -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo -lX11 -lXext   -lX11 -lXt -lXmu  -lR -lm 
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
mkdir -p -- ../../library
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/profile'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/translations'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/translations'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/translations'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
building package 'base'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
mkdir -p -- ../../../library/base/demo
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
mkdir -p -- ../../../library/tools/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
making signals.d from signals.c
making install.d from install.c
making getfmts.d from getfmts.c
making http.d from http.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c text.c -o text.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Rmd5.c -o Rmd5.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c md5.c -o md5.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c signals.c -o signals.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c install.c -o install.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c getfmts.c -o getfmts.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c http.c -o http.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gramLatex.c -o gramLatex.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gramRd.c -o gramRd.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
byte-compiling package 'compiler'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/compiler'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
byte-compiling package 'base'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
byte-compiling package 'tools'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tools'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
mkdir -p -- ../../../library/utils/R
mkdir -p -- ../../../library/utils/Sweave
mkdir -p -- ../../../library/utils/misc
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils/src'
making init.d from init.c
making io.d from io.c
making size.d from size.c
making sock.d from sock.c
making stubs.d from stubs.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
making utils.d from utils.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c io.c -o io.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c size.c -o size.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sock.c -o sock.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c stubs.c -o stubs.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c utils.c -o utils.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
byte-compiling package 'utils'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/utils'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
mkdir -p -- ../../../library/grDevices/R
mkdir -p -- ../../../library/grDevices/afm
mkdir -p -- ../../../library/grDevices/enc
mkdir -p -- ../../../library/grDevices/icc
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src'
making axis_scales.d from axis_scales.c
making devices.d from devices.c
making chull.d from chull.c
making init.d from init.c
making stubs.d from stubs.c
making colors.d from colors.c
making devCairo.d from devCairo.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
making devQuartz.d from devQuartz.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c axis_scales.c -o axis_scales.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chull.c -o chull.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c devices.c -o devices.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c stubs.c -o stubs.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c colors.c -o colors.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c devCairo.c -o devCairo.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c devPicTeX.c -o devPicTeX.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c devPS.c -o devPS.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c devQuartz.c -o devQuartz.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[7]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[8]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
make[9]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
x86_64-alt-linux-gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng15 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cairoBM.c -o cairoBM.o
x86_64-alt-linux-gcc -shared -L../../../../../lib -L/usr/local/lib64 -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng15 -lz -lcairo   -ltiff -ljpeg -lpng -lz -L../../../../../lib -lR -lm 
make[9]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
make[8]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
make[7]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src/cairo'
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
byte-compiling package 'grDevices'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grDevices'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics/src'
making init.d from init.c
making base.d from base.c
making graphics.d from graphics.c
making par.d from par.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making stem.d from stem.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c base.c -o base.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c graphics.c -o graphics.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c par.c -o par.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c plot.c -o plot.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c plot3d.c -o plot3d.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c stem.c -o stem.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
byte-compiling package 'graphics'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/graphics'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats/src'
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making dblcen.d from dblcen.c
making distance.d from distance.c
making hclust-utils.d from hclust-utils.c
making nls.d from nls.c
making rWishart.d from rWishart.c
making HoltWinters.d from HoltWinters.c
making PPsum.d from PPsum.c
making arima.d from arima.c
making burg.d from burg.c
making filter.d from filter.c
making mAR.d from mAR.c
making pacf.d from pacf.c
making starma.d from starma.c
making port.d from port.c
making family.d from family.c
making sbart.d from sbart.c
making approx.d from approx.c
making loglin.d from loglin.c
making lowess.d from lowess.c
making massdist.d from massdist.c
making splines.d from splines.c
making lm.d from lm.c
making complete_cases.d from complete_cases.c
making cov.d from cov.c
making deriv.d from deriv.c
making fft.d from fft.c
making fourier.d from fourier.c
making model.d from model.c
making optim.d from optim.c
making optimize.d from optimize.c
making integrate.d from integrate.c
making random.d from random.c
making distn.d from distn.c
making zeroin.d from zeroin.c
making rcont.d from rcont.c
making influence.d from influence.c
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c kmeans.c -o kmeans.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ansari.c -o ansari.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bandwidths.c -o bandwidths.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chisqsim.c -o chisqsim.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c d2x2xk.c -o d2x2xk.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fexact.c -o fexact.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c kendall.c -o kendall.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ks.c -o ks.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c line.c -o line.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c smooth.c -o smooth.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c prho.c -o prho.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c swilk.c -o swilk.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ksmooth.c -o ksmooth.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c loessc.c -o loessc.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c monoSpl.c -o monoSpl.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c isoreg.c -o isoreg.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Srunmed.c -o Srunmed.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dblcen.c -o dblcen.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c distance.c -o distance.o
In file included from /usr/include/math.h:26:0,
                 from ../../../include/R_ext/Arith.h:37,
                 from distance.c:26:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c hclust-utils.c -o hclust-utils.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c nls.c -o nls.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rWishart.c -o rWishart.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c HoltWinters.c -o HoltWinters.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c PPsum.c -o PPsum.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c arima.c -o arima.o
In file included from /usr/include/math.h:26:0,
                 from ../../../include/R_ext/Arith.h:37,
                 from arima.c:25:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c burg.c -o burg.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c filter.c -o filter.o
In file included from /usr/include/math.h:26:0,
                 from ../../../include/R_ext/Arith.h:37,
                 from filter.c:25:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c mAR.c -o mAR.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pacf.c -o pacf.o
In file included from /usr/include/math.h:26:0,
                 from ../../../include/R_ext/Arith.h:37,
                 from pacf.c:29:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c starma.c -o starma.o
In file included from /usr/include/math.h:26:0,
                 from ../../../include/R_ext/Arith.h:37,
                 from starma.c:24:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c port.c -o port.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c family.c -o family.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sbart.c -o sbart.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c approx.c -o approx.o
In file included from /usr/include/math.h:26:0,
                 from ../../../include/R_ext/Arith.h:37,
                 from approx.c:25:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c loglin.c -o loglin.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lowess.c -o lowess.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c massdist.c -o massdist.o
In file included from /usr/include/math.h:26:0,
                 from ../../../include/R_ext/Arith.h:37,
                 from massdist.c:31:
/usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c splines.c -o splines.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lm.c -o lm.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c complete_cases.c -o complete_cases.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cov.c -o cov.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c deriv.c -o deriv.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fft.c -o fft.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fourier.c -o fourier.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c model.c -o model.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c optim.c -o optim.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c optimize.c -o optimize.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c integrate.c -o integrate.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c random.c -o random.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c distn.c -o distn.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c zeroin.c -o zeroin.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rcont.c -o rcont.o
x86_64-alt-linux-gcc -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c influence.c -o influence.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bsplvd.f -o bsplvd.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bvalue.f -o bvalue.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bvalus.f -o bvalus.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c loessf.f -o loessf.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ppr.f -o ppr.o
loessf.f:59:14:

             j=DBLE(j)/2.D0
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1896:14:

             m=DBLE(l+u)/2.D0
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1398:20:

                   i=phi(pi(ii))
                    1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:927:12:

          lg=DBLE(lg)/2.D0
            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:522:22:

       if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0
                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1204:13:

       ifloor=x
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:834:22:

       if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0
                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1582:18:

                i1=dble((d+2)*(d+1))/2.d0
                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:472:25:

       subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
                         1
Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument]
loessf.f:472:39:

       subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
                                       1
Warning: Unused dummy argument 'nc' at (1) [-Wunused-dummy-argument]
loessf.f:827:31:

       subroutine ehg197(deg,tau,d,f,dk,trl)
                               1
Warning: Unused dummy argument 'tau' at (1) [-Wunused-dummy-argument]
loessf.f:1987:31:

       subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
                               1
Warning: Unused dummy argument 'kappa' at (1) [-Wunused-dummy-argument]
loessf.f:1987:47:

       subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
                                               1
Warning: Unused dummy argument 'nv' at (1) [-Wunused-dummy-argument]
loessf.f:1987:53:

       subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
                                                     1
Warning: Unused dummy argument 'nvmax' at (1) [-Wunused-dummy-argument]
loessf.f:1856:22:

       logical i1,i2,i3,leaf
                      1
Warning: Unused variable 'i3' declared at (1) [-Wunused-variable]
loessf.f:1497:50:

       subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)
                                                  1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1497:53:

       subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)
                                                     1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1648:30:

       subroutine lowese(iv,liv,lv,wv,m,z,s)
                              1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1648:33:

       subroutine lowese(iv,liv,lv,wv,m,z,s)
                                 1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1667:39:

       subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)
                                       1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1667:42:

       subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)
                                          1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1699:30:

       subroutine lowesl(iv,liv,lv,wv,m,z,l)
                              1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1699:33:

       subroutine lowesl(iv,liv,lv,wv,m,z,l)
                                 1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1721:33:

       subroutine lowesr(yy,iv,liv,lv,wv)
                                 1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1721:36:

       subroutine lowesr(yy,iv,liv,lv,wv)
                                    1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
ppr.f:1323:8:

       t=a(ij)
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1328:8:

       t=a(ij)
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1336:8:

       t=a(ij)
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1343:8:

       t=a(ij)
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1354:9:

       tt=a(l)
         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1379:8:

       t=a(i+1)
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:370:10:

         k=sc(j,1)
          1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1088:10:

       ibw=0.5d0*span*n+0.5d0
          1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:396:10:

         k=sc(j,1)
          1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:404:10:

         k=sc(j,1)
          1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:115:8:

       l=sc(lm,1)
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:844:14:

             k=sp(j,1)
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:860:8:

       m=smod(1)+0.1d0
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:861:8:

       p=smod(2)+0.1d0
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:862:8:

       q=smod(3)+0.1d0
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:863:8:

       n=smod(4)+0.1d0
        1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:864:9:

       mu=smod(5)+0.1d0
         1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
ppr.f:1229:42:

       integer iparms(3), i, nk, ip, isetup,ier
                                          1
Warning: Unused variable 'isetup' declared at (1) [-Wunused-variable]
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qsbart.f -o qsbart.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sgram.f -o sgram.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sinerp.f -o sinerp.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sslvrg.f -o sslvrg.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c stxwx.f -o stxwx.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c hclust.f -o hclust.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c kmns.f -o kmns.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c eureka.f -o eureka.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c stl.f -o stl.o
f95 -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing -ffloat-store -c portsrc.f -o portsrc.o
f95  -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lminfl.f -o lminfl.o
portsrc.f:6340:0:

      *        MAXLST,NCOMP,NUMINC,NUMLST,NUMORD,NUMWGT
 ^
Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:6339:0:

       INTEGER DEG,HEAD,IC,IP,IPL,IPU,IR,JCOL,JP,JPL,JPU,L,MAXINC,
 ^
Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5328:0:

       IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
 ^
Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5463:0:

               IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310
 ^
Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10090:0:

       V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
 ^
Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10008:0:

       IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK)
 ^
Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10003:0:

       LK = DMAX1(LK, PHI*W(PHIPIN))
 ^
Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10144:0:

       IF (KA .GE. KAMIN) GO TO 340
 ^
Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11900:0:

       V(NREDUC) = NRED
 ^
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11903:0:

       V(DST0) = DNWTST
 ^
Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2390:0:

       V(NREDUC) = NRED
 ^
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2389:0:

  60   V(DST0) = DS0
 ^
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:7892:0:

       V(NREDUC) = NRED
 ^
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:7891:0:

  90   V(DST0) = DS0
 ^
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8370:0:

  210  IV(FDH) = HES
 ^
Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:3456:0:

       IF (LIV .LT. MIV2) GO TO 300
 ^
Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11737:0:

  270  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
 ^
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11694:0:

       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
 ^
Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:11694:0: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:440:0:

  300  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
 ^
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:348:0:

       CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1))
 ^
Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:348:0: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized]
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/datasets'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/datasets'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c do_substitute_direct.c -o do_substitute_direct.o
making utils.d from utils.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c methods_list_dispatch.c -o methods_list_dispatch.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c slot.c -o slot.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c class_support.c -o class_support.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c tests.c -o tests.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c utils.c -o utils.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
byte-compiling 'methods'
initializing class and method definitions ... done
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/methods'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
mkdir -p -- ../../../library/grid/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid/src'
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making matrix.d from matrix.c
making register.d from register.c
making state.d from state.c
making unit.d from unit.c
making util.d from util.c
making viewport.d from viewport.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gpar.c -o gpar.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c grid.c -o grid.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c just.c -o just.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c layout.c -o layout.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c matrix.c -o matrix.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c register.c -o register.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c state.c -o state.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c unit.c -o unit.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c util.c -o util.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c viewport.c -o viewport.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
byte-compiling package 'grid'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/grid'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
building package 'splines'
mkdir -p -- ../../../library/splines
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
mkdir -p -- ../../../library/splines/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines/src'
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c splines.c -o splines.o
making splines.d from splines.c
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o splines.so splines.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines/src'
mkdir -p -- ../../../../library/splines/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
byte-compiling package 'splines'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/splines'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats4'
mkdir -p -- ../../../library/stats4/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats4'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats4'
byte-compiling package 'stats4'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats4'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/stats4'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk/src'
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/include  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/include  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c tcltk.c -o tcltk.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I/usr/include  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c tcltk_unix.c -o tcltk_unix.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.5 -L/usr/lib64 -ltk8.5 -lX11 -lm -L../../../../lib -lR
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk/src'
mkdir -p -- ../../../../library/tcltk/libs
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk/src'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk'
byte-compiling package 'tcltk'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/tcltk'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
building package 'parallel'
mkdir -p -- ../../../library/parallel
mkdir -p -- ../../../library/parallel/doc
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
mkdir -p -- ../../../library/parallel/R
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
make[5]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel/src'
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
making init.d from init.c
making rngstream.d from rngstream.c
making fork.d from fork.c
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rngstream.c -o rngstream.o
x86_64-alt-linux-gcc -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fork.c -o fork.o
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[6]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel/src'
mkdir -p -- ../../../../library/parallel/libs
make[6]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel/src'
make[5]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel/src'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
make[4]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
byte-compiling package 'parallel'
make[4]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/parallel'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/base'
installing parsed NAMESPACE files
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
you should 'make docs' now ...
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2'
configuring Java ...
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc'

*** Cannot find any Java interpreter
*** Please make sure 'java' is on your PATH or set JAVA_HOME correspondingly
make[1]: [stamp-java] Error 1 (ignored)
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2'
creating NEWS
creating NEWS.pdf
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-FAQ.html will be missing
creating doc/manual/version.texi
'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-admin.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-data.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-exts.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-intro.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-ints.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
file R-lang.html will be missing
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
installing parsed Rd
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
  methods
  utils
  graphics
  datasets
  grDevices
  grid
  tools
  splines
  tcltk
  compiler
  stats4
  parallel
  stats
  base
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
building/updating package metadata ...
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
writing package indices
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
building all R object docs
  converting help for package 'base'
    Arithmetic                              html  
Rd warning: /usr/src/RPM/BUILD/R-3.1.2/src/library/base/man/Arithmetic.Rd:154: missing file link 'Ops'
    AsIs                                    html  
    Bessel                                  html  
    CallExternal                            html  
    Colon                                   html  
    Comparison                              html  
Rd warning: /usr/src/RPM/BUILD/R-3.1.2/src/library/base/man/Comparison.Rd:103: missing file link 'Ops'
    Constants                               html  
    Control                                 html  
    Cstack_info                             html  
    DateTimeClasses                         html  
    Dates                                   html  
    Defunct                                 html  
    Deprecated                              html  
    Encoding                                html  
    EnvVar                                  html  
    Extract                                 html  
    Extract.data.frame                      html  
    Extract.factor                          html  
    Extremes                                html  
    Foreign-internal                        html  
    Foreign                                 html  
    Hyperbolic                              html  
    ISOdatetime                             html  
    Internal                                html  
    InternalMethods                         html  
    La_version                              html  
    Last.value                              html  
    Log                                     html  
    Logic                                   html  
Rd warning: /usr/src/RPM/BUILD/R-3.1.2/src/library/base/man/Logic.Rd:104: missing file link 'Ops'
    LongVectors                             html  
    MathFun                                 html  
    Memory-limits                           html  
    Memory                                  html  
    NA                                      html  
    NULL                                    html  
    NumericConstants                        html  
    Ops.Date                                html  
    Paren                                   html  
    Platform                                html  
    Primitive                               html  
    Quotes                                  html  
    Random-user                             html  
    Random                                  html  
    RdUtils                                 html  
    Recall                                  html  
    Reserved                                html  
    Rhome                                   html  
    Round                                   html  
    Special                                 html  
    Startup                                 html  
    Syntax                                  html  
    Sys.getenv                              html  
    Sys.getpid                              html  
    Sys.glob                                html  
    Sys.info                                html  
    Sys.localeconv                          html  
    Sys.readlink                            html  
    Sys.setFileTime                         html  
    Sys.setenv                              html  
    Sys.sleep                               html  
    Sys.time                                html  
    Sys.which                               html  
    Trig                                    html  
    UseMethod                               html  
    Vectorize                               html  
    Version                                 html  
    abbreviate                              html  
    agrep                                   html  
    all                                     html  
    all.equal                               html  
    allnames                                html  
    any                                     html  
    aperm                                   html  
    append                                  html  
    apply                                   html  
    args                                    html  
    array                                   html  
    as.Date                                 html  
    as.POSIXlt                              html  
Rd warning: /usr/src/RPM/BUILD/R-3.1.2/src/library/base/man/as.POSIXlt.Rd:126: missing file link 'format.POSIXlt'
    as.data.frame                           html  
    as.environment                          html  
    as.function                             html  
    assign                                  html  
    assignOps                               html  
    attach                                  html  
    attr                                    html  
    attributes                              html  
    autoload                                html  
    backsolve                               html  
    base-defunct                            html  
    base-deprecated                         html  
    base-internal                           html  
    base-package                            html  
    basename                                html  
    bincode                                 html  
    bindenv                                 html  
    bitwise                                 html  
    body                                    html  
    bquote                                  html  
    browser                                 html  
    browserText                             html  
    builtins                                html  
    by                                      html  
    c                                       html  
    call                                    html  
    callCC                                  html  
    capabilities                            html  
    cat                                     html  
    cbind                                   html  
    char.expand                             html  
    character                               html  
    charmatch                               html  
    chartr                                  html  
    chol                                    html  
    chol2inv                                html  
    class                                   html  
    col                                     html  
    colSums                                 html  
    colnames                                html  
    commandArgs                             html  
    comment                                 html  
    complex                                 html  
    conditions                              html  
    conflicts                               html  
    connections                             html  
    contributors                            html  
    copyright                               html  
    crossprod                               html  
    cumsum                                  html  
    cut.POSIXt                              html  
    cut                                     html  
    data.class                              html  
    data.frame                              html  
    data.matrix                             html  
    dataframeHelpers                        html  
    date                                    html  
    dcf                                     html  
    debug                                   html  
    delayedAssign                           html  
    deparse                                 html  
    deparseOpts                             html  
    det                                     html  
    detach                                  html  
    dev                                     html  
    diag                                    html  
    diff                                    html  
    difftime                                html  
    dim                                     html  
    dimnames                                html  
    do.call                                 html  
    dontCheck                               html  
    double                                  html  
    dput                                    html  
    drop                                    html  
    droplevels                              html  
    dump                                    html  
    duplicated                              html  
    dynload                                 html  
    eapply                                  html  
    eigen                                   html  
    encodeString                            html  
    environment                             html  
    eval                                    html  
    exists                                  html  
    expand.grid                             html  
    expression                              html  
    factor                                  html  
    file.access                             html  
    file.choose                             html  
    file.info                               html  
    file.path                               html  
    file.show                               html  
    files                                   html  
    files2                                  html  
    find.package                            html  
    findInterval                            html  
    force                                   html  
    formals                                 html  
    format                                  html  
    format.info                             html  
    format.pval                             html  
    formatDL                                html  
    formatc                                 html  
    function                                html  
    funprog                                 html  
    gc                                      html  
    gc.time                                 html  
    gctorture                               html  
    get                                     html  
    getCallingDLL                           html  
    getDLLRegisteredRoutines                html  
    getLoadedDLLs                           html  
    getNativeSymbolInfo                     html  
    gettext                                 html  
    getwd                                   html  
    gl                                      html  
    grep                                    html  
    grepRaw                                 html  
    groupGeneric                            html  
    gzcon                                   html  
    hexmode                                 html  
    iconv                                   html  
    icuSetCollate                           html  
    identical                               html  
    identity                                html  
    ifelse                                  html  
    integer                                 html  
    interaction                             html  
    interactive                             html  
    invisible                               html  
    is.finite                               html  
    is.function                             html  
    is.language                             html  
    is.object                               html  
    is.recursive                            html  
    is.single                               html  
    is.unsorted                             html  
    isR                                     html  
    isS4                                    html  
    isSymmetric                             html  
    jitter                                  html  
    kappa                                   html  
    kronecker                               html  
    l10n_info                               html  
    labels                                  html  
    lapply                                  html  
    lazyload                                html  
    length                                  html  
    levels                                  html  
    libPaths                                html  
    library                                 html  
    library.dynam                           html  
    license                                 html  
    list                                    html  
    list.files                              html  
    list2env                                html  
    load                                    html  
    locales                                 html  
    logical                                 html  
    lower.tri                               html  
    ls                                      html  
    make.names                              html  
    make.unique                             html  
    mapply                                  html  
    margin.table                            html  
    mat.or.vec                              html  
    match                                   html  
    match.arg                               html  
    match.call                              html  
    match.fun                               html  
    matmult                                 html  
    matrix                                  html  
    maxCol                                  html  
    mean                                    html  
    memCompress                             html  
    memory.profile                          html  
    merge                                   html  
    message                                 html  
    missing                                 html  
    mode                                    html  
    name                                    html  
    names                                   html  
    nargs                                   html  
    nchar                                   html  
    nlevels                                 html  
    noquote                                 html  
    norm                                    html  
    normalizePath                           html  
    notyet                                  html  
    nrow                                    html  
    ns-dblcolon                             html  
    ns-hooks                                html  
    ns-internal                             html  
    ns-load                                 html  
    ns-reflect                              html  
    ns-topenv                               html  
    numeric                                 html  
    numeric_version                         html  
    octmode                                 html  
    on.exit                                 html  
    options                                 html  
    order                                   html  
    outer                                   html  
    parse                                   html  
    paste                                   html  
    path.expand                             html  
    pmatch                                  html  
    polyroot                                html  
    pos.to.env                              html  
    pretty                                  html  
    print                                   html  
Rd warning: /usr/src/RPM/BUILD/R-3.1.2/src/library/base/man/print.Rd:84: missing file link '.print.via.format'
    print.dataframe                         html  
    print.default                           html  
    prmatrix                                html  
    proc.time                               html  
    prod                                    html  
    prop.table                              html  
    pushBack                                html  
    qr                                      html  
    qraux                                   html  
    quit                                    html  
    range                                   html  
    rank                                    html  
    rapply                                  html  
    raw                                     html  
    rawConnection                           html  
    rawConversion                           html  
    readBin                                 html  
    readChar                                html  
    readLines                               html  
    readRDS                                 html  
    readRenviron                            html  
    readline                                html  
    reg.finalizer                           html  
    regex                                   html  
    regmatches                              html  
    rep                                     html  
    replace                                 html  
    rev                                     html  
    rle                                     html  
    rm                                      html  
    round.POSIXt                            html  
    row                                     html  
    row.names                               html  
    rowsum                                  html  
    sQuote                                  html  
    sample                                  html  
    save                                    html  
    scale                                   html  
    scan                                    html  
    search                                  html  
    seek                                    html  
    seq.Date                                html  
    seq.POSIXt                              html  
    seq                                     html  
    sequence                                html  
    serialize                               html  
    setTimeLimit                            html  
    sets                                    html  
    shQuote                                 html  
    showConnections                         html  
    sign                                    html  
    sink                                    html  
    slice.index                             html  
    slotOp                                  html  
    socketSelect                            html  
    solve                                   html  
    sort                                    html  
    source                                  html  
    split                                   html  
    sprintf                                 html  
    srcfile                                 html  
    standardGeneric                         html  
    stop                                    html  
    stopifnot                               html  
    strptime                                html  
    strsplit                                html  
    strtoi                                  html  
    strtrim                                 html  
    structure                               html  
    strwrap                                 html  
    subset                                  html  
    substitute                              html  
    substr                                  html  
    sum                                     html  
    summary                                 html  
    svd                                     html  
    sweep                                   html  
    switch                                  html  
    sys.parent                              html  
    sys.source                              html  
    system                                  html  
    system.file                             html  
    system.time                             html  
    system2                                 html  
    t                                       html  
    table                                   html  
    tabulate                                html  
    tapply                                  html  
    taskCallback                            html  
    taskCallbackManager                     html  
    taskCallbackNames                       html  
    tempfile                                html  
    textconnections                         html  
    tilde                                   html  
    timezones                               html  
    toString                                html  
    trace                                   html  
    traceback                               html  
    tracemem                                html  
    transform                               html  
    try                                     html  
    typeof                                  html  
    unique                                  html  
    unlink                                  html  
    unlist                                  html  
    unname                                  html  
    userhooks                               html  
    utf8Conversion                          html  
    vector                                  html  
    warning                                 html  
    warnings                                html  
    weekday.POSIXt                          html  
    which                                   html  
    which.min                               html  
    with                                    html  
    withVisible                             html  
    write                                   html  
    writeLines                              html  
    xtfrm                                   html  
    zMachine                                html  
    zScript                                 html  
    zapsmall                                html  
    zpackages                               html  
    zutils                                  html  
    Signals                                 html  
  converting help for package 'tools'
    HTMLheader                              html  
    HTMLlinks                               html  
    QC                                      html  
    Rd2HTML                                 html  
    Rd2txt_options                          html  
    RdTextFilter                            html  
    Rdiff                                   html  
    Rdindex                                 html  
    Rdutils                                 html  
    SweaveTeXFilter                         html  
    add_datalist                            html  
    assertCondition                         html  
    bibstyle                                html  
    buildVignette                           html  
    buildVignettes                          html  
    charsets                                html  
    checkFF                                 html  
    checkMD5sums                            html  
    checkPoFiles                            html  
    checkRd                                 html  
    checkRdaFiles                           html  
    checkTnF                                html  
    checkVignettes                          html  
    check_packages_in_dir                   html  
Rd warning: /usr/src/RPM/BUILD/R-3.1.2/src/library/tools/man/check_packages_in_dir.Rd:96: missing file link 'parLapply'
    codoc                                   html  
    compactPDF                              html  
    delimMatch                              html  
    dependsOnPkgs                           html  
    encoded                                 html  
    fileutils                               html  
    find_gs_cmd                             html  
    getDepList                              html  
    getVignetteInfo                         html  
    installFoundDepends                     html  
    makeLazyLoading                         html  
    make_translations_pkg                   html  
    md5sum                                  html  
    package.dependencies                    html  
    package_dependencies                    html  
    parseLatex                              html  
    parse_Rd                                html  
    print.via.format                        html  
    pskill                                  html  
    psnice                                  html  
    read.00Index                            html  
    showNonASCII                            html  
    startDynamicHelp                        html  
    testInstalledPackage                    html  
    texi2dvi                                html  
    toHTML                                  html  
    toRd                                    html  
    tools-defunct                           html  
    tools-deprecated                        html  
    tools-package                           html  
    undoc                                   html  
    update_pkg_po                           html  
    vignetteDepends                         html  
    vignetteEngine                          html  
    writePACKAGES                           html  
    xgettext                                html  
  converting help for package 'utils'
    BATCH                                   html  
    INSTALL                                 html  
    PkgUtils                                html  
    Question                                html  
    REMOVE                                  html  
    RHOME                                   html  
    RShowDoc                                html  
    RSiteSearch                             html  
    Rprof                                   html  
    Rprofmem                                html  
    Rscript                                 html  
    Rtangle                                 html  
    RweaveLatex                             html  
    SHLIB                                   html  
    Sweave                                  html  
    SweaveSyntConv                          html  
    SweaveUtils                             html  
    URLencode                               html  
    View                                    html  
    adist                                   html  
    alarm                                   html  
    apropos                                 html  
    aregexec                                html  
    aspell-utils                            html  
    aspell                                  html  
    available.packages                      html  
    bibentry                                html  
    browseEnv                               html  
    browseURL                               html  
    browseVignettes                         html  
    bug.report                              html  
    capture.output                          html  
    changedFiles                            html  
    chooseBioCmirror                        html  
    chooseCRANmirror                        html  
    citEntry                                html  
    citation                                html  
    cite                                    html  
    close.socket                            html  
    combn                                   html  
    compareVersion                          html  
    contrib.url                             html  
    count.fields                            html  
    create.post                             html  
    data                                    html  
    dataentry                               html  
    debugger                                html  
    demo                                    html  
    download.file                           html  
    download.packages                       html  
    edit                                    html  
    edit.data.frame                         html  
    example                                 html  
    file.edit                               html  
    filetest                                html  
    findLineNum                             html  
    fix                                     html  
    flush.console                           html  
    format                                  html  
    getAnywhere                             html  
    getFromNamespace                        html  
    getParseData                            html  
    getS3method                             html  
    glob2rx                                 html  
    globalVariables                         html  
    head                                    html  
    help                                    html  
    help.request                            html  
    help.search                             html  
    help.start                              html  
    install.packages                        html  
    installed.packages                      html  
    localeToCharset                         html  
    ls_str                                  html  
    maintainer                              html  
    make.packages.html                      html  
    make.socket                             html  
    menu                                    html  
    methods                                 html  
    mirrorAdmin                             html  
    modifyList                              html  
    news                                    html  
    object.size                             html  
    package.skeleton                        html  
    packageDescription                      html  
    packageName                             html  
    packageStatus                           html  
    page                                    html  
    person                                  html  
    process.events                          html  
    prompt                                  html  
    promptData                              html  
    promptPackage                           html  
    rcompgen                                html  
    read.DIF                                html  
    read.fortran                            html  
    read.fwf                                html  
    read.socket                             html  
    read.table                              html  
    recover                                 html  
    relist                                  html  
    remove.packages                         html  
    removeSource                            html  
    roman                                   html  
    rtags                                   html  
    savehistory                             html  
    select.list                             html  
    sessionInfo                             html  
    setRepositories                         html  
    sourceutils                             html  
    stack                                   html  
    str                                     html  
    summaryRprof                            html  
    tar                                     html  
    toLatex                                 html  
    txtProgressBar                          html  
    type.convert                            html  
    untar                                   html  
    unzip                                   html  
    update.packages                         html  
    url.show                                html  
    utils-defunct                           html  
    utils-deprecated                        html  
    utils-package                           html  
    vignette                                html  
    write.table                             html  
    zip                                     html  
    COMPILE                                 html  
    LINK                                    html  
    memory.size                             html  
    nsl                                     html  
  converting help for package 'grDevices'
    Devices                                 html  
    Hershey                                 html  
    Japanese                                html  
    Type1Font                               html  
    adjustcolor                             html  
    as.graphicsAnnot                        html  
    as.raster                               html  
    axisTicks                               html  
    boxplot.stats                           html  
    cairo                                   html  
    check.options                           html  
    chull                                   html  
    cm                                      html  
    col2rgb                                 html  
    colorRamp                               html  
    colors                                  html  
    contourLines                            html  
    convertColor                            html  
    densCols                                html  
    dev                                     html  
    dev.capabilities                        html  
    dev.capture                             html  
    dev.flush                               html  
    dev.interactive                         html  
    dev.size                                html  
    dev2                                    html  
    dev2bitmap                              html  
    devAskNewPage                           html  
    embedFonts                              html  
    extendrange                             html  
    getGraphicsEvent                        html  
    grDevices-package                       html  
    gray                                    html  
    gray.colors                             html  
    hcl                                     html  
    hsv                                     html  
    make.rgb                                html  
    n2mfrow                                 html  
    nclass                                  html  
    palette                                 html  
    palettes                                html  
    pdf                                     html  
    pdf.options                             html  
    pictex                                  html  
    plotmath                                html  
    postscript                              html  
    postscriptFonts                         html  
    pretty.Date                             html  
    ps.options                              html  
    recordGraphics                          html  
    recordplot                              html  
    rgb                                     html  
    rgb2hsv                                 html  
    trans3d                                 html  
    xfig                                    html  
    xy.coords                               html  
    xyTable                                 html  
    xyz.coords                              html  
    png                                     html  
    quartz                                  html  
    quartzFonts                             html  
    savePlot                                html  
    x11                                     html  
    x11Fonts                                html  
  converting help for package 'graphics'
    abline                                  html  
    arrows                                  html  
    assocplot                               html  
    axTicks                                 html  
    axis.POSIXct                            html  
    axis                                    html  
    barplot                                 html  
    box                                     html  
    boxplot                                 html  
    boxplot.matrix                          html  
    bxp                                     html  
    cdplot                                  html  
    clip                                    html  
    contour                                 html  
    convertXY                               html  
    coplot                                  html  
    curve                                   html  
    dotchart                                html  
    filled.contour                          html  
    fourfoldplot                            html  
    frame                                   html  
    graphics-defunct                        html  
    graphics-package                        html  
    grid                                    html  
    hist.POSIXt                             html  
    hist                                    html  
    identify                                html  
    image                                   html  
    layout                                  html  
    legend                                  html  
    lines                                   html  
    locator                                 html  
    matplot                                 html  
    mosaicplot                              html  
    mtext                                   html  
    pairs                                   html  
    panel.smooth                            html  
    par                                     html  
    persp                                   html  
    pie                                     html  
    plot                                    html  
    plot.dataframe                          html  
    plot.default                            html  
    plot.design                             html  
    plot.factor                             html  
    plot.formula                            html  
    plot.table                              html  
    plot.window                             html  
    plot.xy                                 html  
    plothistogram                           html  
    points                                  html  
    polygon                                 html  
    polypath                                html  
    rasterImage                             html  
    rect                                    html  
    rug                                     html  
    screen                                  html  
    segments                                html  
    smoothScatter                           html  
    spineplot                               html  
    stars                                   html  
    stem                                    html  
    stripchart                              html  
    strwidth                                html  
    sunflowerplot                           html  
    symbols                                 html  
    text                                    html  
    title                                   html  
    units                                   html  
    xspline                                 html  
    zAxis                                   html  
  converting help for package 'stats'
    AIC                                     html  
    ARMAacf                                 html  
    ARMAtoMA                                html  
    Beta                                    html  
    Binomial                                html  
    Cauchy                                  html  
    Chisquare                               html  
    Distributions                           html  
    Exponential                             html  
    Fdist                                   html  
    GammaDist                               html  
    Geometric                               html  
    HoltWinters                             html  
    Hypergeometric                          html  
    IQR                                     html  
    KalmanLike                              html  
    Logistic                                html  
    Lognormal                               html  
    Multinom                                html  
    NLSstAsymptotic                         html  
    NLSstClosestX                           html  
    NLSstLfAsymptote                        html  
    NLSstRtAsymptote                        html  
    NegBinomial                             html  
    Normal                                  html  
    Poisson                                 html  
    SSD                                     html  
    SSasymp                                 html  
    SSasympOff                              html  
    SSasympOrig                             html  
    SSbiexp                                 html  
    SSfol                                   html  
    SSfpl                                   html  
    SSgompertz                              html  
    SSlogis                                 html  
    SSmicmen                                html  
    SSweibull                               html  
    SignRank                                html  
    StructTS                                html  
    TDist                                   html  
    Tukey                                   html  
    TukeyHSD                                html  
    Uniform                                 html  
    Weibull                                 html  
    Wilcoxon                                html  
    acf                                     html  
    acf2AR                                  html  
    add1                                    html  
    addmargins                              html  
    aggregate                               html  
    alias                                   html  
    anova                                   html  
    anova.glm                               html  
    anova.lm                                html  
    anova.mlm                               html  
    ansari.test                             html  
    aov                                     html  
    approxfun                               html  
    ar                                      html  
    ar.ols                                  html  
    arima                                   html  
    arima.sim                               html  
    arima0                                  html  
    as.hclust                               html  
    asOneSidedFormula                       html  
    ave                                     html  
    bandwidth                               html  
    bartlett.test                           html  
    binom.test                              html  
    biplot                                  html  
    biplot.princomp                         html  
    birthday                                html  
    box.test                                html  
    cancor                                  html  
    case.names                              html  
    checkMFClasses                          html  
    chisq.test                              html  
    cmdscale                                html  
    coef                                    html  
    complete.cases                          html  
    confint                                 html  
    constrOptim                             html  
    contrast                                html  
    contrasts                               html  
    convolve                                html  
    cophenetic                              html  
    cor                                     html  
    cor.test                                html  
    cov.wt                                  html  
    cpgram                                  html  
    cutree                                  html  
    decompose                               html  
    delete.response                         html  
    dendrapply                              html  
    dendrogram                              html  
    density                                 html  
    deriv                                   html  
    deviance                                html  
    df.residual                             html  
    diffinv                                 html  
    dist                                    html  
    dummy.coef                              html  
    ecdf                                    html  
    eff.aovlist                             html  
    effects                                 html  
    embed                                   html  
    expand.model.frame                      html  
    extractAIC                              html  
    factanal                                html  
    factor.scope                            html  
    family                                  html  
    fft                                     html  
    filter                                  html  
    fisher.test                             html  
    fitted.values                           html  
    fivenum                                 html  
    fligner.test                            html  
    formula                                 html  
    formula.nls                             html  
    friedman.test                           html  
    ftable                                  html  
    ftable.formula                          html  
    getInitial                              html  
    glm                                     html  
    glm.control                             html  
    glm.summaries                           html  
    hclust                                  html  
    heatmap                                 html  
    identify.hclust                         html  
    influence.measures                      html  
    integrate                               html  
    interaction.plot                        html  
    is.empty                                html  
    isoreg                                  html  
    kernapply                               html  
    kernel                                  html  
    kmeans                                  html  
    kruskal.test                            html  
    ks.test                                 html  
    ksmooth                                 html  
    lag                                     html  
    lag.plot                                html  
    line                                    html  
    listof                                  html  
    lm                                      html  
    lm.influence                            html  
    lm.summaries                            html  
    lmfit                                   html  
    loadings                                html  
    loess                                   html  
    loess.control                           html  
    logLik                                  html  
    loglin                                  html  
    lowess                                  html  
    ls.diag                                 html  
    ls.print                                html  
    lsfit                                   html  
    mad                                     html  
    mahalanobis                             html  
    make.link                               html  
    makepredictcall                         html  
    manova                                  html  
    mantelhaen.test                         html  
    mauchly.test                            html  
    mcnemar.test                            html  
    median                                  html  
    medpolish                               html  
    model.extract                           html  
    model.frame                             html  
    model.matrix                            html  
    model.tables                            html  
    monthplot                               html  
    mood.test                               html  
    na.action                               html  
    na.contiguous                           html  
    na.fail                                 html  
    nafns                                   html  
    naprint                                 html  
    nextn                                   html  
    nlm                                     html  
    nlminb                                  html  
    nls                                     html  
    nls.control                             html  
    nobs                                    html  
    numericDeriv                            html  
    offset                                  html  
    oneway.test                             html  
    optim                                   html  
    optimize                                html  
    order.dendrogram                        html  
    p.adjust                                html  
    pairwise.prop.test                      html  
    pairwise.t.test                         html  
    pairwise.table                          html  
    pairwise.wilcox.test                    html  
    plot.HoltWinters                        html  
    plot.acf                                html  
    plot.density                            html  
    plot.isoreg                             html  
    plot.lm                                 html  
    plot.ppr                                html  
    plot.profile.nls                        html  
    plot.spec                               html  
    plot.stepfun                            html  
    plot.ts                                 html  
    poisson.test                            html  
    poly                                    html  
    power                                   html  
    power.anova.test                        html  
    power.prop.test                         html  
    power.t.test                            html  
    pp.test                                 html  
    ppoints                                 html  
    ppr                                     html  
    prcomp                                  html  
    predict.HoltWinters                     html  
    predict                                 html  
    predict.arima                           html  
    predict.glm                             html  
    predict.lm                              html  
    predict.loess                           html  
    predict.nls                             html  
    predict.smooth.spline                   html  
    preplot                                 html  
    princomp                                html  
    print.power.htest                       html  
    print.ts                                html  
    printCoefmat                            html  
    profile                                 html  
    profile.nls                             html  
    proj                                    html  
    prop.test                               html  
    prop.trend.test                         html  
    qqnorm                                  html  
    quade.test                              html  
    quantile                                html  
    r2dtable                                html  
    rWishart                                html  
    read.ftable                             html  
    rect.hclust                             html  
    relevel                                 html  
    reorder.dendrogram                      html  
    reorder.factor                          html  
    replications                            html  
    reshape                                 html  
    residuals                               html  
    runmed                                  html  
    scatter.smooth                          html  
    screeplot                               html  
    sd                                      html  
    se.contrast                             html  
    selfStart                               html  
    setNames                                html  
    shapiro.test                            html  
    simulate                                html  
    smooth                                  html  
    smooth.spline                           html  
    smoothEnds                              html  
    sortedXyData                            html  
    spec.ar                                 html  
    spec.pgram                              html  
    spec.taper                              html  
    spectrum                                html  
    splinefun                               html  
    start                                   html  
    stat.anova                              html  
    stats-defunct                           html  
    stats-deprecated                        html  
    stats-package                           html  
    step                                    html  
    stepfun                                 html  
    stl                                     html  
    stlmethods                              html  
    summary.aov                             html  
    summary.glm                             html  
    summary.lm                              html  
    summary.manova                          html  
    summary.nls                             html  
    summary.princomp                        html  
    supsmu                                  html  
    symnum                                  html  
    t.test                                  html  
    termplot                                html  
    terms                                   html  
    terms.formula                           html  
    terms.object                            html  
    time                                    html  
    toeplitz                                html  
    ts-methods                              html  
    ts                                      html  
    ts.plot                                 html  
    ts.union                                html  
    tsSmooth                                html  
    tsdiag                                  html  
    tsp                                     html  
    uniroot                                 html  
    update                                  html  
    update.formula                          html  
    var.test                                html  
    varimax                                 html  
    vcov                                    html  
    weighted.mean                           html  
    weighted.residuals                      html  
    weights                                 html  
    wilcox.test                             html  
    window                                  html  
    xtabs                                   html  
    zC                                      html  
  converting help for package 'datasets'
    AirPassengers                           html  
    BJsales                                 html  
    BOD                                     html  
    ChickWeight                             html  
    DNase                                   html  
    EuStockMarkets                          html  
    Formaldehyde                            html  
    HairEyeColor                            html  
    Harman23.cor                            html  
    Harman74.cor                            html  
    Indometh                                html  
    InsectSprays                            html  
    JohnsonJohnson                          html  
    LakeHuron                               html  
    LifeCycleSavings                        html  
    Loblolly                                html  
    Nile                                    html  
    Orange                                  html  
    OrchardSprays                           html  
    PlantGrowth                             html  
    Puromycin                               html  
    Theoph                                  html  
    Titanic                                 html  
    ToothGrowth                             html  
    UCBAdmissions                           html  
    UKDriverDeaths                          html  
    UKLungDeaths                            html  
    UKgas                                   html  
    USAccDeaths                             html  
    USArrests                               html  
    USJudgeRatings                          html  
    USPersonalExpenditure                   html  
    VADeaths                                html  
    WWWusage                                html  
    WorldPhones                             html  
    ability.cov                             html  
    airmiles                                html  
    airquality                              html  
    anscombe                                html  
    attenu                                  html  
    attitude                                html  
    austres                                 html  
    beavers                                 html  
    cars                                    html  
    chickwts                                html  
    co2                                     html  
    crimtab                                 html  
    datasets-package                        html  
    discoveries                             html  
    esoph                                   html  
    euro                                    html  
    eurodist                                html  
    faithful                                html  
    freeny                                  html  
    infert                                  html  
    iris                                    html  
    islands                                 html  
    lh                                      html  
    longley                                 html  
    lynx                                    html  
    morley                                  html  
    mtcars                                  html  
    nhtemp                                  html  
    nottem                                  html  
    npk                                     html  
    occupationalStatus                      html  
    precip                                  html  
    presidents                              html  
    pressure                                html  
    quakes                                  html  
    randu                                   html  
    rivers                                  html  
    rock                                    html  
    sleep                                   html  
    stackloss                               html  
    state                                   html  
    sunspot.month                           html  
    sunspot.year                            html  
    sunspots                                html  
    swiss                                   html  
    treering                                html  
    trees                                   html  
    uspop                                   html  
    volcano                                 html  
    warpbreaks                              html  
    women                                   html  
    zCO2                                    html  
  converting help for package 'methods'
    BasicClasses                            html  
    Classes                                 html  
    Documentation                           html  
    EmptyMethodsList-class                  html  
    EnvironmentClass                        html  
    GenericFunctions                        html  
    LanguageClasses                         html  
    LinearMethodsList-class                 html  
    MethodDefinition-class                  html  
    MethodSupport                           html  
    MethodWithNext-class                    html  
    Methods                                 html  
    MethodsList-class                       html  
    MethodsList                             html  
    NextMethod                              html  
    ObjectsWithPackage-class                html  
    RClassUtils                             html  
    RMethodUtils                            html  
    S3Part                                  html  
    S4groupGeneric                          html  
    SClassExtension-class                   html  
    StructureClasses                        html  
    TraceClasses                            html  
    as                                      html  
    callGeneric                             html  
    canCoerce                               html  
    cbind2                                  html  
    className                               html  
    classRepresentation-class               html  
    classesToAM                             html  
    dotsMethods                             html  
    evalSource                              html  
    findClass                               html  
    findMethods                             html  
    fixPrevious                             html  
    genericFunction-class                   html  
    getClass                                html  
    getMethod                               html  
    getPackageName                          html  
    hasArg                                  html  
    implicitGeneric                         html  
    inheritedSlotNames                      html  
    initialize-methods                      html  
    is                                      html  
    isSealedMethod                          html  
    languageEl                              html  
    localRefClass                           html  
    method.skeleton                         html  
    methodUtilities                         html  
    methods-defunct                         html  
    methods-deprecated                      html  
    methods-package                         html  
    new                                     html  
    nonStructure-class                      html  
    promptClass                             html  
    promptMethods                           html  
    refClass                                html  
    representation                          html  
    selectSuperClasses                      html  
    setClass                                html  
    setClassUnion                           html  
    setGeneric                              html  
    setLoadActions                          html  
    setMethod                               html  
    setOldClass                             html  
    setSClass                               html  
    show                                    html  
    showMethods                             html  
    signature-class                         html  
    slot                                    html  
    stdRefClass                             html  
    substituteDirect                        html  
    testInheritedMethods                    html  
    validObject                             html  
    zBasicFunsList                          html  
  converting help for package 'grid'
    Grid                                    html  
    absolute.size                           html  
    arrow                                   html  
    calcStringMetric                        html  
    current.viewport                        html  
    dataViewport                            html  
    depth                                   html  
    drawDetails                             html  
    editDetails                             html  
    explode                                 html  
    gEdit                                   html  
    gPath                                   html  
    getNames                                html  
    gpar                                    html  
    grid-defunct                            html  
    grid-internal                           html  
    grid-package                            html  
    grid.DLapply                            html  
    grid.add                                html  
    grid.bezier                             html  
    grid.cap                                html  
    grid.circle                             html  
    grid.clip                               html  
    grid.convert                            html  
    grid.copy                               html  
    grid.curve                              html  
    grid.delay                              html  
    grid.display.list                       html  
    grid.draw                               html  
    grid.edit                               html  
    grid.force                              html  
    grid.frame                              html  
    grid.function                           html  
    grid.get                                html  
    grid.grab                               html  
    grid.grep                               html  
    grid.grill                              html  
    grid.grob                               html  
    grid.layout                             html  
    grid.lines                              html  
    grid.locator                            html  
    grid.ls                                 html  
    grid.move.to                            html  
    grid.newpage                            html  
    grid.null                               html  
    grid.pack                               html  
    grid.path                               html  
    grid.place                              html  
    grid.plot.and.legend                    html  
    grid.points                             html  
    grid.polygon                            html  
    grid.pretty                             html  
    grid.raster                             html  
    grid.record                             html  
    grid.rect                               html  
    grid.refresh                            html  
    grid.remove                             html  
    grid.reorder                            html  
    grid.roundrect                          html  
    grid.segments                           html  
    grid.set                                html  
    grid.show.layout                        html  
    grid.show.viewport                      html  
    grid.text                               html  
    grid.xaxis                              html  
    grid.xspline                            html  
    grid.yaxis                              html  
    grobName                                html  
    grobWidth                               html  
    grobX                                   html  
    legendGrob                              html  
    makeContent                             html  
    plotViewport                            html  
    resolveRasterSize                       html  
    showGrob                                html  
    showViewport                            html  
    stringWidth                             html  
    unit                                    html  
    unit.c                                  html  
    unit.length                             html  
    unit.pmin                               html  
    unit.rep                                html  
    valid.just                              html  
    validDetails                            html  
    viewport                                html  
    viewports                               html  
    vpPath                                  html  
    widthDetails                            html  
    xDetails                                html  
    xsplinePoints                           html  
  converting help for package 'splines'
    asVector                                html  
    backSpline                              html  
    bs                                      html  
    interpSpline                            html  
    ns                                      html  
    periodicSpline                          html  
    polySpline                              html  
    predict.bSpline                         html  
    predict.bs                              html  
    splineDesign                            html  
    finding level-2 HTML links ... done

Rd warning: /usr/src/RPM/BUILD/R-3.1.2/src/library/splines/man/splineDesign.Rd:39: missing link 'sparseMatrix-class'
    splineKnots                             html  
    splineOrder                             html  
    splines-package                         html  
    xyVector                                html  
  converting help for package 'stats4'
    coef-methods                            html  
    confint-methods                         html  
    logLik-methods                          html  
    mle-class                               html  
    mle                                     html  
    plot-methods                            html  
    profile-methods                         html  
    profile.mle-class                       html  
    show-methods                            html  
    stats4-package                          html  
    summary-methods                         html  
    summary.mle-class                       html  
    update-methods                          html  
    vcov-methods                            html  
  converting help for package 'tcltk'
    TclInterface                            html  
    TkCommands                              html  
    TkWidgetcmds                            html  
    TkWidgets                               html  
    tclServiceMode                          html  
    tcltk-defunct                           html  
    tcltk-package                           html  
    tkProgressBar                           html  
    tkStartGUI                              html  
    tk_choose.dir                           html  
    tk_choose.files                         html  
    tk_messageBox                           html  
    tk_select.list                          html  
    tkpager                                 html  
  converting help for package 'compiler'
    compile                                 html  
  converting help for package 'parallel'
    RngStream                               html  
    clusterApply                            html  
    detectCores                             html  
    makeCluster                             html  
    parallel-package                        html  
    splitIndices                            html  
    children                                html  
    mcaffinity                              html  
    mcfork                                  html  
    mclapply                                html  
    mcparallel                              html  
    pvec                                    html  
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/Recommended'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/Recommended'
begin installing recommended package codetools
begin installing recommended package MASS
begin installing recommended package lattice
begin installing recommended package survival
* installing *source* package 'codetools' ...
** package 'codetools' successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'codetools'
    finding HTML links ... done
    checkUsage                              html  
    codetools                               html  
    findGlobals                             html  
    showTree                                html  
** building package indices
** testing if installed package can be loaded
* DONE (codetools)
Making 'packages.html' ... done
begin installing recommended package foreign
* installing *source* package 'foreign' ...
** package 'foreign' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpCXZ01p/R.INSTALL183351f8fce9/foreign/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c R_systat.c -o R_systat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Rdbfread.c -o Rdbfread.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Rdbfwrite.c -o Rdbfwrite.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c SASxport.c -o SASxport.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c avl.c -o avl.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dbfopen.c -o dbfopen.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c file-handle.c -o file-handle.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c format.c -o format.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c minitab.c -o minitab.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pfm-read.c -o pfm-read.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sfm-read.c -o sfm-read.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c spss.c -o spss.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c stataread.c -o stataread.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpCXZ01p/R.INSTALL183351f8fce9/foreign/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/foreign/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'foreign'
    finding HTML links ... done
    lookup.xport                            html  
    read.S                                  html  
    read.arff                               html  
    read.dbf                                html  
    read.dta                                html  
    read.epiinfo                            html  
    read.mtp                                html  
    read.octave                             html  
    read.spss                               html  
    read.ssd                                html  
    read.systat                             html  
    read.xport                              html  
    write.arff                              html  
    write.dbf                               html  
    write.dta                               html  
    write.foreign                           html  
** building package indices
** testing if installed package can be loaded
* DONE (foreign)
Making 'packages.html' ... done
begin installing recommended package KernSmooth
* installing *source* package 'KernSmooth' ...
** package 'KernSmooth' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmppjNSXA/R.INSTALL18f921c1be17/KernSmooth/src'
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c blkest.f -o blkest.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cp.f -o cp.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dgedi.f -o dgedi.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dgefa.f -o dgefa.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dgesl.f -o dgesl.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c linbin.f -o linbin.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c linbin2D.f -o linbin2D.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c locpoly.f -o locpoly.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rlbin.f -o rlbin.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sdiag.f -o sdiag.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sstdiag.f -o sstdiag.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmppjNSXA/R.INSTALL18f921c1be17/KernSmooth/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/KernSmooth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KernSmooth'
    finding HTML links ... done
    bkde                                    html  
    bkde2D                                  html  
    bkfe                                    html  
    dpih                                    html  
    dpik                                    html  
    dpill                                   html  
    locpoly                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (KernSmooth)
Making 'packages.html' ... done
begin installing recommended package rpart
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpM8ujGi/R.INSTALL1805c3a5958/MASS/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c MASS.c -o MASS.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lqs.c -o lqs.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpM8ujGi/R.INSTALL1805c3a5958/MASS/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MASS'
    finding HTML links ... done
    Aids2                                   html  
    Animals                                 html  
    Boston                                  html  
    Cars93                                  html  
    Cushings                                html  
    DDT                                     html  
    GAGurine                                html  
    Insurance                               html  
    MASS-internal                           html  
    Melanoma                                html  
    Null                                    html  
    OME                                     html  
    Pima.tr                                 html  
    Rabbit                                  html  
    Rubber                                  html  
    SP500                                   html  
    Sitka                                   html  
    Sitka89                                 html  
    Skye                                    html  
    Traffic                                 html  
    UScereal                                html  
    UScrime                                 html  
    VA                                      html  
    abbey                                   html  
    accdeaths                               html  
    addterm                                 html  
    anorexia                                html  
    anova.negbin                            html  
    area                                    html  
    bacteria                                html  
    bandwidth.nrd                           html  
    bcv                                     html  
    beav1                                   html  
    beav2                                   html  
    biopsy                                  html  
    birthwt                                 html  
    boxcox                                  html  
    cabbages                                html  
    caith                                   html  
    cats                                    html  
    cement                                  html  
    chem                                    html  
    con2tr                                  html  
    confint                                 html  
    contr.sdif                              html  
    coop                                    html  
    corresp                                 html  
    cov.rob                                 html  
    cov.trob                                html  
    cpus                                    html  
    crabs                                   html  
    deaths                                  html  
    denumerate                              html  
    dose.p                                  html  
    drivers                                 html  
    dropterm                                html  
    eagles                                  html  
    epil                                    html  
    eqscplot                                html  
    farms                                   html  
    fgl                                     html  
    fitdistr                                html  
    forbes                                  html  
    fractions                               html  
    galaxies                                html  
    gamma.dispersion                        html  
    gamma.shape.glm                         html  
    gehan                                   html  
    genotype                                html  
    geyser                                  html  
    gilgais                                 html  
    ginv                                    html  
    glm.convert                             html  
    glm.nb                                  html  
    glmmPQL                                 html  
    hills                                   html  
    hist.scott                              html  
    housing                                 html  
    huber                                   html  
    hubers                                  html  
    immer                                   html  
    isoMDS                                  html  
    kde2d                                   html  
    lda                                     html  
    ldahist                                 html  
    leuk                                    html  
    lm.gls                                  html  
    lm.ridge                                html  
    loglm                                   html  
    loglm1                                  html  
    logtrans                                html  
    lqs                                     html  
    mammals                                 html  
    mca                                     html  
    mcycle                                  html  
    menarche                                html  
    michelson                               html  
    minn38                                  html  
    motors                                  html  
    muscle                                  html  
    mvrnorm                                 html  
    negative.binomial                       html  
    newcomb                                 html  
    nlschools                               html  
    npk                                     html  
    npr1                                    html  
    oats                                    html  
    painters                                html  
    pairs.lda                               html  
    parcoord                                html  
    petrol                                  html  
    phones                                  html  
    plot.lda                                html  
    plot.mca                                html  
    plot.profile                            html  
    polr                                    html  
    predict.glmmPQL                         html  
    predict.lda                             html  
    predict.lqs                             html  
    predict.mca                             html  
    predict.qda                             html  
    profile.glm                             html  
    qda                                     html  
    quine                                   html  
    rational                                html  
    renumerate                              html  
    rlm                                     html  
    rms.curv                                html  
    rnegbin                                 html  
    road                                    html  
    rotifer                                 html  
    sammon                                  html  
    ships                                   html  
    shoes                                   html  
    shrimp                                  html  
    shuttle                                 html  
    snails                                  html  
    stdres                                  html  
    steam                                   html  
    stepAIC                                 html  
    stormer                                 html  
    studres                                 html  
    summary.loglm                           html  
    summary.negbin                          html  
    summary.rlm                             html  
    survey                                  html  
    synth.tr                                html  
    theta.md                                html  
    topo                                    html  
    truehist                                html  
    ucv                                     html  
    waders                                  html  
    whiteside                               html  
    width.SJ                                html  
    write.matrix                            html  
    wtloss                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (MASS)
Making 'packages.html' ... done
begin installing recommended package nnet
* installing *source* package 'lattice' ...
** package 'lattice' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpNgnT2h/R.INSTALL17ff1ea6c29f/lattice/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c threeDplot.c -o threeDplot.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpNgnT2h/R.INSTALL17ff1ea6c29f/lattice/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/lattice/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'lattice'
    finding HTML links ... done
    Lattice                                 html  
    Rows                                    html  
    axis.default                            html  
    banking                                 html  
    barchart.table                          html  
    barley                                  html  
    cloud                                   html  
    draw.colorkey                           html  
    draw.key                                html  
    environmental                           html  
    ethanol                                 html  
    histogram                               html  
    interaction                             html  
    lattice.options                         html  
    latticeParseFormula                     html  
    level.colors                            html  
    levelplot                               html  
    llines                                  html  
    lset                                    html  
    make.groups                             html  
    melanoma                                html  
    oneway                                  html  
    packet.panel.default                    html  
    panel.axis                              html  
    panel.barchart                          html  
    panel.bwplot                            html  
    panel.cloud                             html  
    panel.densityplot                       html  
    panel.dotplot                           html  
    panel.functions                         html  
    panel.histogram                         html  
    panel.levelplot                         html  
    panel.loess                             html  
    panel.number                            html  
    panel.pairs                             html  
    panel.parallel                          html  
    panel.qqmath                            html  
    panel.qqmathline                        html  
    panel.smoothScatter                     html  
    panel.spline                            html  
    panel.stripplot                         html  
    panel.superpose                         html  
    panel.violin                            html  
    panel.xyplot                            html  
    prepanel.default                        html  
    prepanel.functions                      html  
    print.trellis                           html  
    qq                                      html  
    qqmath                                  html  
    rfs                                     html  
    shingles                                html  
    simpleKey                               html  
    simpleTheme                             html  
    singer                                  html  
    splom                                   html  
    strip.default                           html  
    tmd                                     html  
    trellis.device                          html  
    trellis.object                          html  
    trellis.par.get                         html  
    update.trellis                          html  
    utilities.3d                            html  
    xyplot                                  html  
    xyplot.ts                               html  
** building package indices
** testing if installed package can be loaded
* DONE (lattice)
Making 'packages.html' ... done
begin installing recommended package spatial
* installing *source* package 'nnet' ...
** package 'nnet' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpFmxuxb/R.INSTALL198a388bbc40/nnet/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c nnet.c -o nnet.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpFmxuxb/R.INSTALL198a388bbc40/nnet/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nnet'
    finding HTML links ... done
    class.ind                               html  
    multinom                                html  
    nnet.Hess                               html  
    nnet                                    html  
    predict.nnet                            html  
    which.is.max                            html  
** building package indices
** testing if installed package can be loaded
* DONE (nnet)
Making 'packages.html' ... done
begin installing recommended package Matrix
* installing *source* package 'rpart' ...
** package 'rpart' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/Rtmpr5AKj6/R.INSTALL193369270043/rpart/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c anova.c -o anova.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c anovapred.c -o anovapred.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c branch.c -o branch.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c bsplit.c -o bsplit.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c choose_surg.c -o choose_surg.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fix_cp.c -o fix_cp.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c free_tree.c -o free_tree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gini.c -o gini.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c graycode.c -o graycode.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c insert_split.c -o insert_split.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c make_cp_list.c -o make_cp_list.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c make_cp_table.c -o make_cp_table.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c mysort.c -o mysort.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c nodesplit.c -o nodesplit.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c partition.c -o partition.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c poisson.c -o poisson.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pred_rpart.c -o pred_rpart.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c print_tree.c -o print_tree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rpart.c -o rpart.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rpart_callback.c -o rpart_callback.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rpartexp.c -o rpartexp.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rpartexp2.c -o rpartexp2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rpcountup.c -o rpcountup.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rpmatrix.c -o rpmatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rundown.c -o rundown.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rundown2.c -o rundown2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c surrogate.c -o surrogate.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c usersplit.c -o usersplit.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c xpred.c -o xpred.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c xval.c -o xval.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/Rtmpr5AKj6/R.INSTALL193369270043/rpart/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/rpart/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rpart'
    finding HTML links ... done
    car.test.frame                          html  
    car90                                   html  
    cu.summary                              html  
    kyphosis                                html  
    labels.rpart                            html  
    meanvar.rpart                           html  
    na.rpart                                html  
    path.rpart                              html  
    plot.rpart                              html  
    plotcp                                  html  
    post.rpart                              html  
    predict.rpart                           html  
    print.rpart                             html  
    printcp                                 html  
    prune.rpart                             html  
    residuals.rpart                         html  
    rpart-internal                          html  
    rpart                                   html  
    rpart.control                           html  
    rpart.exp                               html  
    rpart.object                            html  
    rsq.rpart                               html  
    snip.rpart                              html  
    solder                                  html  
    stagec                                  html  
    summary.rpart                           html  
    text.rpart                              html  
    xpred.rpart                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpart)
Making 'packages.html' ... done
begin installing recommended package nlme
* installing *source* package 'spatial' ...
** package 'spatial' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpP7V0Hj/R.INSTALL19bf2d03356c/spatial/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c krc.c -o krc.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pps.c -o pps.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpP7V0Hj/R.INSTALL19bf2d03356c/spatial/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'spatial'
    finding HTML links ... done
    Kaver                                   html  
    Kenvl                                   html  
    Kfn                                     html  
    Psim                                    html  
    SSI                                     html  
    Strauss                                 html  
    anova.trls                              html  
    correlogram                             html  
    expcov                                  html  
    ppgetregion                             html  
    ppinit                                  html  
    pplik                                   html  
    ppregion                                html  
    predict.trls                            html  
    prmat                                   html  
    semat                                   html  
    surf.gls                                html  
    surf.ls                                 html  
    trls.influence                          html  
    trmat                                   html  
    variogram                               html  
** building package indices
** testing if installed package can be loaded
* DONE (spatial)
Making 'packages.html' ... done
begin installing recommended package cluster
* installing *source* package 'survival' ...
** package 'survival' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpQaB70h/R.INSTALL18021d920041/survival/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agexact.c -o agexact.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agfit4.c -o agfit4.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agfit5.c -o agfit5.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agmart.c -o agmart.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agmart2.c -o agmart2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agscore.c -o agscore.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agsurv3.c -o agsurv3.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agsurv4.c -o agsurv4.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c agsurv5.c -o agsurv5.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chinv2.c -o chinv2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chinv3.c -o chinv3.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cholesky2.c -o cholesky2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cholesky3.c -o cholesky3.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chsolve2.c -o chsolve2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chsolve3.c -o chsolve3.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c concordance1.c -o concordance1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cox_Rcallback.c -o cox_Rcallback.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxcount1.c -o coxcount1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxdetail.c -o coxdetail.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxexact.c -o coxexact.o
coxexact.c: In function 'coxexact':
coxexact.c:303:22: warning: 'sstart' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 d0 = coxd0(ndeath, nrisk, score+sstart, dmem0, maxdeath);
                      ^
coxexact.c:191:18: warning: 'nrisk' may be used uninitialized in this function [-Wmaybe-uninitialized]
             nrisk++;
                  ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxfit5.c -o coxfit5.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxfit6.c -o coxfit6.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxmart.c -o coxmart.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxmart2.c -o coxmart2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxph_wtest.c -o coxph_wtest.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxsafe.c -o coxsafe.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxscho.c -o coxscho.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxscore.c -o coxscore.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dmatrix.c -o dmatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c doloop.c -o doloop.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c msurv.c -o msurv.o
msurv.c: In function 'msurv':
msurv.c:16:12: warning: unused variable 'ntime' [-Wunused-variable]
     int    ntime, nstate, n;
            ^
msurv.c:50:42: warning: 'k2' may be used uninitialized in this function [-Wmaybe-uninitialized]
         while (eflag==1 && i2>=0 && etime[k2] >=time) {
                                          ^
msurv.c:13:19: warning: 'i2' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int    eflag, i2, k2;
                   ^
msurv.c:12:21: warning: 'isort' may be used uninitialized in this function [-Wmaybe-uninitialized]
     int    *dsort, *isort;
                     ^
msurv.c:50:42: warning: 'etime' may be used uninitialized in this function [-Wmaybe-uninitialized]
         while (eflag==1 && i2>=0 && etime[k2] >=time) {
                                          ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pyears1.c -o pyears1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pyears2.c -o pyears2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pyears3b.c -o pyears3b.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pystep.c -o pystep.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survConcordance.c -o survConcordance.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survdiff2.c -o survdiff2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survfit4.c -o survfit4.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survfitci.c -o survfitci.o
survfitci.c: In function 'survfitci':
survfitci.c:189:33: warning: 'umat' may be used uninitialized in this function [-Wmaybe-uninitialized]
                             umat[j][k] -= (p[kk]/ws[kk])* hmat[kk][k];
                                 ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survpenal.c -o survpenal.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survreg6.c -o survreg6.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survreg7.c -o survreg7.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survregc1.c -o survregc1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c survregc2.c -o survregc2.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o concordance1.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o init.o msurv.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpQaB70h/R.INSTALL18021d920041/survival/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'survival'
    finding HTML links ... done
    Surv                                    html  
    aareg                                   html  
    agreg.fit                               html  
    aml                                     html  
    anova.coxph                             html  
    attrassign                              html  
    basehaz                                 html  
    bladder                                 html  
    cch                                     html  
    cgd                                     html  
    clogit                                  html  
    cluster                                 html  
    colon                                   html  
    cox.zph                                 html  
    coxph                                   html  
    coxph.control                           html  
    coxph.detail                            html  
    coxph.object                            html  
    coxph.wtest                             html  
    dsurvreg                                html  
    flchain                                 html  
    frailty                                 html  
    heart                                   html  
    is.ratetable                            html  
    kidney                                  html  
    lines.survfit                           html  
    logan                                   html  
    lung                                    html  
    mgus                                    html  
    model.frame.coxph                       html  
    model.matrix.coxph                      html  
    nwtco                                   html  
    ovarian                                 html  
    pbc                                     html  
    pbcseq                                  html  
    plot.aareg                              html  
    plot.cox.zph                            html  
    plot.survfit                            html  
    predict.coxph                           html  
    predict.survreg                         html  
    print.aareg                             html  
    print.summary.coxph                     html  
    print.summary.survexp                   html  
    print.summary.survfit                   html  
    print.survfit                           html  
    pspline                                 html  
    pyears                                  html  
    quantile.survfit                        html  
    ratetable                               html  
    ratetableDate                           html  
    rats                                    html  
    rats2                                   html  
    residuals.coxph                         html  
    residuals.survreg                       html  
    ridge                                   html  
    stanford2                               html  
    strata                                  html  
    summary.aareg                           html  
    summary.coxph                           html  
    summary.survexp                         html  
    summary.survfit                         html  
    survConcordance                         html  
    survSplit                               html  
    survdiff                                html  
    survexp                                 html  
    survexp.fit                             html  
    survexp.us                              html  
    survfit                                 html  
    survfit.coxph                           html  
    survfit.formula                         html  
    survfit.object                          html  
    survfitcoxph.fit                        html  
    survival-internal                       html  
    survobrien                              html  
    survreg                                 html  
    survreg.control                         html  
    survreg.distributions                   html  
    survreg.object                          html  
    survregDtest                            html  
    tcut                                    html  
    tobin                                   html  
    untangle.specials                       html  
    uspop2                                  html  
    veteran                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
Making 'packages.html' ... done
begin installing recommended package class
* installing *source* package 'cluster' ...
** package 'cluster' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c clara.c -o clara.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c daisy.f -o daisy.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dysta.f -o dysta.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c fanny.c -o fanny.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c mona.f -o mona.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pam.c -o pam.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sildist.c -o sildist.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c spannel.c -o spannel.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c twins.c -o twins.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cluster'
    finding HTML links ... done
    agnes                                   html  
    agnes.object                            html  
    agriculture                             html  
    animals                                 html  
    bannerplot                              html  
    chorSub                                 html  
    clara                                   html  
    clara.object                            html  
    clusGap                                 html  
    clusplot.default                        html  
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/clusplot.default.Rd:208: missing file link 'cov.mve'
    clusplot.partition                      html  
    cluster-internal                        html  
    coef.hclust                             html  
    daisy                                   html  
    diana                                   html  
    dissimilarity.object                    html  
    ellipsoidhull                           html  
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/ellipsoidhull.Rd:36: missing file link 'cov.mve'
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/ellipsoidhull.Rd:86: missing file link 'cov.mve'
    fanny                                   html  
    fanny.object                            html  
    flower                                  html  
    lower.to.upper.tri.inds                 html  
    mona                                    html  
    mona.object                             html  
    pam                                     html  
    pam.object                              html  
    partition.object                        html  
    plantTraits                             html  
    plot.agnes                              html  
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/plot.agnes.Rd:73: missing file link 'plot.dendrogram'
    plot.diana                              html  
    plot.mona                               html  
    plot.partition                          html  
    pltree                                  html  
    pltree.twins                            html  
    pluton                                  html  
    predict.ellipsoid                       html  
    print.agnes                             html  
    print.clara                             html  
    print.diana                             html  
    print.dissimilarity                     html  
Rd warning: /usr/src/tmp/RtmpaCibDs/R.INSTALL1a074e029f9/cluster/man/print.dissimilarity.Rd:27: missing file link 'print.dist'
    print.fanny                             html  
    print.mona                              html  
    print.pam                               html  
    ruspini                                 html  
    silhouette                              html  
    sizeDiss                                html  
    summary.agnes                           html  
    summary.clara                           html  
    summary.diana                           html  
    summary.mona                            html  
    summary.pam                             html  
    twins.object                            html  
    volume.ellipsoid                        html  
    votes.repub                             html  
    xclara                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (cluster)
Making 'packages.html' ... done
begin installing recommended package boot
* installing *source* package 'class' ...
** package 'class' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/Rtmp021oNH/R.INSTALL1ad0799d6abd/class/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c class.c -o class.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/Rtmp021oNH/R.INSTALL1ad0799d6abd/class/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'class'
    finding HTML links ... done
    SOM                                     html  
    batchSOM                                html  
    condense                                html  
    knn                                     html  
    knn.cv                                  html  
    knn1                                    html  
    lvq1                                    html  
    lvq2                                    html  
    lvq3                                    html  
    lvqinit                                 html  
    lvqtest                                 html  
    multiedit                               html  
    olvq1                                   html  
    reduce.nn                               html  
    somgrid                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (class)
Making 'packages.html' ... done
* installing *source* package 'boot' ...
** package 'boot' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'boot'
    finding HTML links ... done
    EEF.profile                             html  
    Imp.Estimates                           html  
    abc.ci                                  html  
    acme                                    html  
    aids                                    html  
    aircondit                               html  
    amis                                    html  
    aml                                     html  
    beaver                                  html  
    bigcity                                 html  
    boot-practicals                         html  
    boot                                    html  
    boot.array                              html  
    boot.ci                                 html  
    brambles                                html  
    breslow                                 html  
    calcium                                 html  
    cane                                    html  
    capability                              html  
    catsM                                   html  
    cav                                     html  
    cd4                                     html  
    cd4.nested                              html  
    censboot                                html  
    channing                                html  
    claridge                                html  
    cloth                                   html  
    co.transfer                             html  
    coal                                    html  
    control                                 html  
    corr                                    html  
    cum3                                    html  
    cv.glm                                  html  
    darwin                                  html  
    dogs                                    html  
    downs.bc                                html  
    ducks                                   html  
    empinf                                  html  
    envelope                                html  
    exp.tilt                                html  
    fir                                     html  
    freq.array                              html  
    frets                                   html  
    glm.diag                                html  
    glm.diag.plots                          html  
    gravity                                 html  
    hirose                                  html  
    imp.weights                             html  
    inv.logit                               html  
    islay                                   html  
    jack.after.boot                         html  
    k3.linear                               html  
    linear.approx                           html  
    lines.saddle.distn                      html  
    logit                                   html  
    manaus                                  html  
    melanoma                                html  
    motor                                   html  
    neuro                                   html  
    nitrofen                                html  
    nodal                                   html  
    norm.ci                                 html  
    nuclear                                 html  
    paulsen                                 html  
    plot.boot                               html  
    poisons                                 html  
    polar                                   html  
    print.boot                              html  
    print.bootci                            html  
    print.saddle.distn                      html  
    print.simplex                           html  
    remission                               html  
    saddle                                  html  
    saddle.distn                            html  
    saddle.distn.object                     html  
    salinity                                html  
    simplex                                 html  
    simplex.object                          html  
    smooth.f                                html  
    sunspot                                 html  
    survival                                html  
    tau                                     html  
    tilt.boot                               html  
    tsboot                                  html  
    tuna                                    html  
    urine                                   html  
    var.linear                              html  
    wool                                    html  
** building package indices
** testing if installed package can be loaded
* DONE (boot)
Making 'packages.html' ... done
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpRs3bjG/R.INSTALL19f357052816/nlme/src'
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chol.f -o chol.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c corStruct.c -o corStruct.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gnls.c -o gnls.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c matrix.c -o matrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c nlOptimizer.c -o nlOptimizer.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c nlme.c -o nlme.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c nlmefit.c -o nlmefit.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c nls.c -o nls.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include   -fvisibility=hidden -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c pdMat.c -o pdMat.o
f95   -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c rs.f -o rs.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpRs3bjG/R.INSTALL19f357052816/nlme/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nlme'
    finding HTML links ... done
    ACF                                     html  
    ACF.gls                                 html  
    ACF.lme                                 html  
    Alfalfa                                 html  
    Assay                                   html  
    BodyWeight                              html  
    Cefamandole                             html  
    Coef                                    html  
    Covariate                               html  
    Covariate.varFunc                       html  
    Dialyzer                                html  
    Dim                                     html  
    Dim.corSpatial                          html  
    Dim.corStruct                           html  
    Dim.pdMat                               html  
    Earthquake                              html  
    Extract.pdMat                           html  
    Fatigue                                 html  
    Gasoline                                html  
    Glucose                                 html  
    Glucose2                                html  
    Gun                                     html  
    IGF                                     html  
    Initialize                              html  
    Initialize.corStruct                    html  
    Initialize.glsStruct                    html  
    Initialize.lmeStruct                    html  
    Initialize.reStruct                     html  
    Initialize.varFunc                      html  
    LDEsysMat                               html  
    Machines                                html  
    MathAchSchool                           html  
    MathAchieve                             html  
    Matrix                                  html  
    Matrix.pdMat                            html  
    Matrix.reStruct                         html  
    Meat                                    html  
    Milk                                    html  
    Muscle                                  html  
    Names                                   html  
    Names.formula                           html  
    Names.pdBlocked                         html  
    Names.pdMat                             html  
    Names.reStruct                          html  
    Nitrendipene                            html  
    Oats                                    html  
    Orthodont                               html  
    Ovary                                   html  
    Oxboys                                  html  
    Oxide                                   html  
    PBG                                     html  
    Phenobarb                               html  
    Pixel                                   html  
    Quinidine                               html  
    Rail                                    html  
    RatPupWeight                            html  
    Relaxin                                 html  
    Remifentanil                            html  
    Soybean                                 html  
    Spruce                                  html  
    Tetracycline1                           html  
    Tetracycline2                           html  
    VarCorr                                 html  
    Variogram                               html  
    Variogram.corExp                        html  
    Variogram.corGaus                       html  
    Variogram.corLin                        html  
    Variogram.corRatio                      html  
    Variogram.corSpatial                    html  
    Variogram.corSpher                      html  
    Variogram.default                       html  
    Variogram.gls                           html  
    Variogram.lme                           html  
    Wafer                                   html  
    Wheat                                   html  
    Wheat2                                  html  
    allCoef                                 html  
    anova.gls                               html  
    anova.lme                               html  
    as.matrix.corStruct                     html  
    as.matrix.pdMat                         html  
    as.matrix.reStruct                      html  
    asOneFormula                            html  
    asTable                                 html  
    augPred                                 html  
    balancedGrouped                         html  
    bdf                                     html  
    coef.corStruct                          html  
    coef.gnls                               html  
    coef.lmList                             html  
    coef.lme                                html  
    coef.modelStruct                        html  
    coef.pdMat                              html  
    coef.reStruct                           html  
    coef.varFunc                            html  
    collapse                                html  
    collapse.groupedData                    html  
    compareFits                             html  
    comparePred                             html  
    corAR1                                  html  
    corARMA                                 html  
    corCAR1                                 html  
    corClasses                              html  
    corCompSymm                             html  
    corExp                                  html  
    corFactor                               html  
    corFactor.corStruct                     html  
    corGaus                                 html  
    corLin                                  html  
    corMatrix                               html  
    corMatrix.corStruct                     html  
    corMatrix.pdMat                         html  
    corMatrix.reStruct                      html  
    corNatural                              html  
    corRatio                                html  
    corSpatial                              html  
    corSpher                                html  
    corSymm                                 html  
    ergoStool                               html  
    fdHess                                  html  
    fitted.glsStruct                        html  
    fitted.gnlsStruct                       html  
    fitted.lmList                           html  
    fitted.lme                              html  
    fitted.lmeStruct                        html  
    fitted.nlmeStruct                       html  
    fixed.effects                           html  
    fixef.lmList                            html  
    formula.pdBlocked                       html  
    formula.pdMat                           html  
    formula.reStruct                        html  
    gapply                                  html  
    getCovariate                            html  
    getCovariate.corStruct                  html  
    getCovariate.data.frame                 html  
    getCovariate.varFunc                    html  
    getCovariateFormula                     html  
    getData                                 html  
    getData.gls                             html  
    getData.lmList                          html  
    getData.lme                             html  
    getGroups                               html  
    getGroups.corStruct                     html  
    getGroups.data.frame                    html  
    getGroups.gls                           html  
    getGroups.lmList                        html  
    getGroups.lme                           html  
    getGroups.varFunc                       html  
    getGroupsFormula                        html  
    getResponse                             html  
    getResponseFormula                      html  
    getVarCov                               html  
    gls-internal                            html  
    gls                                     html  
    glsControl                              html  
    glsObject                               html  
    glsStruct                               html  
    gnls                                    html  
    gnlsControl                             html  
    gnlsObject                              html  
    gnlsStruct                              html  
    groupedData                             html  
    gsummary                                html  
    intervals                               html  
    intervals.gls                           html  
    intervals.lmList                        html  
    intervals.lme                           html  
    isBalanced                              html  
    isInitialized                           html  
    lmList                                  html  
    lmList.groupedData                      html  
    lme                                     html  
    lme.groupedData                         html  
    lme.lmList                              html  
    lmeControl                              html  
    lmeObject                               html  
    lmeStruct                               html  
    logDet                                  html  
    logDet.corStruct                        html  
    logDet.pdMat                            html  
    logDet.reStruct                         html  
    logLik.corStruct                        html  
    logLik.glsStruct                        html  
    logLik.gnls                             html  
    logLik.gnlsStruct                       html  
    logLik.lmList                           html  
    logLik.lme                              html  
    logLik.lmeStruct                        html  
    logLik.reStruct                         html  
    logLik.varFunc                          html  
    model.matrix.reStruct                   html  
    needUpdate                              html  
    needUpdate.modelStruct                  html  
    nlme                                    html  
    nlme.nlsList                            html  
    nlmeControl                             html  
    nlmeObject                              html  
    nlmeStruct                              html  
    nlsList                                 html  
    nlsList.selfStart                       html  
    pairs.compareFits                       html  
    pairs.lmList                            html  
    pairs.lme                               html  
    pdBlocked                               html  
    pdClasses                               html  
    pdCompSymm                              html  
    pdConstruct                             html  
    pdConstruct.pdBlocked                   html  
    pdDiag                                  html  
    pdFactor                                html  
    pdFactor.reStruct                       html  
    pdIdent                                 html  
    pdLogChol                               html  
    pdMat                                   html  
    pdMatrix                                html  
    pdMatrix.reStruct                       html  
    pdNatural                               html  
    pdSymm                                  html  
    phenoModel                              html  
    plot.ACF                                html  
    plot.Variogram                          html  
    plot.augPred                            html  
    plot.compareFits                        html  
    plot.gls                                html  
    plot.intervals.lmList                   html  
    plot.lmList                             html  
    plot.lme                                html  
    plot.nffGroupedData                     html  
    plot.nfnGroupedData                     html  
    plot.nmGroupedData                      html  
    plot.ranef.lmList                       html  
    plot.ranef.lme                          html  
    pooledSD                                html  
    predict.gls                             html  
    predict.gnls                            html  
    predict.lmList                          html  
    predict.lme                             html  
    predict.nlme                            html  
    print.summary.pdMat                     html  
    print.varFunc                           html  
    qqnorm.gls                              html  
    qqnorm.lme                              html  
    quinModel                               html  
    random.effects                          html  
    ranef.lmList                            html  
    ranef.lme                               html  
    reStruct                                html  
    recalc                                  html  
    recalc.corStruct                        html  
    recalc.modelStruct                      html  
    recalc.reStruct                         html  
    recalc.varFunc                          html  
    residuals.gls                           html  
    residuals.glsStruct                     html  
    residuals.gnlsStruct                    html  
    residuals.lmList                        html  
    residuals.lme                           html  
    residuals.lmeStruct                     html  
    residuals.nlmeStruct                    html  
    simulate.lme                            html  
    solve.pdMat                             html  
    solve.reStruct                          html  
    splitFormula                            html  
    summary.corStruct                       html  
    summary.gls                             html  
    summary.lmList                          html  
    summary.lme                             html  
    summary.modelStruct                     html  
    summary.nlsList                         html  
    summary.pdMat                           html  
    summary.varFunc                         html  
    update.modelStruct                      html  
    update.varFunc                          html  
    varClasses                              html  
    varComb                                 html  
    varConstPower                           html  
    varExp                                  html  
    varFixed                                html  
    varFunc                                 html  
    varIdent                                html  
    varPower                                html  
    varWeights                              html  
    varWeights.glsStruct                    html  
    varWeights.lmeStruct                    html  
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
Making 'packages.html' ... done
* installing *source* package 'Matrix' ...
** package 'Matrix' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c CHMfactor.c -o CHMfactor.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Csparse.c -o Csparse.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c TMatrix_as.c -o TMatrix_as.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Tsparse.c -o Tsparse.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c Mutils.c -o Mutils.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c chm_common.c -o chm_common.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cs.c -o cs.o
cs.c: In function 'cs_qr':
cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
     csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
                  ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c cs_utils.c -o cs_utils.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dense.c -o dense.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dgCMatrix.c -o dgCMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dgTMatrix.c -o dgTMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dgeMatrix.c -o dgeMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dpoMatrix.c -o dpoMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dppMatrix.c -o dppMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dsCMatrix.c -o dsCMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dsyMatrix.c -o dsyMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dspMatrix.c -o dspMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dtCMatrix.c -o dtCMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dtTMatrix.c -o dtTMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dtrMatrix.c -o dtrMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c dtpMatrix.c -o dtpMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c factorizations.c -o factorizations.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ldense.c -o ldense.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c lgCMatrix.c -o lgCMatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sparseQR.c -o sparseQR.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c abIndex.c -o abIndex.o
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD/Lib'
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD'
( cd Source ; make clean )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD/Source'
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD'
( cd Source ; make clean )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD/Source'
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD/Source'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/SuiteSparse_config'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/SuiteSparse_config'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD'
( cd Lib ; make )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_aat.c -o cholmod_aat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_add.c -o cholmod_add.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_band.c -o cholmod_band.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_common.c -o cholmod_common.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_complex.c -o cholmod_complex.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_error.c -o cholmod_error.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_factor.c -o cholmod_factor.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_memory.c -o cholmod_memory.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_version.c -o cholmod_version.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                      ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Check/cholmod_read.c -o cholmod_read.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Check/cholmod_write.c -o cholmod_write.o
../Check/cholmod_write.c: In function 'cholmod_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^
../Check/cholmod_check.c: In function 'check_factor.constprop':
../Check/cholmod_check.c:1934:48: warning: 'psxend' may be used uninitialized in this function [-Wmaybe-uninitialized]
                     || (for_cholesky && psxend - psx != nsrow * nscol))
                                                ^
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
../Core/cholmod_copy.c: In function 'cholmod_l_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                      ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
../Check/cholmod_write.c: In function 'cholmod_l_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^
../Check/cholmod_check.c: In function 'check_factor.constprop':
../Check/cholmod_check.c:1934:48: warning: 'psxend' may be used uninitialized in this function [-Wmaybe-uninitialized]
                     || (for_cholesky && psxend - psx != nsrow * nscol))
                                                ^
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o 
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD/Lib'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/CHOLMOD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD'
( cd Source ; make lib )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c colamd_global.c -o colamd_global.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c colamd.c -o colamd.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD/Source'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/COLAMD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD'
( cd Source ; make lib )
make[5]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_global.c -o amd_i_global.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o 
make[5]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD/Source'
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/AMD'
make[4]: Entering directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/SuiteSparse_config'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG -DNTIMER -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[4]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src/SuiteSparse_config'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'image' from package 'graphics' in package 'Matrix'
Creating a generic function for 'solve' from package 'base' in package 'Matrix'
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix'
Creating a generic function for 'determinant' from package 'base' in package 'Matrix'
Creating a generic function for 'update' from package 'stats' in package 'Matrix'
Creating a generic function for 'as.vector' from package 'base' in package 'Matrix'
Creating a generic function for 't' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'as.matrix' from package 'base' in package 'Matrix'
Creating a generic function for 'as.array' from package 'base' in package 'Matrix'
Creating a generic function for 'head' from package 'utils' in package 'Matrix'
Creating a generic function for 'tail' from package 'utils' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'mean' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'isSymmetric' from package 'base' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'chol' from package 'base' in package 'Matrix'
Creating a generic function for 'norm' from package 'base' in package 'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package 'Matrix'
Creating a generic function for 'all.equal' from package 'base' in package 'Matrix'
Creating a generic function for 'diff' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc"
Creating a generic function for 'colSums' from package 'base' in package 'Matrix'
Creating a generic function for 'colMeans' from package 'base' in package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package 'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix'
in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix'
Creating a generic function for 'qr' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package 'Matrix'
Creating a generic function for 'crossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'print' from package 'base' in package 'Matrix'
Creating a generic function for 'summary' from package 'base' in package 'Matrix'
Creating a generic function for 'which' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
Creating a generic function for 'format' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
** help
*** installing help indices
  converting help for package 'Matrix'
    finding HTML links ... done
    BunchKaufman-methods                    html  
    CAex                                    html  
    CHMfactor-class                         html  
    Cholesky-class                          html  
    Cholesky                                html  
    CsparseMatrix-class                     html  
    Diagonal                                html  
    Hilbert                                 html  
    KNex                                    html  
    KhatriRao                               html  
    LU-class                                html  
    Matrix-class                            html  
    Matrix                                  html  
    MatrixFactorization-class               html  
    RsparseMatrix-class                     html  
    Schur-class                             html  
    Schur                                   html  
    SparseM-conv                            html  
    Subassign-methods                       html  
    TsparseMatrix-class                     html  
    USCounties                              html  
    Xtrct-methods                           html  
    abIndex-class                           html  
Rd warning: /usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/man/abIndex-class.Rd:81: missing file link 'Ops'
    abIseq                                  html  
    all-methods                             html  
    all.equal-methods                       html  
    atomicVector-class                      html  
    band                                    html  
    bandSparse                              html  
    bdiag                                   html  
    cBind                                   html  
    chol                                    html  
    chol2inv-methods                        html  
    colSums                                 html  
    compMatrix-class                        html  
    condest                                 html  
    dMatrix-class                           html  
    ddenseMatrix-class                      html  
    ddiMatrix-class                         html  
    denseMatrix-class                       html  
    dgCMatrix-class                         html  
    dgRMatrix-class                         html  
    dgTMatrix-class                         html  
    dgeMatrix-class                         html  
    diagU2N                                 html  
    diagonalMatrix-class                    html  
    dpoMatrix-class                         html  
    drop0                                   html  
    dsCMatrix-class                         html  
    dsRMatrix-class                         html  
    dsparseMatrix-class                     html  
    dsyMatrix-class                         html  
    dtCMatrix-class                         html  
    dtRMatrix-class-def                     html  
    dtpMatrix-class                         html  
    dtrMatrix-class                         html  
    expand                                  html  
    expm                                    html  
    externalFormats                         html  
    facmul                                  html  
    forceSymmetric                          html  
    formatSparseM                           html  
    generalMatrix-class                     html  
    graph2T                                 html  
    image-methods                           html  
Rd warning: /usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/man/image-methods.Rd:48: missing file link 'panel.levelplot.raster'
    indMatrix-class                         html  
    index-class                             html  
    invPerm                                 html  
    is.na-methods                           html  
    is.null.DN                              html  
    isSymmetric-methods                     html  
    isTriangular                            html  
    kronecker-methods                       html  
    ldenseMatrix-class                      html  
    ldiMatrix-class                         html  
    lgeMatrix-class                         html  
    lsparseMatrix-classes                   html  
    lsyMatrix-class                         html  
    ltrMatrix-class                         html  
    lu                                      html  
    matrix-products                         html  
Rd warning: /usr/src/tmp/RtmpwID6Zg/R.INSTALL19da12b4a4df/Matrix/man/matrix-products.Rd:325: missing file link 'tcrossprod'
    nMatrix-class                           html  
    ndenseMatrix-class                      html  
    nearPD                                  html  
    ngeMatrix-class                         html  
    nnzero                                  html  
    norm                                    html  
    nsparseMatrix-classes                   html  
    nsyMatrix-class                         html  
    ntrMatrix-class                         html  
    number-class                            html  
    pMatrix-class                           html  
    printSpMatrix                           html  
    qr-methods                              html  
    rankMatrix                              html  
    rcond                                   html  
    rep2abI                                 html  
    replValue-class                         html  
    rleDiff-class                           html  
    rsparsematrix                           html  
    solve-methods                           html  
    spMatrix                                html  
    sparse.model.matrix                     html  
    sparseLU-class                          html  
    sparseMatrix-class                      html  
    sparseMatrix                            html  
    sparseQR-class                          html  
    sparseVector-class                      html  
    sparseVector                            html  
    symmetricMatrix-class                   html  
    symmpart                                html  
    triangularMatrix-class                  html  
    unpack                                  html  
    unused-classes                          html  
    updown                                  html  
** building package indices
Loading required package: Matrix
** installing vignettes
   'Comparisons.Rnw' 
   'Design-issues.Rnw' 
   'Intro2Matrix.Rnw' 
   'Introduction.Rnw' 
   'sparseModels.Rnw' 
** testing if installed package can be loaded
* DONE (Matrix)
Making 'packages.html' ... done
begin installing recommended package mgcv
* installing *source* package 'mgcv' ...
** package 'mgcv' successfully unpacked and MD5 sums checked
** libs
make[3]: Entering directory `/usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/src'
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c coxph.c -o coxph.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c gdi.c -o gdi.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c magic.c -o magic.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c mat.c -o mat.o
coxph.c: In function 'coxlpl':
coxph.c:309:39: warning: 'd2ldA_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 d2ldA_p[l + off * *p] +=  d2gamma[i+ off * *n] * X[i + *n * l] * X[ i + *n *l];
                                       ^
coxph.c:302:47: warning: 'd1A_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
               d1A_p[k + *p * l + m * *p * *p] += xx * X[i + *n * k] * X[i + *n * l];             
                                               ^
coxph.c:381:27: warning: 'd1b_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
     R_chk_free(d1gamma_p);R_chk_free(d1b_p);
                           ^
coxph.c:380:5: warning: 'd1eta' may be used uninitialized in this function [-Wmaybe-uninitialized]
     R_chk_free(d1eta);R_chk_free(d1gamma);
     ^
coxph.c:381:5: warning: 'd1gamma_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
     R_chk_free(d1gamma_p);R_chk_free(d1b_p);
     ^
coxph.c:380:23: warning: 'd1gamma' may be used uninitialized in this function [-Wmaybe-uninitialized]
     R_chk_free(d1eta);R_chk_free(d1gamma);
                       ^
coxph.c:293:35: warning: 'd2b_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
               d2b_p[l + off * *p] +=  d2gamma[i+ off * *n] * X[i + *n * l];
                                   ^
coxph.c:195:22: warning: 'd2gamma_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *d2eta,*d2gamma,*d2gamma_p,*d2b_p,
                      ^
coxph.c:309:50: warning: 'd2gamma' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 d2ldA_p[l + off * *p] +=  d2gamma[i+ off * *n] * X[i + *n * l] * X[ i + *n *l];
                                                  ^
coxph.c:386:5: warning: 'd2eta' may be used uninitialized in this function [-Wmaybe-uninitialized]
     R_chk_free(d2eta);R_chk_free(d2gamma);
     ^
coxph.c:348:36: warning: 'A_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
     d2H[l + off * *p] += xx3 * (A_p[l + *p *l] * d1gamma_p[k] + 
                                    ^
coxph.c:192:6: warning: 'b_p' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *b_p,*A_p,*p1,*p2,*p3,*p4,
      ^
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c matrix.c -o matrix.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c mgcv.c -o mgcv.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c misc.c -o misc.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c mvn.c -o mvn.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c qp.c -o qp.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c soap.c -o soap.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c sparse-smooth.c -o sparse-smooth.o
x86_64-alt-linux-gcc -I/usr/src/RPM/BUILD/R-3.1.2/include -DNDEBUG  -I/usr/local/include    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -c tprs.c -o tprs.o
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.1.2/lib -L/usr/local/lib64 -o mgcv.so coxph.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.1.2/lib -lR
make[3]: Leaving directory `/usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/src'
installing to /usr/src/RPM/BUILD/R-3.1.2/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mgcv'
    finding HTML links ... done
    Beta                                    html  
    Predict.matrix                          html  
    Predict.matrix.cr.smooth                html  
    Predict.matrix.soap.film                html  
    Rrank                                   html  
    Tweedie                                 html  
    anova.gam                               html  
    bam                                     html  
Rd warning: /usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/man/bam.Rd:13: missing file link 'parallel'
Rd warning: /usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/man/bam.Rd:120: missing file link 'parLapply'
Rd warning: /usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/man/bam.Rd:165: missing file link 'makeForkCluster'
    bam.update                              html  
    cSplineDes                              html  
    choose.k                                html  
    columb                                  html  
    concurvity                              html  
    coxph                                   html  
    exclude.too.far                         html  
    extract.lme.cov                         html  
    family.mgcv                             html  
    fix.family.link                         html  
    fixDependence                           html  
    formXtViX                               html  
    formula.gam                             html  
    fs.test                                 html  
    full.score                              html  
    gam                                     html  
    gam.check                               html  
    gam.control                             html  
    gam.convergence                         html  
    gam.fit                                 html  
    gam.fit3                                html  
    gam.models                              html  
    gam.outer                               html  
    gam.scale                               html  
    gam.selection                           html  
    gam.side                                html  
    gam.vcomp                               html  
    gam2objective                           html  
    gamObject                               html  
    gamSim                                  html  
    gamm                                    html  
    gaulss                                  html  
    get.var                                 html  
    in.out                                  html  
    inSide                                  html  
    influence.gam                           html  
    initial.sp                              html  
    interpret.gam                           html  
    ldTweedie                               html  
    linear.functional.terms                 html  
    logLik.gam                              html  
    ls.size                                 html  
    magic                                   html  
    magic.post.proc                         html  
    mgcv-FAQ                                html  
    mgcv-package                            html  
    mgcv-parallel                           html  
Rd warning: /usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/man/mgcv-parallel.Rd:7: missing file link 'parallel'
    model.matrix.gam                        html  
    mono.con                                html  
    mroot                                   html  
    mvn                                     html  
    negbin                                  html  
    new.name                                html  
    notExp                                  html  
    notExp2                                 html  
    null.space.dimension                    html  
    ocat                                    html  
    pcls                                    html  
    pdIdnot                                 html  
    pdTens                                  html  
    pen.edf                                 html  
    place.knots                             html  
    plot.gam                                html  
    polys.plot                              html  
    predict.bam                             html  
Rd warning: /usr/src/tmp/RtmprNiBIc/R.INSTALL1c8e1a8e1901/mgcv/man/predict.bam.Rd:71: missing file link 'parLapply'
    predict.gam                             html  
    print.gam                               html  
    qq.gam                                  html  
    rTweedie                                html  
    random.effects                          html  
    residuals.gam                           html  
    rig                                     html  
    s                                       html  
    scat                                    html  
    slanczos                                html  
    smooth.construct                        html  
    smooth.construct.ad.smooth.spec         html  
    smooth.construct.cr.smooth.spec         html  
    smooth.construct.ds.smooth.spec         html  
    smooth.construct.fs.smooth.spec         html  
    smooth.construct.mrf.smooth.spec        html  
    smooth.construct.ps.smooth.spec         html  
    smooth.construct.re.smooth.spec         html  
    smooth.construct.so.smooth.spec         html  
    smooth.construct.sos.smooth.spec        html  
    smooth.construct.t2.smooth.spec         html  
    smooth.construct.tensor.smooth.spec     html  
    smooth.construct.tp.smooth.spec         html  
    smooth.terms                            html  
    smoothCon                               html  
    sp.vcov                                 html  
    spasm.construct                         html  
    step.gam                                html  
    summary.gam                             html  
    t2                                      html  
    te                                      html  
    tensor.prod.model.matrix                html  
    uniquecombs                             html  
    vcov.gam                                html  
    vis.gam                                 html  
    ziP                                     html  
    ziplss                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (mgcv)
Making 'packages.html' ... done
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/Recommended'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library/Recommended'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
building/updating vignettes for package 'grid' ...
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2'
+ '[' -n 4 ']'
+ make -j4 pdf info
make: Entering directory `/usr/src/RPM/BUILD/R-3.1.2'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
creating doc/manual/version.tex
ERROR: 'makeinfo' v4.7 or later needed but missing on your system.
make[2]: *** [R-FAQ.info] Error 1
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[1]: *** [info] Error 2
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make: [info] Error 2 (ignored)
collecting LaTeX docs for package 'base' ...
collecting LaTeX docs for package 'utils' ...
collecting LaTeX docs for package 'grDevices' ...
collecting LaTeX docs for package 'tools' ...
Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX ............
...collecting LaTeX docs for package 'graphics' ...
..
.Converting parsed Rd's to LaTeX ..collecting LaTeX docs for package 'stats' ...
.Converting parsed Rd's to LaTeX ..........
...collecting LaTeX docs for package 'datasets' ...
..Converting parsed Rd's to LaTeX .......
.......collecting LaTeX docs for package 'methods' ...
....Converting parsed Rd's to LaTeX .
..collecting LaTeX docs for package 'grid' ...
.Converting parsed Rd's to LaTeX ............................
....collecting LaTeX docs for package 'splines' ...

..Converting parsed Rd's to LaTeX .collecting LaTeX docs for package 'stats4' ...
..
..Converting parsed Rd's to LaTeX ...
..collecting LaTeX docs for package 'tcltk' ...
..collecting LaTeX docs for package 'compiler' ...
Converting parsed Rd's to LaTeX ..Converting parsed Rd's to LaTeX 
...
..collecting LaTeX docs for package 'MASS' ...
collecting LaTeX docs for package 'parallel' ...
.Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX ....
collecting LaTeX docs for package 'lattice' ...
..Converting parsed Rd's to LaTeX .......
....collecting LaTeX docs for package 'Matrix' ...
....Converting parsed Rd's to LaTeX ...................
collecting LaTeX docs for package 'nlme' ...
.
.Converting parsed Rd's to LaTeX 
.collecting LaTeX docs for package 'survival' ...
collecting LaTeX docs for package 'boot' ...
.Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX ...............................
.collecting LaTeX docs for package 'cluster' ...

..collecting LaTeX docs for package 'codetools' ...
..
Converting parsed Rd's to LaTeX collecting LaTeX docs for package 'foreign' ...
.Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'KernSmooth' ...
Converting parsed Rd's to LaTeX ..Converting parsed Rd's to LaTeX 
.collecting LaTeX docs for package 'rpart' ...

.collecting LaTeX docs for package 'class' ...
Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX .....
collecting LaTeX docs for package 'nnet' ...
...
collecting LaTeX docs for package 'spatial' ...
...
Converting parsed Rd's to LaTeX .collecting LaTeX docs for package 'mgcv' ...
Converting parsed Rd's to LaTeX .
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi
.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi
Converting parsed Rd's to LaTeX ....This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1
[1] Chapter 2 [2]. Cross reference values unknown; you must run TeX again.
[3] [4] [5] [6] [7] [8] [9] Chapter 3 [10]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,
Underfull \hbox (badness 7685) in paragraph at lines 1121--1125
 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[11 markup, glyphs,
page headings, tables,] conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, [12] formatting, and turning on texinfo input format.)
(/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/cache/texmf/fonts/map/pdftex/
updmap/pdftex.map
Underfull \hbox (badness 10000) in paragraph at lines 1261--1265
[]@textrm Running @texttt make[] @textrm in @textttsl R_HOME@texttt /src/gnuwin
32/bitmap[] @textrm or @texttt make bitmapdll[] @textrm in

Underfull \hbox (badness 10000) in paragraph at lines 1261--1265
@textttsl R_HOME@texttt /src/gnuwin32[] @textrm should build @texttt Rbitmap.dl
l[] @textrm and in-stall it un-der @textttsl R_
[13]
Underfull \hbox (badness 10000) in paragraph at lines 1348--1352
[]@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de
vel[] @textrm and @texttt make
[14}]] [-1] Chapter 1 [15]
Cross reference values unknown; you must run TeX again. Chapter 4 [16] [1] Chapter 2 [2] [17] Chapter 5 [18
[3]].. Chapter 6 [19] [4] [20 [5]] [21] [6] [7 [22]] [8]
Overfull \hbox (29.11234pt too wide) in paragraph at lines 2121--2131
[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[23 [9]] [24] [10] Chapter 3 [11 [25]] Chapter 7 [26] [12] [13] [27 [14]] [15] [28] Chapter 8 [29 [16]]
[17 Chapter 9 [30]] [18] [31] Chapter 4 [19
[32]] Appendix A [33] [20 [34]] Chapter 5 [21] [35] [22] [36] [23] [37] [24] [25] [38] Chapter 6
[26] [39 [27]] Chapter 7 [28 [40]] [41] [29] Appendix B
[42 [30]] [43 [31]] [32] [44] [33] [45 [34]] [35 [46]] Appendix C [47] [36 [48]] [49] [37] [50] [38 [51]]
[39] [52] [40] [53] [41 [54]]
Overfull \hbox (45.05586pt too wide) in paragraph at lines 4762--4762
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig[] 
[55 [42]] Chapter 8 [43]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 4913--4913
 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Con
tents/Home[] 
[56] [57 Chapter 9 [44]] [58] [45]
Underfull \hbox (badness 10000) in paragraph at lines 5131--5134
[]@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe
r per-for-mance:
[59] Chapter 10 [46] [47 [60]] )</
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmb10.pfb></usr/share/texmf-texl
ive/fonts/type1/bluesky/cm/cmbx12.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmcsc10.pfb [61></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmex10.pfb
]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-
texlive/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1
/bluesky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pf
b></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmsl10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.p
fb [62></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texm
f-texlive/fonts/type1/bluesky/cm/cmti10.pfb></usr/share/texmf-texlive/fonts/typ
e1/bluesky/cm/cmtt10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt1
2.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb></usr/share/te
xmf-texlive/fonts/type1/bluesky/latex-fonts/lcircle1.pfb> [63
Output written on R-FAQ.pdf (49 pages, 351735 bytes).
Transcript written on R-FAQ.log.
] Appendix D [64] [65] [66]
(Function and variable index) [67] (Concept index) [68]
(Environment variable index) [69]. [70] )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmcsc10.pfb></usr
/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/
cm/cmr8.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb></usr/sha
re/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb></usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb.></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmtt9.pfb>
Output written on R-admin.pdf (73 pages, 443107 bytes).
Transcript written on R-admin.log.

TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi
This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,. formatting, and turning on texinfo input format.) (./R-FAQ.auxThis is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(./R-admin.aux)
(/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/cache/texmf/fonts/map/pdftex/
updmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc)
Chapter 1 [1] Chapter 2 [2]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex))
(./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map. [3]}] [4
[2] (./R-admin.toc] [-1 [5]] [-2 [6]] [7) [-3]] (./R-admin.toc) (./R-admin.toc [8)] Chapter 1
[1 [9]] Chapter 2 [2] [10] Chapter 3 [11]
[12] [13] [14] [3] [15] [4 [16]] [17] [5 [18]] Chapter 4 [19 [6]] [7] [20] [8] Chapter 5 [21] [9] Chapter 3 [10] [22]
[23]
Underfull \hbox (badness 7685) in paragraph at lines 1121--1125
 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[11] [24] [12 [25]] Chapter 6 [26]
Underfull \hbox (badness 10000) in paragraph at lines 1261--1265
[]@textrm Running @texttt make[] @textrm in @textttsl R_HOME@texttt /src/gnuwin
32/bitmap[] @textrm or @texttt make bitmapdll[] @textrm in

Underfull \hbox (badness 10000) in paragraph at lines 1261--1265
@textttsl R_HOME@texttt /src/gnuwin32[] @textrm should build @texttt Rbitmap.dl
l[] @textrm and in-stall it un-der @textttsl R_
[13] [27] Chapter 7
Underfull \hbox (badness 10000) in paragraph at lines 1348--1352
[]@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de
vel[] @textrm and @texttt make
[14 [28]] [15] [29 Chapter 4 [16]] [30] [17 [31]] [32 Chapter 5 [18]] [33 Chapter 6 [19]]
[34] [20 [35]] [21 [36]] [37 [22]] [38
Overfull \hbox (29.11234pt too wide) in paragraph at lines 2121--2131
[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[23]] [39 [24]] [40 [25]] Chapter 7 [41] [26] [42] Chapter 8 [43.] Chapter 9 [44 [27]
[45]] Chapter 10 [46] [47] [28 )</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmb
10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb>]</usr/share/
texmf-texlive/fonts/type1/bluesky/cm/cmcsc10.pfb></usr/share/texmf-texlive/font
s/type1/bluesky/cm/cmex10.pfb Chapter 8></usr/share/texmf-texlive/fonts/type1/bluesky/cm/
cmmi10.pfb [29></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb]></usr/sh
are/texmf-texlive/fonts/type1/bluesky/cm/cmmi7.pfb></usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm
/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share
/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb Chapter 9></usr/share/texmf-texlive/font
s/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmsy10.pfb [30></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb]></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmtt12.pfb></usr/share/texmf-texlive/fonts/type1/bluesk
y/cm/cmtt9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/latex-fonts/lcircl
e1.pfb>
Output written on R-FAQ.pdf (51 pages, 405980 bytes).
Transcript written on R-FAQ.log.
 [31]
[32] Appendix A [33] [34] [35] [36] [37] [38] [39] [40] [41] Appendix B
[42] [43]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [44]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, [45] markup, glyphs,
page headings, tables, conditionals, [46 indexing, sectioning,] toc, environments,
defuns, Appendix C. [47] [48] macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, [49] [50] formatting, and turning on texinfo input format.)
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [51] [52] [53]}] [2] [-1]
(Acknowledgements) [54]
Underfull \hbox (badness 10000) in paragraph at lines 88--88
 [][]@textbf DBI

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 88--88
 @texttt package=DBI[]@textrm )[][]| 

Overfull \hbox (8.53186pt too wide) in paragraph at lines 89--89
 [][]@textbf dataframes2xls

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt org /

Overfull \hbox (67.73643pt too wide) in paragraph at lines 89--89
 @texttt package=dataframes2xls[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 [][]@textbf foreign

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 90--90
 @texttt package=foreign[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 [][]@textbf gdata

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91
 @texttt package=gdata[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 [][]@textbf hdf5

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt org /

Overfull \hbox (10.24956pt too wide) in paragraph at lines 92--92
 @texttt package=hdf5[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf ncdf

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (13.29123pt too wide) in paragraph at lines 93--93
 @texttt package=ncdf[]@textrm )[][],

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf ncdf4

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93
 @texttt package=ncdf4[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 [][]@textbf rJava

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 94--94
 @texttt package=rJava[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 [][]@textbf RJDBC

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 95--95
 @texttt package=RJDBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 [][]@textbf RMySQL

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @textrm (@texttt http: / /

Underfull 
Overfull \hbox (45.05586pt too wide) in paragraph at lines 4762--4762
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig[] 
[55]\hbox (badness 10000) in paragraph at lines 96--96
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt org /

Overfull \hbox (21.74693pt too wide) in paragraph at lines 96--96
 @texttt package=RMySQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 [][]@textbf RNetCDF

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97
 @texttt package=RNetCDF[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 [][]@textbf RODBC

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 98--98
 @texttt package=RODBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 [][]@textbf ROracle

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 99--99
 @texttt package=ROracle[]@textrm )[][]| 

Overfull \hbox (2.70708pt too wide) in paragraph at lines 100--100
 [][]@textbf RPostgreSQL

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @texttt org /

Overfull \hbox (50.49037pt too wide) in paragraph at lines 100--100
 @texttt package=RPostgreSQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 [][]@textbf RSQLite

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 103--103
 @texttt package=RSQLite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 [][]@textbf WriteXLS

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt org /

Overfull \hbox (33.24431pt too wide) in paragraph at lines 105--105
 @texttt package=WriteXLS[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 [][]@textbf XLConnect

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @texttt org /

Overfull \hbox (38.993pt too wide) in paragraph at lines 106--106
 @texttt package=XLConnect[]@textrm )[][]| 

Overfull \hbox (2.49414pt too wide) in paragraph at lines 107--107
 [][]@textbf xlsReadWrite

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @texttt org /

Overfull \hbox (56.23906pt too wide) in paragraph at lines 107--107
 @texttt package=xlsReadWrite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 [][]@textbf XML

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 108--108
 @texttt package=XML[]@textrm )[][]| 
[1] [2] Chapter 1 [3
Overfull \hbox (22.06111pt too wide) in paragraph at lines 4913--4913
 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Con
tents/Home[] 
[56]] Cross reference values unknown; you must run TeX again. [57] [58]
[4
Underfull \hbox (badness 10000) in paragraph at lines 5131--5134
[]@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe
r per-for-mance:
[59]] [60] [5] [61] [62] [6] [63] Appendix D [64] Chapter 2 [7 [65]] [8] [9 [66]]
(Function and variable index) [67] (./R-admin.vrs [10) (Concept index) [68]]
(./R-admin.cps [11) (Environment variable index)] [69] (./R-admin.ens [12]) [70 Chapter 3 [13]] )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmcsc10.pfb></usr
/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmmi9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/
cm/cmr9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb [14></usr/s
hare/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb]></usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmti10.pfb Chapter 4>
[15</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb]></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb>
Output written on R-admin.pdf (75 pages, 529734 bytes).
Transcript written on R-admin.log.
 [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23.]
[24] [25] [26] Chapter 8 [27] Chapter 9 [28]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,
Underfull \hbox (badness 10000) in paragraph at lines 2341--2345
[]@textrm 32-bit Win-dows pack-age [][]@textbf xlsReadWrite @textrm (@texttt ht
tp: / / CRAN . R-project . org /
Appendix A [29] markup, glyphs,
page headings, (Function and variable index) tables, [30 conditionals, indexing,] sectioning, (Concept index) [31 toc,] environments,
defuns,
[32] macros, )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb cross references, insertions, (./epsf.tex>
This is `epsf.tex' v2.7.4 <14 February 2011>
)</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb localization,></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-texlive/
fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmr9.pfb formatting, and turning on texinfo input format.>) (./R-FAQ.aux</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmti10.pfb></usr/share/texmf-texlive/fonts/type1/bluesk
y/cm/cmtt10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.pfb></u
sr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb>
Output written on R-data.pdf (35 pages, 272731 bytes).
Transcript written on R-data.log.
)
(/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/cache/texmf/fonts/map/pdftex/
updmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc)
Chapter 1 [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [10] Chapter 3 [11.]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,
[12] [13] markup, [14 glyphs,]
page headings, tables, conditionals, indexing, sectioning, toc, environments, [15
defuns,] macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, [16] [17] formatting, and turning on texinfo input format. [18)
(./R-admin.aux] Chapter 4 [19] [20] Chapter 5 [21] [22]
[23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31)] (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) [32
(./version.texi) [1]{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [33]
[34]}]
[2] (./R-admin.toc [35] [-1] [36] [-2] [37]) [-3] (./R-admin.toc) (./R-admin.toc) Chapter 1 [38] [39
[1]] Chapter 2 [2] [40] [41 [3]] [42This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
] Chapter 8 [4 [43]]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, [5] Chapter 9 [44] [6]
[45 markup, glyphs, [7
page headings,] tables, conditionals,] indexing, sectioning, Chapter 10 [46 toc, environments,] [47] )</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmb
10.pfb> [8</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb]></usr/share/
texmf-texlive/fonts/type1/bluesky/cm/cmcsc10.pfb></usr/share/texmf-texlive/font
s/type1/bluesky/cm/cmex10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/
cmmi10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb
defuns, [9 macros,></usr/sh
are/texmf-texlive/fonts/type1/bluesky/cm/cmmi7.pfb cross references,>]</usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm
/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb Chapter 3 [10></usr/share
/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb insertions,> (./epsf.tex]</usr/share/texmf-texlive/font
s/type1/bluesky/cm/cmsltt10.pfb
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,></usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmtt12.pfb> formatting,</usr/share/texmf-texlive/fonts/type1/bluesk
y/cm/cmtt9.pfb and turning on texinfo input format.) (./R-data.aux
></usr/share/texmf-texlive/fonts/type1/bluesky/latex-fonts/lcircl
e1.pfb>
Underfull \hbox (badness 7685) in paragraph at lines 1121--1125
 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP
TIONS[] @textrm to the value
[11]
Output written on R-FAQ.pdf (51 pages, 405980 bytes).
Transcript written on R-FAQ.log.
. [12]
Underfull \hbox (badness 10000) in paragraph at lines 1261--1265
[]@textrm Running @texttt make[] @textrm in @textttsl R_HOME@texttt /src/gnuwin
32/bitmap[] @textrm or @texttt make bitmapdll[] @textrm in

Underfull \hbox (badness 10000) in paragraph at lines 1261--1265
@textttsl R_HOME@texttt /src/gnuwin32[] @textrm should build @texttt Rbitmap.dl
l[] @textrm and in-stall it un-der @textttsl R_
[13]
Underfull \hbox (badness 10000) in paragraph at lines 1348--1352
[]@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de
vel[] @textrm and @texttt make
[14] [15]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) Chapter 4 [16]) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [17] Chapter 5 [18}]] [2] (./R-data.toc Chapter 6 [19
[-1]]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) [20
Underfull \hbox (badness 10000) in paragraph at lines 88--88
 [][]@textbf DBI

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 88--88
 @texttt package=DBI[]@textrm )[][]| 

Overfull \hbox (8.53186pt too wide) in paragraph at lines 89--89
 [][]@textbf dataframes2xls

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt org /

Overfull \hbox (67.73643pt too wide) in paragraph at lines 89--89
 @texttt package=dataframes2xls[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 [][]@textbf foreign

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 90--90
 @texttt package=foreign[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 [][]@textbf gdata

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91
 @texttt package=gdata[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 [][]@textbf hdf5

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt org /

Overfull \hbox (10.24956pt too wide) in paragraph at lines 92--92
 @texttt package=hdf5[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf ncdf

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (13.29123pt too wide) in paragraph at lines 93--93
 @texttt package=ncdf[]@textrm )[][],

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf ncdf4

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93
 @texttt package=ncdf4[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 [][]@textbf rJava

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 94--94
 @texttt package=rJava[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 [][]@textbf RJDBC

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 95--95
 @texttt package=RJDBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 [][]@textbf RMySQL

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @textrm (@texttt http: / /

Underfull ]\hbox (badness 10000) in paragraph at lines 96--96
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt org /

Overfull \hbox (21.74693pt too wide) in paragraph at lines 96--96
 @texttt package=RMySQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 [][]@textbf RNetCDF

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97
 @texttt package=RNetCDF[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 [][]@textbf RODBC

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 98--98
 @texttt package=RODBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 [][]@textbf ROracle

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 99--99
 @texttt package=ROracle[]@textrm )[][]| 

Overfull \hbox (2.70708pt too wide) in paragraph at lines 100--100
 [][]@textbf RPostgreSQL

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @texttt org /

Overfull \hbox (50.49037pt too wide) in paragraph at lines 100--100
 @texttt package=RPostgreSQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 [][]@textbf RSQLite

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 103--103
 @texttt package=RSQLite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 [][]@textbf WriteXLS

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt org /

Overfull \hbox (33.24431pt too wide) in paragraph at lines 105--105
 @texttt package=WriteXLS[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 [][]@textbf XLConnect

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @texttt org /

Overfull \hbox (38.993pt too wide) in paragraph at lines 106--106
 @texttt package=XLConnect[]@textrm )[][]| 

Overfull \hbox (2.49414pt too wide) in paragraph at lines 107--107
 [][]@textbf xlsReadWrite

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @texttt org /

Overfull \hbox (56.23906pt too wide) in paragraph at lines 107--107
 @texttt package=xlsReadWrite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 [][]@textbf XML

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 108--108
 @texttt package=XML[]@textrm )[][]| 
[1 [21] [2] Chapter 1] [3]TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi
 [22] [4
Overfull \hbox (29.11234pt too wide) in paragraph at lines 2121--2131
[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[23]] [5] [24] [6] [25] Chapter 7 Chapter 2 [26 [7]] [8] [9] [27] [10 [28]] Chapter 8 [29] [11] Chapter 9 [30] [12] [31]
Chapter 3 [13]
[32] Appendix A [33] [34] [14] Chapter 4 [15] [35] [16] [36] [17] [37] [38] [18] [19] [39] [40] [20] [41 Chapter 5 [21]] Appendix B
[42] [43]
Chapter 6 [22.] Chapter 7 [23]
 [44] [24] [45 [25]] [46 [26]] Appendix C [47 Chapter 8 [27] [48]] [49] Chapter 9 [50 [28]] [51] [52
Underfull \hbox (badness 10000) in paragraph at lines 2341--2345
[]@textrm 32-bit Win-dows pack-age [][]@textbf xlsReadWrite @textrm (@texttt ht
tp: / / CRAN . R-project . org /
Appendix A] [29] [53 (Function and variable index) [30]] (./R-data.vrs [54 [31]]
Overfull \hbox (45.05586pt too wide) in paragraph at lines 4762--4762
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig[] 
[55)
(Concept index)] [32] (./R-data.cps
Overfull \hbox (22.06111pt too wide) in paragraph at lines 4913--4913
 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Con
tents/Home[] 
[56]) [33] )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb [57>]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb> [58</usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb>]</usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmmi9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmr10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb
Underfull \hbox (badness 10000) in paragraph at lines 5131--5134
[]@textrm You can tar-get spe-cific Sparc ar-chi-tec-tures for (slightly) highe
r per-for-mance:
[59></usr/s
hare/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb>]</usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmsy10.pfbTEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi
></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb> [60</us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb]></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmtt12.pfb></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmtt9.pfb> [61]
Output written on R-data.pdf (37 pages, 341113 bytes).
Transcript written on R-data.log.
 [62] [63] Appendix D [64] [65] [66]
(Function and variable index) [67] (./R-admin.vrs) (Concept index) [68]
(./R-admin.cps) (Environment variable index) [69] (./R-admin.ens) [70] )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmcsc10.pfb></usr
/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmmi9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/
cm/cmr9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb></usr/s
hare/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmti10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb>
Output written on R-admin.pdf (75 pages, 529734 bytes).
Transcript written on R-admin.log.
This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi
 formatting, and turning on texinfo input format.)
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1]
(Acknowledgements) Chapter 1 [1]
Cross reference values unknown; you must run TeX again. [2] [3] [4] [5]
[6]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [7]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: [8 pdf, fonts,] [9 markup,] glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, [10 cross references, insertions, (./epsf.tex]
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.) (./R-data.aux
 [11] [12] [13] [14)] (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [15] [16] [17}]] [2] (./R-data.toc [18]
[-1]) [-2] (./R-data.toc [19) (./R-data.toc) (Acknowledgements)] [20]
Underfull \hbox (badness 10000) in paragraph at lines 88--88
 [][]@textbf DBI

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 88--88
 @texttt package=DBI[]@textrm )[][]| 

Overfull \hbox (8.53186pt too wide) in paragraph at lines 89--89
 [][]@textbf dataframes2xls

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt org /

Overfull \hbox (67.73643pt too wide) in paragraph at lines 89--89
 @texttt package=dataframes2xls[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 [][]@textbf foreign

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 90--90
 @texttt package=foreign[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 [][]@textbf gdata

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91
 @texttt package=gdata[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 [][]@textbf hdf5

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt org /

Overfull \hbox (10.24956pt too wide) in paragraph at lines 92--92
 @texttt package=hdf5[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf ncdf

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (13.29123pt too wide) in paragraph at lines 93--93
 @texttt package=ncdf[]@textrm )[][],

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf ncdf4

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93
 @texttt package=ncdf4[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 [][]@textbf rJava

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 94--94
 @texttt package=rJava[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 [][]@textbf RJDBC

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 95--95
 @texttt package=RJDBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 [][]@textbf RMySQL

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @textrm (@texttt http: / /

Underfull  [21]\hbox (badness 10000) in paragraph at lines 96--96
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt org /

Overfull \hbox (21.74693pt too wide) in paragraph at lines 96--96
 @texttt package=RMySQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 [][]@textbf RNetCDF

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97
 @texttt package=RNetCDF[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 [][]@textbf RODBC

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 98--98
 @texttt package=RODBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 [][]@textbf ROracle

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 99--99
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 99--99
 @texttt package=ROracle[]@textrm )[][]| 

Overfull \hbox (2.70708pt too wide) in paragraph at lines 100--100
 [][]@textbf RPostgreSQL

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 100--100
 @texttt org /

Overfull \hbox (50.49037pt too wide) in paragraph at lines 100--100
 @texttt package=RPostgreSQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 [][]@textbf RSQLite

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 103--103
 @texttt package=RSQLite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 [][]@textbf WriteXLS

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt org /

Overfull \hbox (33.24431pt too wide) in paragraph at lines 105--105
 @texttt package=WriteXLS[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 [][]@textbf XLConnect

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 106--106
 @texttt org /

Overfull \hbox (38.993pt too wide) in paragraph at lines 106--106
 @texttt package=XLConnect[]@textrm )[][]| 

Overfull \hbox (2.49414pt too wide) in paragraph at lines 107--107
 [][]@textbf xlsReadWrite

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 107--107
 @texttt org /

Overfull \hbox (56.23906pt too wide) in paragraph at lines 107--107
 @texttt package=xlsReadWrite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 [][]@textbf XML

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @textrm (@texttt http: / /

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 108--108
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 108--108
 @texttt package=XML[]@textrm )[][]| 
[1] [2
[22] Chapter 1 [3]] [23]
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2069--2069
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 

Overfull \hbox (31.98314pt too wide) in paragraph at lines 2071--2071
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[24] [25] [4] [26 [5]] [27] [6] [28] [29 Chapter 2 [7]] [30] [8] [9 [31]] [10 [32]] [11 [33]] [12] [34
Chapter 3 [13]] [35] [36 [14]] Chapter 4 [15 [37]] [38 [16]] [17
[39]] [40 [18]]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [41]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: [19 pdf, fonts,] [42] markup, [43 glyphs,
page headings,] tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, [44 cross references, insertions, (./epsf.tex [20]
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,] Chapter 5 [21] [45] formatting, and turning on texinfo input format.)
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [46)] (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [47]
Chapter 6 [22] [48]}] [2 Chapter 7 [49] [23 [-1] Chapter 1]] [50]
[1 [51]] [24] [2 [52]] [25] [3 [53]]
Chapter 2 [54] [4] [26 [55]] Chapter 8 [27 [5 [56]]] [57] [6] [58 Chapter 9] [28] [7 [59]] [8] [60 [9]
Underfull \hbox (badness 10000) in paragraph at lines 2341--2345
[]@textrm 32-bit Win-dows pack-age [][]@textbf xlsReadWrite @textrm (@texttt ht
tp: / / CRAN . R-project . org /
Appendix A [29]] [61 (Function and variable index) [30] (./R-data.vrs [10]] [31 [11 [62]]])
(Concept index) [32] [12 (./R-data.cps [63]]) [13 [33This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
]] [14 [64 )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb]>]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfbentering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]:></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb pdf,></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb fonts,></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmmi9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmr10.pfb [15></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb [65]></usr/s
hare/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb]></usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmsltt10.pfb markup,></usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmsy10.pfb glyphs,
page headings,></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb tables, [16 conditionals,> indexing,</us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb] sectioning,
Underfull \hbox (badness 10000) in paragraph at lines 5752--5759
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[66> toc,</usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmtt12.pfb environments,]></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmtt9.pfb
defuns, macros, [17> cross references, insertions, (./epsf.tex]
This is `epsf.tex' v2.7.4 <14 February 2011>
)
Output written on R-data.pdf (37 pages, 341113 bytes).
Transcript written on R-data.log.
 localization,
[18 [67]] formatting, and turning on texinfo input format.)
Underfull \hbox (badness 10000) in paragraph at lines 5929--5935
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[68
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)]) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [19] [69] [20] Chapter 2 [70 [21}]]] [2] [-1] Chapter 1 Chapter 3 [71] [22
Chapter 2] [1] [23] [72] [2 [73 [24]]] [25] Chapter 3 [26] [74 Cross reference values unknown; you must run TeX again.] [27]
Chapter 4 [28 [75]]
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3 [76 [29]]] [77] Chapter 5 [30] [78] Chapter 6 [31 Chapter 4
[79]] [32] [80 [4]] [81 [33]] [82 [34]] [83] [5 [35]] [36
Underfull \hbox (badness 10000) in paragraph at lines 7180--7189
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[84]]
[37] [85] [6 [38] [86]] [39] [7 [87]] [40 Chapter 3 [8]]
Underfull \hbox (badness 7379) in paragraph at lines 7588--7591
[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few 
files (e.g.
[88 [41]] Chapter 7 [42
Underfull \hbox (badness 10000) in paragraph at lines 7592--7594
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[89]] [9] [43
Overfull \hbox (50.80455pt too wide) in paragraph at lines 7713--7713
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[90 [10]]] Chapter 8 [44 [91]] [11 [92]] [45 [93]] Chapter 5 [12 [94]]
Underfull \hbox (badness 10000) in paragraph at lines 3848--3853
 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[46] [13 [95]] [47 [96 [14]]] [48 [97]] [98 [15]] [49] [99 Chapter 9 [50]] [16] [100 [51]
[17] Chapter 10 [52]] [101 Chapter 11] [53] [18
Chapter 12] [54] [19] [55]
[102] (Function and variable index) [56] [20 [103 (Concept index)]
[57]] [58]
kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+3/600 --dpi 603 ecrm1095
 Chapter 4 [21 [104]] [105] [22]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 9020--9020
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[106] [23 [107]] [108] [24] [109 Chapter 5 [25]] [110] [26 [111]] [27] [112] [113]
[28] [114] [29]
Underfull \hbox (badness 10000) in paragraph at lines 9854--9856
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[115] [30] Chapter 6 [31] [116] [32 [117]] [33 [118]] [119 [34]] [120] [35 [121]] [122]PDF/LaTeX documentation: full reference index ...
 [36 [123]] [124 [37]] [38 [125] Chapter 7]
[39] [126]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 10865--10865
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[127] Chapter 6 [128] Chapter 8 [40] [41] [129] Chapter 9 [42] [130] [43] Chapter 10 [44] [131] [45 [132]]
Underfull \hbox (badness 10000) in paragraph at lines 4343--4345
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46 [133]] [47] [134] [48]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 %&-line parsing enabled.
 [49] [135] [50entering extended mode
(./fullrefman.tex]
LaTeX2e <2005/12/01>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa
n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded.
(/usr/share/texmf-texlive/tex/latex/base/book.cls
Document Class: book 2005/09/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo) (Function and Variable Index) [51])
(../../share/texmf/tex/latex/Rd.sty (Concept Index)
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
[52]
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty [136 Appendix A [53]] [54])
(/usr/share/texmf-texlive/tex/latex/tools/bm.sty )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb)
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty>)</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty>)
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb>
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def</usr/share/texmf-texlive/
fonts/type1/bluesky/cm/cmr7.pfb [137></usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmr9.pfb)]>)</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb></usr/sh
are/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty>
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def</usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/bluesk
y/cm/cmsy9.pfb
[138))>]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty)
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty>
(/etc/texmf/tex/latex/config/color.cfg)</us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmtt9.pfb
Underfull \hbox (badness 10000) in paragraph at lines 12079--12083
 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
 R_orderVector(indx, n,
[139))>
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty])
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)
Output written on R-lang.pdf (57 pages, 291925 bytes).
Transcript written on R-lang.log.

(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty [140
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))]
(/etc/texmf/tex/latex/config/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty) [141
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty]
(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty))) [142
(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty])
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty) [143)]
*hyperref using default driver hpdftex*
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) [144

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 366.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 366.

)] (/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
Underfull \hbox (badness 10000) in paragraph at lines 12511--12517
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7
(/usr/share/texmf-texlive/tex/latex/base/utf8.def [145]
(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu) [146
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu])))
(/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty
(/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty
(/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) Chapter 8
(/etc/texmf/tex/latex/config/graphics.cfg) [147)])
(/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
No file fullrefman.aux.
(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) [148]
(/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texmf-texlive/tex/latex/psnfss/ts1ptm.fd) [149 [1]{/var/cache/texmf/fonts
/map/pdftex/updmap/pdftex.map
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12921--12921
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[150]
Overfull \hbox (33.55849pt too wide) in paragraph at lines 12969--12969
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[151]}] [152 [1] [2]] [1] [2] (./base-pkg.tex
Chapter 1.
(/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd) [153]
Underfull \hbox (badness 4595) in paragraph at lines 40--43
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[3] [154]
Underfull \hbox (badness 4168) in paragraph at lines 94--99
[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one 
char-ac-ter vec-tors. The first en-try is al-ways
[4] [155] [156
Underfull \hbox (badness 10000) in paragraph at lines 131--137
[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
 x \T1/ptm/m/n/10 such that

Underfull \hbox (badness 10000) in paragraph at lines 131--137
\T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base 
^ ulp.digits \T1/ptm/m/n/10 if ei-

Underfull \hbox (badness 6236) in paragraph at lines 131--137
\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m
/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise,

Underfull \hbox (badness 10000) in paragraph at lines 131--137
\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally

Underfull \hbox (badness 10000) in paragraph at lines 137--145
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 137--145
\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if

Underfull \hbox (badness 4328) in paragraph at lines 137--145
\T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is

Underfull \hbox (badness 10000) in paragraph at lines 137--145
\T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma
lly

Underfull \hbox (badness 10000) in paragraph at lines 148--155
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-

Underfull \hbox (badness 10000) in paragraph at lines 148--155
\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5]]
Underfull \hbox (badness 10000) in paragraph at lines 13477--13484
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[157] [6 [158]]
Underfull \hbox (badness 10000) in paragraph at lines 13600--13604
 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [159] (Concept index) [160]
Underfull \hbox (badness 4036) in paragraph at lines 291--295
\T1/ptm/m/n/10 ues \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.
binary"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 an
d
[7] [161]
kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+3/600 --dpi 603 ecrm1095

Underfull \hbox (badness 10000) in paragraph at lines 330--333
[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8]
Underfull \hbox (badness 2359) in paragraph at lines 375--378
[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
Underfull \hbox (badness 1072) in paragraph at lines 505--511
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [13] [14]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 807--807
 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[15] [16] [17] [18] [19]
Underfull \hbox (badness 1838) in paragraph at lines 1094--1097
[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[20] [21] [22]
Underfull \hbox (badness 5862) in paragraph at lines 1302--1308
[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[23] [24] [25] [26] [27]
Underfull \hbox (badness 2865) in paragraph at lines 1665--1669
[]\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/
m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then

Underfull \hbox (badness 10000) in paragraph at lines 1669--1671
[]\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by
[28] [29]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 1808--1808
 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 

Overfull \hbox (19.13934pt too wide) in paragraph at lines 1843--1845
[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x,      parent = emptyenv())

Underfull \hbox (badness 10000) in paragraph at lines 1846--1848
[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[30] [31]
Underfull \hbox (badness 10000) in paragraph at lines 1993--1995
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[32] [33]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2100--2100
 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[34] [35]
Underfull \hbox (badness 1107) in paragraph at lines 2233--2235
[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[36] [37] [38] [39] [40]
Underfull \hbox (badness 5878) in paragraph at lines 2562--2567
[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to 
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-

Underfull \hbox (badness 10000) in paragraph at lines 2562--2567
\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53]
Underfull \hbox (badness 10000) in paragraph at lines 3446--3448
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[54] [55] [56] [57] [58] [59] [60]
Underfull \hbox (badness 4927) in paragraph at lines 3896--3900
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject

Underfull \hbox (badness 2012) in paragraph at lines 3896--3900
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[61]
Underfull \hbox (badness 5260) in paragraph at lines 4004--4009
[]\T1/ptm/m/n/10 Are the \T1/pcr/m/n/10 R.app \T1/ptm/m/n/10 GUI com-po-nents a
nd the [][]\T1/pcr/m/n/10 quartz[][][] \T1/ptm/m/n/10 func-tion op-er-a-

Underfull \hbox (badness 1354) in paragraph at lines 4004--4009
\T1/ptm/m/n/10 tional? Only on some OS X builds. Note that this is dis-tinct fr
om
[62] [63] [64]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4172--4172
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
[65]
Underfull \hbox (badness 10000) in paragraph at lines 4273--4278
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for

Underfull \hbox (badness 10000) in paragraph at lines 4273--4278
[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-

Underfull \hbox (badness 2181) in paragraph at lines 4273--4278
\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
 columns to fac-tors un-less
[66]mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+3/600; nonstopmode; input ecrm1095

Overfull \hbox (9.78043pt too wide) in paragraph at lines 4352--4352
 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[67] [68] [69] [70]
Underfull \hbox (badness 2521) in paragraph at lines 4589--4591
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[71] [72] [73]This is METAFONT, Version 2.718281 (Web2C 7.5.7)
 [74]
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/ecrm1095.mf
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exbase.mf)
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/ecrm.mf [75]
Underfull \hbox (badness 10000) in paragraph at lines 4922--4930
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[76]
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exroman.mf
 Ok (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exaccess.mf
 Ok) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/expseudo.mf
 Ok) [77 (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exruwest.mf] [78] [79
 Ok [192]] [80 [193]] [194] [195] [196] [197] [81 [198] [199]]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [82] [83] [200]
Underfull \hbox (badness 2443) in paragraph at lines 5465--5472
[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 http : / /
[84 [201]] [202]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex [203]
Loading texinfo [version 2015-06-24.23]: pdf, fonts,
[204] [85 [205]] [206] [207] [208] [209] [86 markup,] glyphs,
page headings, tables, [210 conditionals,] indexing, sectioning, [211] [87 toc, [212] environments,] [213]
defuns, [214] macros, [215 cross references,]
[216] insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
)
Underfull \hbox (badness 1635) in paragraph at lines 5777--5780
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class

Underfull \hbox (badness 3009) in paragraph at lines 5781--5784
[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing

Underfull \hbox (badness 1102) in paragraph at lines 5798--5811
[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in

Underfull \hbox (badness 1308) in paragraph at lines 5812--5820
[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[88 localization, [217]] [218] [219] [220] [89] formatting, and turning on texinfo input format.)
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [221] [90 [222)]] (./version.texi) [223])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrlwest.mf
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [91
 Ok [224]] [225] [226] [227] [228]
Underfull \hbox (badness 2158) in paragraph at lines 6032--6036
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 '). Prox-ies can be spe
c-i-fied for HTTP and FTP \T1/pcr/m/n/10 url \T1/ptm/m/n/10 con-nec-tions: see
[92]}]
Underfull \hbox (badness 10000) in paragraph at lines 6120--6123
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is

Underfull \hbox (badness 2057) in paragraph at lines 6120--6123
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[93 [2] (./R-lang.toc] [229] [94 [230] [231]
[-1] [232]]
Underfull \hbox (badness 3815) in paragraph at lines 6284--6290
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-


Underfull \hbox (badness 2343) in paragraph at lines 6284--6290
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1147) in paragraph at lines 6284--6290
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If it is re-quired (it is n
ot rec-om-mended) when writ-ing

Underfull \hbox (badness 10000) in paragraph at lines 6303--6305
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[95 [233] [234]] [235] [-2
[236] [237]] [238] [239] [240]
Underfull \hbox (badness 1067) in paragraph at lines 6345--6352
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[96 [241]) [-3] [242]
Underfull \vbox (badness 10000) has occurred while \output is active [97] (./R-lang.toc]) (./R-lang.toc [243] [244] [245]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6518--6518
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[98) [246] Chapter 1] [247]
[248] Chapter 2 [1 [249] [99]] [250] [251] [252] [100] [2] [253] [101 [254]] [255])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrueast.mf
Cross reference values unknown; you must run TeX again.
 Ok [128] [129] [102] [130] [131] [132] [133]
Underfull \hbox (badness 10000) in paragraph at lines 6844--6846
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[103]
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3 [134] [135]] [136] [104] [137] [138]
Underfull \hbox (badness 4595) in paragraph at lines 6950--6953
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[105 [139]]
[140] [141] [106] [4 [142]] [143] [107 [144]] [145] [146] [147] [148]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7143--7143
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[108 [149] [5]] [150]
Underfull \hbox (badness 8132) in paragraph at lines 7239--7243
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The

Underfull \hbox (badness 4543) in paragraph at lines 7239--7243
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
[109 [151]]
[152] [153] [154]
Underfull \hbox (badness 10000) in paragraph at lines 7258--7269
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing

Underfull \hbox (badness 1062) in paragraph at lines 7258--7269
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be

Overfull \hbox (4.63962pt too wide) in paragraph at lines 7291--7295
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[110 [155]] [6 [156]] [157])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrleast.mf
 Ok [158] [111 [160]] [161] [7 [162 [112]] [163]] [164] [165] Chapter 3 [8] [166] [167] [113] [168] [169] [170] [9
[171 [114]]] [172] [173] [174] [10 [115]] [175] [176]
Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[116 [177]] [178] [11 [179]] [180] [181] [117 [12]] [182]
[183] [184]
Underfull \hbox (badness 5802) in paragraph at lines 7938--7942
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
[118] [185] [186] [119 [187]] [188])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exbraces.mf
 Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8053--8057
\T1/pcr/m/n/10 trace("plot", browser, exit = browser, signature = c("track", "m
issing")) 
[120 [125]
[95] [127] [32]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/expunct.mf]
 Ok [14] [15] [19] [20] [13] [18] [33] [13 [39
Underfull \hbox (badness 10000) in paragraph at lines 8106--8110
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[121] [42] [43]] [44] [46] [47]] [58]
[59] [61] [96] [189] [17] [45] [16] [21] [22])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exaccent.mf
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8187--8187
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO
! "); pi+2})[] 
[122 [14]]
 Ok [0] [1] [2] [3] [4] [123 [5] [6] [7] [8] [9]] [10] [11] [12])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exsign.mf
 Ok [24] [34] [35]
Underfull \hbox (badness 4254) in paragraph at lines 8340--8344
[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
[124 [36] [15] [37]] [64] [191] [159])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrlig.mf
 Ok [25] [26]
Underfull \hbox (badness 1132) in paragraph at lines 8383--8390
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[125 [28]] [16 [27] [29]] [30]
Underfull \hbox (badness 1603) in paragraph at lines 8492--8495
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[126]
[17 [31])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exromp.mf]
 Ok [38] [63] [190])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrulett.mf
 Ok [65] [127mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+3/600; nonstopmode; input ecrm1095
 [18 [66]] [67] [68]] [69] [19 [70]] [128 [71]] [72] [73] [74] [75] [76] [129 [77]] [78]
[79] [20 [80] [81]] [82] [83] [130 [84]] [85] Chapter 4 [21 [86]] [87] [131] [88] [89] [90])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrllett.mf
 Ok [97] [98] [99] [100 [132] [101] [102]] [103] [22 [104] [105]] [106] [133 [107] [108]]
[109]This is METAFONT, Version 2.718281 (Web2C 7.5.7)
 [110] [111] [112] [113] [114] [134 [115]] [116] [117] [118] [119]
Underfull \hbox (badness 1917) in paragraph at lines 9077--9080
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has

Overfull \hbox (36.7804pt too wide) in paragraph at lines 9130--9130
 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 9131--9131
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[135
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/ecrm1095.mf
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exbase.mf [120]]
[121] [122]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrdigit.mf [23
 Ok [48] [49])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/ecrm.mf [50]] [51] [136 [52]] [53] [54] [55] [56] [57])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrligtb.mf
 Ok) ) ) )
(some charht values had to be adjusted by as much as 0.07599pt)
Font metrics written on ecrm1095.tfm.
Output written on ecrm1095.603gf (256 characters, 55528 bytes).
Transcript written on ecrm1095.log.

Underfull \hbox (badness 1168) in paragraph at lines 9231--9236
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[137] [24]
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exroman.mf
 Ok (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exaccess.mf Chapter 5 [138 [25
 Ok) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/expseudo.mf
 Ok)] (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exruwest.mf]
 Ok [192] [26
Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]198
5$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / en . wikipedia .

Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 http : / / en . wikipedia . org / wiki / Double _
[139]] [193] [194] [27 [195]] [140 [196]] [197] [198] [199] [141] [200]
[28]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9588--9588
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[142] [201] [29 [202] [203]]
Underfull \hbox (badness 1629) in paragraph at lines 9661--9665
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[143
[204]] [205] [30 [206] [207]] Chapter 6 [208] [31 [144] [209]] [210] [32
Underfull \hbox (badness 2150) in paragraph at lines 9760--9763
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 3690) in paragraph at lines 9774--9782
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for

Underfull \hbox (badness 10000) in paragraph at lines 9783--9785
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
[145] [211] [212]] [213] [214] [215]
[216] [33
Underfull \hbox (badness 3735) in paragraph at lines 9815--9822
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[146]] [217] [34 [218] [147] [219] [220]] [35]
Underfull \hbox (badness 10000) in paragraph at lines 10010--10013
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[148 [221] [222]] [223])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrlwest.mf [36
 Ok [224]] [149 [37 [225]]] [226] [227] [228] [150] [229] [230] [231] [151 [232]] [233] [234] [235] [152
[236]] [237] [238] [239] [240] [153 [241]] [38] [242]mktexpk: /usr/src/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk: successfully generated.
 Chapter 7
[39] [243] [244] [245] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk [246] [247] [154
[248]>]</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb [249]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb><
 [155/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb] [250]> [251]</usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmr7.pfb [252]></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmr8.pfb [156></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb [253]]> [254]</usr
/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb Chapter 8 [255])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrueast.mf> [40</usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmsltt10.pfb
 Ok [128]]> [41]</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb [129
Underfull \hbox (badness 5288) in paragraph at lines 10669--10671
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of

Underfull \hbox (badness 3039) in paragraph at lines 10679--10684
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
[157]>
]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb> [130]</usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmtt12.pfb [131]> [132] Chapter 9</usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmtt9.pfb [42 [133]>] [134] [135]
Underfull \hbox (badness 10000) in paragraph at lines 10737--10739
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[158
Output written on R-ints.pdf (61 pages, 347601 bytes).
Transcript written on R-ints.log.
 [136]] [137] [43] [138] [159 Chapter 10 [139]] [44]
[140] [141]
Underfull \hbox (badness 4569) in paragraph at lines 10854--10858
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 10854--10858
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[160] [142]
Underfull \hbox (badness 10000) in paragraph at lines 10965--10967
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[161] [143] [144] [45 [145] [162 [146]] [147] [148]] [149]
Underfull \hbox (badness 10000) in paragraph at lines 4343--4345
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46 [163] [150]] [151]
[152] [47 [153] [154]]
Underfull \hbox (badness 4048) in paragraph at lines 11151--11161
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is

Underfull \hbox (badness 3657) in paragraph at lines 11151--11161
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[164 [155]] [156] [157])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrleast.mf
 Ok [158] [165 [48 [160]]] [161] [162] [166 [49 [163]] [164]] [165] [166] [167]
Underfull \hbox (badness 5460) in paragraph at lines 11398--11407
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-

Underfull \hbox (badness 2221) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those

Underfull \hbox (badness 2707) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL

Underfull \hbox (badness 2818) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,

Underfull \hbox (badness 6978) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[167 [50 [168]] [169]] [170] (Function and Variable Index) [168 [51]
[171]] (./R-lang.vrs [172] [173] [169] [174] [175] [176]
[52 [170 [177]] [178] [179]] [180]) [181] (Concept Index) [171 [53]] [182 (./R-lang.cps]
[183]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11761--11761
 []\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[] 
[172 [184]] [185] [186] [187]) [173 [188])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exbraces.mf
 Ok [94] Appendix A [126] [23] [40]] [41] [54 [60] [124] [62] [91] [93] [92] [123] [125]
[95] [127] [32]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/expunct.mf
 Ok [14] [15] [19]] [174 [20] [13]] [18] [55 [33]] [39] [42] [43] )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb [44] [46] [47] [58]
[59] [61]> [96] [189]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb [17] [45] [16] [21]> [175 [22])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exaccent.mf</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb
 Ok [0]></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb] [1]> [2]</usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmmi9.pfb [3] [4]></usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmr10.pfb> [176</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb]></usr/s
hare/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb></usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmsl10.pfb> [5]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmsltt10.pfb [6] [7] [8] [9]>
Underfull \hbox (badness 2221) in paragraph at lines 12121--12127
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[177</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb [10] [11] [12])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exsign.mf></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy9.pfb
 Ok [24] [34] [35]]></usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmti10.pfb [36]> [37]</usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmtt10.pfb [64] [191]> [159])</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrlig.mf
 Ok [25] [26]> [178 [28]] [27]
Output written on R-lang.pdf (60 pages, 413992 bytes).
Transcript written on R-lang.log.
 [29] [30] [179] [31])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exromp.mf
 Ok [38] [63] [190])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrulett.mf
 Ok [65] [66] [67] [180 [68]] [69] [70] [71] [72] [73
Underfull \hbox (badness 2253) in paragraph at lines 12350--12352
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[181] [74]] [75] [76] [77] [78]
[79] [80]
Underfull \hbox (badness 10000) in paragraph at lines 12454--12456
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[182 [81]] [82] [83] [84] [85] [86] [183 [87]] [88] [89] [90])
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrllett.mf
 Ok [97] [98] [99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 12602--12604
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See

[184 [101] [102]] [103] [104] [105] [106] [185 [107] [108]]
[109] [110] [111] [112] [113] [114] [115]
Underfull \hbox (badness 10000) in paragraph at lines 12700--12704
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (30.78088pt too wide) in paragraph at lines 12750--12750
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777") 
[186 [116] [117]] [118] [119] [120] [187
[121] [122]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrdigit.mf
 Ok [48]] [49] [50] [51] [52] [53] [54] [55] [56] [57])
Underfull \hbox (badness 10000) in paragraph at lines 12839--12842
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 12849--12849
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive  TRUE)[] 
[188
(/usr/share/texmf-texlive/fonts/source/jknappen/ec/exrligtb.mf
 Ok) ) ) )
(some charht values had to be adjusted by as much as 0.07599pt)
Font metrics written on ecrm1095.tfm.
Output written on ecrm1095.603gf (256 characters, 55528 bytes).
Transcript written on ecrm1095.log.
]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12932--12932
 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE) 

Underfull \hbox (badness 7238) in paragraph at lines 12950--12957
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 12950--12957
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to

Underfull \hbox (badness 2126) in paragraph at lines 12950--12957
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-

Underfull \hbox (badness 3965) in paragraph at lines 12958--12962
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[189] [190]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13066--13066
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 13067--13067
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[191]
Underfull \hbox (badness 10000) in paragraph at lines 13148--13152
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a

Underfull \hbox (badness 1389) in paragraph at lines 13148--13152
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[192]
Underfull \hbox (badness 1314) in paragraph at lines 13208--13210
[]\T1/ptm/m/n/10 In re-cent ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 most u
n-nec-es-sary copy-ing is avoided: on the other hand us-ing
[193] [194] [195]
Underfull \hbox (badness 1168) in paragraph at lines 13402--13406
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-

Underfull \hbox (badness 2012) in paragraph at lines 13402--13406
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[196]
Underfull \hbox (badness 6944) in paragraph at lines 13496--13499
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 13521--13521
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[197] [198] [199]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13668--13668
 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 

Underfull \hbox (badness 2790) in paragraph at lines 13675--13678
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for

Underfull \hbox (badness 4254) in paragraph at lines 13691--13699
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,

Underfull \hbox (badness 1024) in paragraph at lines 13706--13710
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[200]
Underfull \hbox (badness 10000) in paragraph at lines 13761--13763
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point,

Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives

Underfull \hbox (badness 10000) in paragraph at lines 13772--13780
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[201]
Underfull \hbox (badness 1009) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 is
 not ap-pro-pri-ate for use within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/1
0 meth-ods: use
[202]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13869--13869
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
[203] [204] [205]mktexpk: /usr/src/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk: successfully generated.
 [206] [207] [208] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk> [209] [210</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi7.pfb [211></usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmr10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmr9.pfb [212>]</usr/share/texmf-texlive/fonts/type1/bluesk
y/cm/cmsl10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmss10.pfb [213></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmsy10.pfb]></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmsy7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy9.pfb>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb></usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmti9.pfb [214></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmtt10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.pf
b></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb></usr/share/texmf-
texlive/fonts/type1/bluesky/latex-fonts/lcircle1.pfb
[215>]
Output written on R-exts.pdf (164 pages, 834304 bytes).
Transcript written on R-exts.log.

Underfull \hbox (badness 2418) in paragraph at lines 14776--14780
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,

Underfull \hbox (badness 6510) in paragraph at lines 14783--14786
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle

Underfull \hbox (badness 2326) in paragraph at lines 14811--14818
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[216] [217] [218] [219]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15057--15057
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 

Underfull \hbox (badness 1867) in paragraph at lines 15082--15089
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[220] [221] [222] [223]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15316--15316
 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 15343--15343
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 

Underfull \vbox (badness 10000) has occurred while \output is active [224]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.

Overfull \hbox (0.78088pt too wide) in paragraph at lines 15387--15387
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 

Underfull \hbox (badness 10000) in paragraph at lines 15393--15397
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for

Underfull \hbox (badness 1028) in paragraph at lines 15393--15397
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[225]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, [226] markup, glyphs,
page headings, tables, conditionals, indexing, [227 sectioning,] toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex [228
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,] [229] formatting, and turning on texinfo input format.) [230
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)]) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [231]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15921--15921
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[232] [233}]] [2] (./R-ints.toc [234]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [235]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
[-1
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,]
Underfull \hbox (badness 2435) in paragraph at lines 16174--16176
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /

Underfull \hbox (badness 2285) in paragraph at lines 16227--16229
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /

Overfull \hbox (9.78043pt too wide) in paragraph at lines 16235--16235
 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
[236]) [-2] markup, (./R-ints.toc
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16245--16245
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 16265--16265
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[237) (./R-ints.toc glyphs,
page headings,] tables,) Chapter 1 conditionals, indexing, sectioning, toc, environments, [238
defuns, macros, cross references,] insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, [1 [239]] [240 formatting,] and turning on texinfo input format.) (./R-lang.aux
 [2] [241] [242 [3]] [4] [243] [5
Underfull \hbox (badness 10000) in paragraph at lines 16701--16703
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[244]] [6]
Underfull \hbox (badness 4217) in paragraph at lines 16785--16794
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2057) in paragraph at lines 16800--16816
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[245]
[7] [246] [8] [247] [9] [248] [10 [249]] [250] [11]
Underfull \hbox (badness 4699) in paragraph at lines 17207--17210
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the atomic types (\T1/pcr
/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[251] [12] [252] [13]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17329--17329
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[253] [14]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [254]) (./version.texi)
[1 [15{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map]
Underfull \hbox (badness 4739) in paragraph at lines 17460--17462
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[255] [16 [256]] [17 [257]] [258 [18}]] [2]] (./R-lang.toc [259]
[-1] [260] [19]
Underfull \hbox (badness 1430) in paragraph at lines 17858--17863
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .


Underfull \hbox (badness 10000) in paragraph at lines 17858--17863
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[261 [-2]] [20])
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher

Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would

Underfull \hbox (badness 5008) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to

Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[262 [-3] Chapter 2]
[21 (./R-lang.toc) (./R-lang.toc]) Chapter 1
Underfull \hbox (badness 10000) in paragraph at lines 17979--17986
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If

Underfull \hbox (badness 6364) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-

Underfull \hbox (badness 5064) in paragraph at lines 17979--17986
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with

Underfull \hbox (badness 5908) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with

Underfull \hbox (badness 10000) in paragraph at lines 17995--17997
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[263 [22]] Chapter 2 [1]
Underfull \hbox (badness 1975) in paragraph at lines 18067--18070
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[264] [23] [2 [265]] [24] [266] [25 [267] Chapter 3 [26]] [268]
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3 [27]] Chapter 4 [28
Underfull \hbox (badness 10000) in paragraph at lines 18364--18368
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[269]] [29
Underfull \hbox (badness 10000) in paragraph at lines 18494--18498
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use

Underfull \hbox (badness 1454) in paragraph at lines 18494--18498
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
[270]] Chapter 5
[30] [4 [271 Chapter 6 [31]]] [32
Underfull \hbox (badness 10000) in paragraph at lines 18589--18596
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[272]] [33 [273]] [34] [5
Underfull \hbox (badness 10000) in paragraph at lines 18710--18714
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use

Underfull \hbox (badness 5161) in paragraph at lines 18765--18770
[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the

Underfull \hbox (badness 6592) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of

Underfull \hbox (badness 5133) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed

Underfull \hbox (badness 10000) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[274 [35]]] [36] [275] [37] [276] [38]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 18927--18927
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 18931--18931
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[277] [39] [6
Underfull \hbox (badness 3343) in paragraph at lines 18987--18991
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[278] [40]]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19073--19073
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 19084--19084
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[279] [41] [280
Chapter 7 [42]] [7
Underfull \hbox (badness 6380) in paragraph at lines 19229--19234
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[281 [43]] Chapter 8 [44]]
Underfull \hbox (badness 10000) in paragraph at lines 19258--19261
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1337) in paragraph at lines 19287--19294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be

Underfull \hbox (badness 2229) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or

Underfull \hbox (badness 1043) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in

Underfull \hbox (badness 2564) in paragraph at lines 19306--19309
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[282] Chapter 3
Underfull \hbox (badness 1205) in paragraph at lines 19359--19364
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[283 [45]] [8] [284]
Underfull \hbox (badness 10000) in paragraph at lines 3848--3853
 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[46] [285] [47 [9]] [286] [10 [48]
Underfull \hbox (badness 2469) in paragraph at lines 19668--19674
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,

Underfull \hbox (badness 1939) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing names.

Underfull \hbox (badness 10000) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[287]] [288 [49 [11]]] Chapter 9 [50] [12] [289] [51] Chapter 10 [52] [290 Chapter 11 [53]] [13
Chapter 12] [54] [291] [14] [55
Underfull \hbox (badness 10000) in paragraph at lines 19977--19979
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[292]] (Function and variable index) [56] [293] (./R-ints.vrs [15] [294] [16 [295]] [296 [57
[17]] [18 [297]
Underfull \hbox (badness 1655) in paragraph at lines 20374--20378
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[298]] [19]])
(Concept index) [299 [58]] [20 [300]] Chapter 4 (./R-ints.cps [21 [301]]) [59] [302 )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk] [303] [22></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb [304><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb]> [305] [23</usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmmi9.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb [306]>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb
Underfull \hbox (badness 4366) in paragraph at lines 20965--20971
\T1/pcr/m/n/10 www . bzip . org/$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http 
: / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n
/10 http : / / tukaani .
[307] [24>]</usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmr9.pfb [308> Chapter 5]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb [25]></u
sr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfbThis is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.

Underfull \hbox (badness 10000) in paragraph at lines 21094--21100
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed

Underfull \hbox (badness 6316) in paragraph at lines 21094--21100
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[309] [26]></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmti10.pfb [310> [27]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pf
b>]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 21203--21203
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[311]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.pfb></usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmtt9.pfb
Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-

Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[312
[28>]]
Output written on R-ints.pdf (63 pages, 430533 bytes).
Transcript written on R-ints.log.
 [313 markup,] glyphs, [29
page headings, tables, conditionals, indexing,] [314 sectioning,] toc, environments,
defuns, macros, [30 cross references, insertions, (./epsf.tex] [315
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, Chapter 6] [31] [32 [316] formatting, and turning on texinfo input format.)]
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi [317)
[1 [33{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map]] [34 [318]]
Underfull \hbox (badness 3849) in paragraph at lines 21797--21802
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[319]}] [2] [35 (./R-exts.toc]
Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
[320]
[-1] [321] [36] [322] [-2] [37
Underfull \hbox (badness 10000) in paragraph at lines 22025--22027
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[323]] [-3 [38 [324]] Chapter 7
[39]] [325]) [-4] (./R-exts.toc) (./R-exts.toc [326]) (Acknowledgements)
Chapter 1 [327 [1]] Cross reference values unknown; you must run TeX again. Chapter 8 [40] [2 [328 [41]]] [329] Chapter 9 [42]
[3 [330]]
Underfull \hbox (badness 2197) in paragraph at lines 22624--22628
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by

Underfull \hbox (badness 4048) in paragraph at lines 22624--22628
\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[331] [43] [4]
Underfull \hbox (badness 2846) in paragraph at lines 22638--22642
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-

Underfull \hbox (badness 1990) in paragraph at lines 22638--22642
\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
[332 Chapter 10 [44]] [5]
Underfull \hbox (badness 10000) in paragraph at lines 22722--22728
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.

Underfull \hbox (badness 1168) in paragraph at lines 22722--22728
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
[333] [6] [45 [334]] [7
Underfull \hbox (badness 10000) in paragraph at lines 4343--4345
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46] [335]] [8 [47]]
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of

Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,

Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[336] [9
Underfull \hbox (badness 4120) in paragraph at lines 22997--23004
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from

[337] [48]] [49 [10
Underfull \hbox (badness 1694) in paragraph at lines 23107--23110
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[338]]] [339] [50] [11] [340 (Function and Variable Index) [51]] (./R-lang.vrs [12
Underfull \hbox (badness 1603) in paragraph at lines 23346--23348
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[341]]
[52 [342] [13]]) (Concept Index) [53]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 23464--23473
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[343 [14 (./R-lang.cps]] [15
Underfull \hbox (badness 5475) in paragraph at lines 23559--23569
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 3271) in paragraph at lines 23578--23581
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able

Underfull \hbox (badness 10000) in paragraph at lines 23593--23595
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[344) Appendix A]] [54 [16] [345] [55]] )
(see the transcript file for additional information)</usr/share/texmf-texlive/f
onts/type1/bluesky/cm/cmb10.pfb [17>]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmbx12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb [346></usr/
share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb] [18></usr/share/texmf-texlive
/fonts/type1/bluesky/cm/cmmi9.pfb>]</usr/share/texmf-texlive/fonts/type1/bluesky
/cm/cmr10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/s
hare/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb>
[19
Underfull \hbox (badness 3138) in paragraph at lines 23833--23839
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4132) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "http://www.bioconductor.org"\
T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror

Underfull \hbox (badness 4001) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T
1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 1194) in paragraph at lines 23845--23848
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 1389) in paragraph at lines 23869--23871
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[347</usr/share/texmf-texlive/fo
nts/type1/bluesky/cm/cmsl10.pfb>]</usr/share/texmf-texlive/fonts/type1/bluesky/c
m/cmsltt10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb [20></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmtt10.pfb]></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmtt9.pfb
Underfull \hbox (badness 10000) in paragraph at lines 23886--23892
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by

Underfull \hbox (badness 1009) in paragraph at lines 23897--23900
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 23907--23914
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see

Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 23916--23923
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Overfull \hbox (34.78088pt too wide) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";

Underfull \hbox (badness 1881) in paragraph at lines 23930--23935
[]\T1/ptm/m/n/10 a char-ac-ter string, the path of the com-mand used for un-zip
-ping help files, or
[348 [21>]] [349
Output written on R-lang.pdf (60 pages, 409837 bytes).
Transcript written on R-lang.log.
] [22 [350]] [23 [351]]
Underfull \vbox (badness 10000) has occurred while \output is active [352]
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2069--2069
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 

Overfull \hbox (31.98314pt too wide) in paragraph at lines 2071--2071
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[24] [25
Underfull \hbox (badness 10000) in paragraph at lines 24227--24231
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 24227--24231
\T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[353]] [26 [354]] [27] [355] [28] [356] [29]
Underfull \hbox (badness 4341) in paragraph at lines 24550--24552
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[357] [30] [358] [31] [359] [360] [361] [32] [362] [33] [363] [34
Underfull \hbox (badness 10000) in paragraph at lines 24977--24981
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[364]]
Underfull \hbox (badness 1796) in paragraph at lines 25040--25043
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[365 [35]] [366] [36] [367] [37]
Underfull \hbox (badness 10000) in paragraph at lines 25235--25238
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[368] [38] [369]TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi

[39 [370]] [40 [371]] [41] [372This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
] [373 [42]]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: [374] pdf, fonts, [43] [375] [44 markup, glyphs,
page headings,] tables, conditionals, indexing, [376 sectioning,] toc, environments,
defuns, macros, [45 cross references, insertions, (./epsf.tex]
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,
Underfull \hbox (badness 1226) in paragraph at lines 25855--25860
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[377] [46]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25900--25900
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[378] [47] formatting, [379 and turning on texinfo input format.) (./R-ints.aux
] [48] [380] [49] [381 [50]]
Underfull \hbox (badness 7415) in paragraph at lines 26181--26185
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use

Overfull \hbox (42.18039pt too wide) in paragraph at lines 26202--26202
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[382 [51]] [383] [52]
Underfull \hbox (badness 2418) in paragraph at lines 26350--26361
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[384] [385 [53]]
Chapter 2 [386] [54]
Underfull \hbox (badness 1533) in paragraph at lines 26583--26586
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[387] [55
Underfull \hbox (badness 1337) in paragraph at lines 26680--26683
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[388]] [56
Underfull \hbox (badness 1038) in paragraph at lines 26745--26755
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[389]] [57
Underfull \hbox (badness 10000) in paragraph at lines 26756--26759
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[390]]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [58]
Underfull \hbox (badness 1117) in paragraph at lines 26840--26846
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[391) (./version.texi)]
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [392 [59]] [393] [60]}] [394 [2] [395] [61] (./R-ints.toc] [396]
[-1 [62]
Underfull \hbox (badness 4048) in paragraph at lines 27210--27215
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to

Underfull \hbox (badness 4582) in paragraph at lines 27210--27215
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:

Underfull \hbox (badness 1824) in paragraph at lines 27210--27215
\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[397]]) [-2 [398]] (./R-ints.toc) (./R-ints.toc [63) Chapter 1] [399] [400] [1 [64]] [401] [2 [402]] [65] [403]
Underfull \hbox (badness 10000) in paragraph at lines 5752--5759
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[66 [404]] [3]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27743--27743
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[405] [4] [406 [67]] [5] [407]
Underfull \hbox (badness 10000) in paragraph at lines 5929--5935
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[68] [6 [408]] [69]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 28025--28027
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[409
[7]] [70 [8 [410]]] Chapter 3 [71] [9
Underfull \hbox (badness 7558) in paragraph at lines 28234--28238
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 5417) in paragraph at lines 28250--28253
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
[411] [72]] [73]
Underfull \hbox (badness 10000) in paragraph at lines 28254--28256
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /

Underfull \hbox (badness 10000) in paragraph at lines 28257--28259
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[412] [10] [413 [74]] [414] [11] [75] [415] [76] [12 [77 [416]]] [78] [13 Chapter 4]
[79] [417] [14 [80]]
Underfull \hbox (badness 10000) in paragraph at lines 28664--28668
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[418] [81] [82 [15 [419]]] [83] [420] [16
Underfull \hbox (badness 10000) in paragraph at lines 7180--7189
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[84]] [421] [17] [85 [422]] [86 [18]] [423] [87 [424]] [19
Underfull \hbox (badness 7379) in paragraph at lines 7588--7591
[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few 
files (e.g.
[88 [425]]] [426 [20]
Underfull \hbox (badness 10000) in paragraph at lines 7592--7594
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[89]] [427 Chapter 2
[21]]
Overfull \hbox (50.80455pt too wide) in paragraph at lines 7713--7713
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[90] [22 [91 [428]]] [23] [429] [92] [93] [24 Chapter 5 [94]]
Underfull \hbox (badness 10000) in paragraph at lines 29470--29473
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,

Underfull \hbox (badness 1430) in paragraph at lines 29470--29473
\T1/pcr/m/n/10 save(list = ls(all = TRUE), file =     ".RData")\T1/ptm/m/n/10 .
 It is also what hap-
[430] [25] Chapter 3 [26] [431] [95] [27 [96] [432]] Chapter 4 [28]
Underfull \hbox (badness 2302) in paragraph at lines 29681--29688
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3815) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[433 [97]] [29] [98
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29733--29733
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[434] Chapter 5
[30]] Chapter 6 [99 [31]]
Underfull \hbox (badness 1158) in paragraph at lines 29834--29839
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 29861--29867
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1953) in paragraph at lines 29861--29867
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[435] [32 [100]]
Underfull \hbox (badness 10000) in paragraph at lines 29937--29942
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by

Underfull \hbox (badness 6725) in paragraph at lines 29937--29942
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[436] [33 [101]] [34
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30019--30019
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[437]] [35] [438
[102 [36]]] [103 [37 [439]]] [104 [440 [38]]] [39]
Underfull \hbox (badness 2809) in paragraph at lines 30282--30288
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment

Underfull \hbox (badness 7759) in paragraph at lines 30289--30292
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[441 [105]] [40 [442]]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 9020--9020
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[106 [41] [443]]
Chapter 7 [42] [107 [444]] [108 [445]] [446 [43]] [109 Chapter 8 [44]] [447] [110] [448 [111] [45]] [449 [112]]
Underfull \hbox (badness 10000) in paragraph at lines 3848--3853
 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c
hoice of
[46] [450] [113] [451 [47] [114]] [452
Underfull \hbox (badness 10000) in paragraph at lines 9854--9856
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[115] [48]]
Underfull \hbox (badness 1735) in paragraph at lines 31079--31085
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent

Underfull \hbox (badness 4303) in paragraph at lines 31095--31098
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[453] [116] [117 [454]] [49] Chapter 9 [50] [455 [118]] [119] [51 [120] [456 Chapter 10]] [52] Chapter 11 [121 [53]] [122 [457]
Chapter 12 [54]] [123] [458 [55 [124]]] (Function and variable index) [459 [56] [125] (./R-ints.vrs]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [460 [126]]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 10865--10865
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[127]
Underfull \hbox (badness 2512) in paragraph at lines 31636--31638
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[461 [57]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf,] fonts, [462 Chapter 6 [128)
(Concept index)] [58]] (./R-ints.cps [463 markup,] glyphs,)
page headings, tables, [59 [129 conditionals, indexing,] sectioning,] [464 )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk toc, environments,>
defuns,] macros,</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb
Underfull \vbox (badness 10000) has occurred while \output is active [465 cross references,>] insertions,</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb (./epsf.tex [130>
This is `epsf.tex' v2.7.4 <14 February 2011>
)<
 localization,/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb]></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmmi9.pfb
[466></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb]>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32030--32030
 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 32045--32045
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[467></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmr8.pfb]></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmr9.pfb formatting, and turning on texinfo input format.>)</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb
(./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)> [131</u
sr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb [468]></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmsy10.pfb])></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmti10.pfb (./version.texi)></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pf
b
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map> [469</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.pfb></usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmtt9.pfb [132]>] [470
Output written on R-ints.pdf (63 pages, 430533 bytes).
Transcript written on R-ints.log.
] [133] [471]
Underfull \hbox (badness 1087) in paragraph at lines 32416--32418
[]\T1/ptm/m/n/10 Markus Kuhn, ``ASCII and Uni-code quo-ta-tion marks''. [][]$\T
1/pcr/m/n/10 http : / / www . cl . cam . ac . uk /
[472] [134}]] [2] [-1] (Preface)
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32480--32480
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 32481--32481
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[473]
Cross reference values unknown; you must run TeX again. Chapter 1 [1] [474] [135] [2 [475]]
Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want

Underfull \hbox (badness 8113) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call

Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,

Underfull \hbox (badness 6542) in paragraph at lines 32696--32706
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on

Underfull \hbox (badness 5189) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-

Underfull \hbox (badness 4193) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or

Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,

Underfull \hbox (badness 1496) in paragraph at lines 32740--32746
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
[476
[3]] [136]
Underfull \hbox (badness 1728) in paragraph at lines 32753--32760
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[477] [4] [478] [137] [479] [5] Chapter 2
[138 [6]] [480]
Underfull \hbox (badness 10000) in paragraph at lines 12079--12083
 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
 R_orderVector(indx, n,
[139
Underfull \hbox (badness 10000) in paragraph at lines 33049--33055
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[481]] [482 [7]] [140
Underfull \hbox (badness 1163) in paragraph at lines 33224--33231
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6

Underfull \hbox (badness 8132) in paragraph at lines 33224--33231
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[483]] [8 [484]] [141] [485] [142
Underfull \hbox (badness 1142) in paragraph at lines 33440--33446
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
[486]]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 33455--33455
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[487 [9]] [143] [488] [144 [10]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12517
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [145]] [489] [146] Chapter 8
Overfull \hbox (6.78088pt too wide) in paragraph at lines 33707--33707
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[490 [11 [147]]]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33751--33751
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[491 Chapter 3 [12]] [148] [492] [149] [13 [493
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12921--12921
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[150]]] [494
Overfull \hbox (33.55849pt too wide) in paragraph at lines 12969--12969
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[151]] [14] [495
Chapter 4] [15] [152] [496 [153]] [16] [497 [154]] Chapter 5 [17]
Underfull \hbox (badness 10000) in paragraph at lines 34212--34215
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
[498] [155] [156]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34259--34259
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[499]
Underfull \hbox (badness 10000) in paragraph at lines 13477--13484
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[157 [18]] [158 [19 [500]]]
Underfull \hbox (badness 10000) in paragraph at lines 13600--13604
 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [159] (./R-exts.vrs [501] [20] [502] [160
Underfull \hbox (badness 2762) in paragraph at lines 34489--34498
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less

Underfull \hbox (badness 1466) in paragraph at lines 34489--34498
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple

Overfull \hbox (31.3804pt too wide) in paragraph at lines 34548--34548
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[503] [21]] [504] [505 [161] [22]]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34688--34688
 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[506] [23
Underfull \hbox (badness 3219) in paragraph at lines 34770--34775
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple

Underfull \hbox (badness 1107) in paragraph at lines 34770--34775
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[507]]) (Concept index)
[162
Underfull \hbox (badness 2452) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes

Underfull \hbox (badness 10000) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[508]] [24 (./R-exts.cps] [509
Chapter 6] [25] [163 [510] [26]])
Underfull \hbox (badness 10000) in paragraph at lines 35040--35044
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and

Underfull \hbox (badness 1584) in paragraph at lines 35055--35058
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[511 [164]] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk [512>]</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb [27 [513></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi12.pfb]]></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi9.pfb>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb [28>]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 35248--35248
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[514</usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmr7.pfb]></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmr8.pfb Chapter 7></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb [29]></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb [515]></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmsltt10.pfb> [30</usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmss10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb
></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pfb
Underfull \hbox (badness 1082) in paragraph at lines 35377--35380
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[516>]</usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmsy9.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmti10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti9.pfb
 [517></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pfb] [31>]< Chapter 8/usr/share/texmf-
texlive/fonts/type1/bluesky/cm/cmtt12.pfb [32]></usr/share/texmf-texlive/fonts/type1
/bluesky/cm/cmtt9.pfb [518></usr/share/texmf-texlive/fonts/type1/bluesky/latex-fonts
/lcircle1.pfb]>
Output written on R-exts.pdf (170 pages, 1013871 bytes).
Transcript written on R-exts.log.

Underfull \hbox (badness 1038) in paragraph at lines 35565--35568
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[519] [33] <./i
mages/hist.pdf> [520 [34]] <./images/ecdf.pdf> <./images/QQ.pdf> [35] [521] [36] <./images/
ice.pdf> [522 [37]] [38] Chapter 9 [39] [523]
Underfull \hbox (badness 1515) in paragraph at lines 35904--35907
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[524] [40]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36020--36020
 []\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c
("no", 
[525 Chapter 10] [41]
Underfull \hbox (badness 1924) in paragraph at lines 36039--36042
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[526 [42]]
Underfull \hbox (badness 4096) in paragraph at lines 36123--36126
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[527] [528 [43]] [529] [44]
Underfull \hbox (badness 10000) in paragraph at lines 36363--36365
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[530] [45]
[46
Underfull \hbox (badness 10000) in paragraph at lines 36443--36446
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$http : / / developer .
[531]] [47] [532]
Underfull \hbox (badness 5475) in paragraph at lines 36564--36568
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http : / /
[533 [48]] [49] Chapter 11
Underfull \hbox (badness 10000) in paragraph at lines 36626--36630
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http :
[534 [50]] [51 [535]] [52] [536] [537 [53]] [538] [54] [539]
Underfull \hbox (badness 5637) in paragraph at lines 37038--37047
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the Ol-son/IANA

Underfull \hbox (badness 1629) in paragraph at lines 37038--37047
\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
 in the file sys-tem varies,
[540] [55]
Underfull \hbox (badness 3460) in paragraph at lines 37092--37094
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Time _ zone$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / www . twinsun . com /
[541] [56] [542] [57 [543]] [58]
Underfull \hbox (badness 10000) in paragraph at lines 37299--37301
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[544] [545
[59]] [546 [60]] [547] [548] [61] [549] Chapter 12 [62]
Underfull \hbox (badness 6542) in paragraph at lines 37718--37720
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[550] [551 [63]]
Underfull \hbox (badness 1708) in paragraph at lines 37841--37849
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 3713) in paragraph at lines 37841--37849
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less

Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-

Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like

Underfull \hbox (badness 3281) in paragraph at lines 37850--37854
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-

Underfull \hbox (badness 4859) in paragraph at lines 37864--37869
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[552] [64]
Underfull \hbox (badness 3895) in paragraph at lines 37926--37938
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in

Underfull \hbox (badness 1303) in paragraph at lines 37926--37938
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[553] [65] [554] [66] [555]
Underfull \hbox (badness 1515) in paragraph at lines 38113--38118
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[556 [67]] [557 [68]]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 38252--38252
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[558 [69]] [70] [559] <./image
s/fig11.pdf> [71 [560]] <./images/fig12.pdf> [72] [73 [561]] [562 [74]] [75 [563]] Chapter 13 [76]
Underfull \hbox (badness 1803) in paragraph at lines 38707--38710
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),

Underfull \hbox (badness 2334) in paragraph at lines 38711--38718
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and

Underfull \hbox (badness 4726) in paragraph at lines 38737--38741
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be

Underfull \hbox (badness 1122) in paragraph at lines 38737--38741
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[564] [565]
[77 [566]] Chapter 14 [78]
Underfull \hbox (badness 3668) in paragraph at lines 38915--38917
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[567] [79] [568
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and

Underfull \hbox (badness 7064) in paragraph at lines 6647--6652
 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they 
may work in
[80]] Appendix A [81] [569] [82] [570 [83]]
Underfull \hbox (badness 6220) in paragraph at lines 39189--39194
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,

Underfull \hbox (badness 3098) in paragraph at lines 39189--39194
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,

Underfull \hbox (badness 1533) in paragraph at lines 39189--39194
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,

Underfull \hbox (badness 6592) in paragraph at lines 39205--39210
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[571 Appendix B] [84]
Underfull \hbox (badness 1603) in paragraph at lines 39224--39228
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[572] [85] [573 [86]] [87 [574]] [88] [575] [576 [89]]
[90 [577] Appendix C] [91] [92
Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to

Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[578]] Appendix D [93] Appendix E [94] Appendix F
Underfull \hbox (badness 2846) in paragraph at lines 39729--39733
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[579 [95]]
[96] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk>
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39769--39769
 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 

Underfull \hbox (badness 3209) in paragraph at lines 39790--39794
[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[580])</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb (./compiler-pkg.tex></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx7.pfb></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmcsc10.pfb
Chapter 2.
[581>]</usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmex10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pf
b></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi7.pfb></usr/share/texmf-
texlive/fonts/type1/bluesky/cm/cmmi9.pfb [582></usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmr10.pfb]> [583]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb) (./datasets-pkg.tex [584]>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmr9.pfb></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmsl10.pfb
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[585>]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl9.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmsy10.pfb [586></usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmsy7.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy9.pfb
></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb [587>]</usr/share/texmf-
texlive/fonts/type1/bluesky/cm/cmti9.pfb></usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmtt10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.p
fb [588><]/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb></usr/share/texmf
-texlive/fonts/type1/bluesky/latex-fonts/lcircle1.pfb> [589
Output written on R-intro.pdf (99 pages, 530709 bytes).
Transcript written on R-intro.log.
]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 294--294
 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[590]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368
 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
[591] [592] [593] [594] [595]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 691--694
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[596] [597]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 824--827
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[598] [599] [600] [601]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[602] [603] [604] [605] [606]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1432--1432
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[607] [608]
Underfull \hbox (badness 10000) in paragraph at lines 1517--1520
[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2903) in paragraph at lines 1517--1520
\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[609]
Underfull \hbox (badness 1325) in paragraph at lines 1598--1603
[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[610] [611]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1705--1708
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1799--1799
 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807
 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[613]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [614]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1923--1923
 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1924--1924
 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[615] [616] markup, glyphs,
page headings, tables, [617 conditionals, indexing,] sectioning, toc, environments,
defuns, macros, [618 cross references, insertions,] (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2127--2130
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[619] [620 formatting, and turning on texinfo input format.]) (./R-exts.aux
 [621] [622] [623] [624] [625] [626]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2666--2669
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[627]
Overfull \vbox (13.87083pt too high) has occurred while \output is active
[628]
Underfull \vbox (badness 1789) has occurred while \output is active [629]
[630]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[631] [632]
Overfull \vbox (17.12102pt too high) has occurred while \output is active
[633]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3083--3083
 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[634] [635] [636] [637] [638] [639] [640]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3540--3540
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[641]
Underfull \hbox (badness 5175) in paragraph at lines 3639--3642
[]\T1/ptm/m/n/10 Files for all 182 dis-tricts in 1888 and other years have been
 avail-able at [][]$\T1/pcr/m/n/10 http :

Underfull \hbox (badness 10000) in paragraph at lines 3639--3642
\T1/pcr/m/n/10 / / opr . princeton . edu / archive / eufert / switz . html$[][]
 \T1/ptm/m/n/10 or [][]$\T1/pcr/m/n/10 http : / / opr .
[642]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 3689--3692
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[643]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[644]
Overfull \vbox (27.49593pt too high) has occurred while \output is active
[645]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3891--3891
 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 

Underfull \hbox (badness 10000) in paragraph at lines 3920--3923
[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
[646]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [647]) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [648] [649] [650]}] [2] (./R-exts.toc [651]
[-1 [652]] [653] [-2 [654]] [655] [-3
Underfull \vbox (badness 10000) has occurred while \output is active [656]])
[657 [-4]] (./R-exts.tocThis is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
) (./R-exts.toc [658]) (./grDevices-pkg.tex) (Acknowledgements)entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]:
Chapter 1 [1 pdf,] fonts,
Chapter 4.
[659] [660 [2]] markup, glyphs,
page headings, tables, [661 conditionals, indexing,] sectioning, toc, environments,
defuns, [662 macros,] cross references, insertions, [3 (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,] [663] [4] formatting, and turning on texinfo input format.)
(./R-intro.aux [5
Underfull \hbox (badness 10000) in paragraph at lines 366--374
[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to

Underfull \hbox (badness 10000) in paragraph at lines 366--374
[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[664]] [665] [6]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462
 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[666] [7 [667]] [8] [668] [9 [669]] [670] [10] [671] [672 [11]] [673] [674 [12]]
Underfull \hbox (badness 5175) in paragraph at lines 1058--1060
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[675 [13]]
Underfull \hbox (badness 1325) in paragraph at lines 1120--1126
\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[676] [14
Underfull \hbox (badness 10000) in paragraph at lines 1161--1163
[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /

Overfull \hbox (25.98041pt too wide) in paragraph at lines 1213--1213
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[677]] [15
Underfull \hbox (badness 1173) in paragraph at lines 1255--1258
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[678]]
[16] [679] [17] [680] [18]
Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on

Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of

Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
[681] [19]
Underfull \hbox (badness 2221) in paragraph at lines 1515--1518
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[682] [20]) [21
Underfull \hbox (badness 10000) in paragraph at lines 1584--1588
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when

Underfull \hbox (badness 10000) in paragraph at lines 1584--1588
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[683 (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)]])
(./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [684 [22]] [685
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2069--2069
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
[23]]
Underfull \hbox (badness 1565) in paragraph at lines 1743--1748
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not

Underfull \hbox (badness 1354) in paragraph at lines 1743--1748
\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[686
Overfull \hbox (31.98314pt too wide) in paragraph at lines 2071--2071
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[24}]]]
[2] (./R-intro.toc [25]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1826--1826
 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 

Underfull \hbox (badness 1184) in paragraph at lines 1867--1877
[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-

Underfull \hbox (badness 2057) in paragraph at lines 1867--1877
\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[687 [26 [-1]]] [27 [688]] [-2] [28
Underfull \hbox (badness 10000) in paragraph at lines 1972--1974
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[689]] [29 [-3] [690]]) [-4] (./R-intro.toc) (./R-intro.toc
Underfull \hbox (badness 6758) in paragraph at lines 2133--2136
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[691 [30])
(Preface)] Chapter 1 [1] [692 [31]]
Underfull \hbox (badness 2326) in paragraph at lines 2240--2250
\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place

Underfull \hbox (badness 2318) in paragraph at lines 2240--2250
\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0

Underfull \hbox (badness 2460) in paragraph at lines 2240--2250
\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing

Underfull \hbox (badness 1221) in paragraph at lines 2240--2250
\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[693] [32 [2
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2324--2324
 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
[694]]] [695] [33 [3]] [696 [34]] [4] [697] [35] [698] [5
Underfull \hbox (badness 10000) in paragraph at lines 2650--2651

[699 [36]] Chapter 2 [6]] [700] [37 [701]] [702 [7] [38]] [703
[39]] [8] [704 [40]]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3056--3056
 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 3057--3057
 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[705] [41
Underfull \hbox (badness 1210) in paragraph at lines 3088--3090
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[706] [9]] [707 [42]] [10 [43] [708]]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3302--3302
 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[709] [11 [44]
Chapter 3] [12 [710]] [45]
Underfull \hbox (badness 3525) in paragraph at lines 3409--3412
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

Underfull \hbox (badness 1968) in paragraph at lines 3423--3425
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[711 [13]] [46] [712 [47] [14]] [713 Chapter 4] [15] [48 [714]] [16] [49
Underfull \hbox (badness 5939) in paragraph at lines 3717--3722
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[715]] Chapter 5 [17 [50]] [716] [51 [717]] [18] [19] [52] [718] [719]
Chapter 2 [20 [53]] [720] [54] [721]
[21 [55]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4200--4200
 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[722]] [56]
Underfull \hbox (badness 1502) in paragraph at lines 4247--4252
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[723] [57 [22] [724]]
Underfull \hbox (badness 4765) in paragraph at lines 4407--4409
[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if

Overfull \hbox (9.78043pt too wide) in paragraph at lines 4421--4421
 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[725 [58]] [23]
Underfull \hbox (badness 5077) in paragraph at lines 4461--4467
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as

Underfull \hbox (badness 1342) in paragraph at lines 4477--4479
[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[726 [59]] [24
Underfull \hbox (badness 1874) in paragraph at lines 4554--4562
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[727] [60 Chapter 6] [25]]
Underfull \hbox (badness 1755) in paragraph at lines 4621--4623
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[728] [26] [61 [729]]
Underfull \hbox (badness 7344) in paragraph at lines 4792--4794
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso

Underfull \hbox (badness 7397) in paragraph at lines 4803--4807
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[730 [27] [62]] [731] [28] Chapter 7
Underfull \hbox (badness 1552) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
[732 [29 [63]]] [30
Underfull \hbox (badness 4686) in paragraph at lines 4959--4965
\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for

Underfull \hbox (badness 10000) in paragraph at lines 4984--4992
[]\T1/pcr/m/n/10 Baekmuk-Batang \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m/n
/10 ftp : / / ftp . mizi . com / pub / baekmuk/$[][]\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 4984--4992
\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m
/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \vbox (badness 10000) has occurred while \output is active [733]] [64
Underfull \hbox (badness 7344) in paragraph at lines 5003--5005
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[734]] [31]
Chapter 8 [32 [735]]
Underfull \hbox (badness 10000) in paragraph at lines 5752--5759
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[65] [736] [33]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5194--5194
 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 

Underfull \hbox (badness 1648) in paragraph at lines 5200--5204
[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[737 <./images/hist.pdf>] [34 [66]] <./images/ecdf.pdf>
Underfull \hbox (badness 10000) in paragraph at lines 5280--5282
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[738 <./images/QQ.p
df> [35]]
Underfull \hbox (badness 10000) in paragraph at lines 5929--5935
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[67] [36
Underfull \hbox (badness 1072) in paragraph at lines 5316--5322
[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[739]] <./images/ice.pdf> [37] [740 [38 [68]] Chapter 9 [39]] [741] [69] [742 Chapter 3] [40 [70]] Chapter 10
[41
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5610--5610
 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 

Underfull \hbox (badness 10000) in paragraph at lines 5623--5626
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[743]] [71] [744] [72] [42] [745] [73] [746] [43] [747 [74]] [44] [75 [748]] [76] [45] [77]
Underfull \hbox (badness 1189) in paragraph at lines 6019--6021
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[749 [46 Chapter 4]
[78]] [750] [79] [47
Underfull \hbox (badness 10000) in paragraph at lines 6117--6119
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and

Underfull \hbox (badness 10000) in paragraph at lines 6156--6163
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and

Underfull \hbox (badness 1584) in paragraph at lines 6156--6163
\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[751] [80]] [81]
Underfull \hbox (badness 3088) in paragraph at lines 6240--6244
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[752] [82 [48]]
Underfull \hbox (badness 10000) in paragraph at lines 7180--7189
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[83
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6285--6285
 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 

Underfull \hbox (badness 10000) in paragraph at lines 6317--6320
[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[753 [49]]] Chapter 11 [50] [754] [84] [51
Underfull \hbox (badness 5637) in paragraph at lines 6408--6414
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1721) in paragraph at lines 6441--6444
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[755] [85] [756]] [86] [52 [757]]
Underfull \hbox (badness 7379) in paragraph at lines 7588--7591
[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few 
files (e.g.
[87]
Underfull \hbox (badness 6157) in paragraph at lines 6593--6596
\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via

Underfull \hbox (badness 1231) in paragraph at lines 6604--6606
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[758]
Underfull \hbox (badness 10000) in paragraph at lines 7592--7594
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[88] [53 [759]] [760]) (./graphics-pkg.tex
Overfull \hbox (50.80455pt too wide) in paragraph at lines 7713--7713
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[89] [90]
Chapter 5.

Underfull \hbox (badness 10000) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[761]
[54] [762 [91]] [92] Chapter 5 [93] [763] [55 [764]] [94
Underfull \hbox (badness 1412) in paragraph at lines 286--291
[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[765]] [95 [56]] [766 [96] [57]] [97 [767 [58]]] [98
Underfull \hbox (badness 2726) in paragraph at lines 465--471
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[768] [59]] [99 [769]] [60] [100 [770]]
Underfull \hbox (badness 10000) in paragraph at lines 655--659
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or

Underfull \hbox (badness 3250) in paragraph at lines 655--659
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if

Underfull \hbox (badness 2735) in paragraph at lines 683--690
[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[771] [101
Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[772]] [61
[102]] [773 Chapter 12] [103] [62]
Underfull \hbox (badness 1062) in paragraph at lines 849--852
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[774] [775] [104] [63 [776]]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 9020--9020
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[105] [777] [64] [106 [778]] [779 [65] [107]] [780 [66]] [108]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1274--1274
 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 

Underfull \hbox (badness 1024) in paragraph at lines 1319--1327
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
[781
[67]] [109]
Underfull \hbox (badness 1248) in paragraph at lines 1347--1353
\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground

Underfull \hbox (badness 6893) in paragraph at lines 1347--1353
\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and

Underfull \hbox (badness 3375) in paragraph at lines 1353--1355
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),

Overfull \hbox (19.3703pt too wide) in paragraph at lines 1375--1379
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[782 [110]] [68
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1423--1423
 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1424--1424
 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1430--1430
 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 1431--1431
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[783]] [111] [69 [784]] [112 [70] [785]] [113 <./images/fig11.pdf>] [71 [786]] <./images/fig12.pdf>
Underfull \hbox (badness 10000) in paragraph at lines 9854--9856
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[114 [72] [787]
[73]] [115]
Underfull \hbox (badness 10000) in paragraph at lines 1731--1737
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
[788 [74 [116]]]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1768--1768
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[789] [75] [117] [118
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1860--1860
 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[790 Chapter 13] [76]] [119] [791 [120]] [121]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1989--1989
 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1994--1994
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[792 [122 [77]]] Chapter 14 [78] [123] [793 [79]] [794
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and

Underfull \hbox (badness 7064) in paragraph at lines 6647--6652
 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they 
may work in
[80] [124]] Appendix A [81] [125 [795]] [82]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 10865--10865
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[126 [796] [83]] Chapter 6
Underfull \hbox (badness 1009) in paragraph at lines 2277--2284
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[797 Appendix B [127 [84]]] [798] [128 [85 [799]]] [800] [129] [86] [801] [87] [88
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2605--2605
 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[802]] [130 [89]] [803] [131
Underfull \hbox (badness 5878) in paragraph at lines 2763--2767
\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy

Underfull \hbox (badness 10000) in paragraph at lines 2791--2794
[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[804
[90]]] Appendix C [91] [132 [805]]
Underfull \hbox (badness 10000) in paragraph at lines 2869--2872
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[806 [133]] [92] [807 Appendix D] [93] (./R-intro.vrs [808] [94
Underfull \hbox (badness 1755) in paragraph at lines 3121--3125
[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[809] [134]]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the

Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther

Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[810] [95 [135 [811]]]) [812 Appendix E]
[96
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3379--3379
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 3398--3398
 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[813]] (./R-intro.cps [136]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3402--3402
 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[814 [97]
[137]]) Appendix F [98] [815 [99]
Underfull \hbox (badness 10000) in paragraph at lines 12079--12083
 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
 R_orderVector(indx, n,
[138 )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk]]></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb>
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3578--3578
 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 3579--3579
 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[816</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb]><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx7.pfb
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3616--3616
 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [817><]/usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmcsc10.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmex10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pf
b
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3668--3668
 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 3688--3688
 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[818>] [139</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmmi7.pfb]></usr/share/texmf-texlive/fonts/type1
/bluesky/cm/cmmi9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pf
b
Underfull \hbox (badness 10000) in paragraph at lines 3751--3755
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for
[819></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb]></usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmr8.pfb [140></usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmr9.pfb>]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb [820>]<
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl9.pfb></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pf
b
Underfull \hbox (badness 1867) in paragraph at lines 3903--3907
[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[821></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb] [141>]</usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmti9.pfb></usr/share/texmf-texlive/fonts/type1
/bluesky/cm/cmtt10.pfb [822>]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.
pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb [142> [823</usr/share/texm
f-texlive/fonts/type1/bluesky/latex-fonts/lcircle1.pfb>]]
Output written on R-intro.pdf (105 pages, 673913 bytes).
Transcript written on R-intro.log.
 [143
Underfull \hbox (badness 3930) in paragraph at lines 4066--4068
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[824]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12517
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7] [144] [825] [145] Chapter 8 [146 [826]] [147 [827]] [148]
Underfull \hbox (badness 1924) in paragraph at lines 4354--4359
[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[828]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12921--12921
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[149]
Underfull \hbox (badness 1286) in paragraph at lines 4376--4379
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing

Underfull \hbox (badness 2529) in paragraph at lines 4383--4386
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used: see
[829]
Overfull \hbox (33.55849pt too wide) in paragraph at lines 12969--12969
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[150
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4468--4468
 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 4472--4472
 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[830]] [151]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4516--4516
 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[831] [152]
Underfull \hbox (badness 1264) in paragraph at lines 4590--4603
\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[832 [153]] [833 [154]] [155]
Underfull \hbox (badness 10000) in paragraph at lines 13477--13484
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[156
Underfull \hbox (badness 7925) in paragraph at lines 4727--4733
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[834]] [157]
Underfull \hbox (badness 10000) in paragraph at lines 13600--13604
 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [158
Underfull \hbox (badness 10000) in paragraph at lines 4857--4860


</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf, id=14567, 28
9.08pt x 289.08pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf>] [835 (./R-exts.vrs </u
sr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf>]
Underfull \hbox (badness 10000) in paragraph at lines 4918--4920


</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf, id=14580, 25
9.97125pt x 332.24126pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>
Underfull \vbox (badness 10000) has occurred while \output is active [836]
[837 [159 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>]]
[838]
Underfull \hbox (badness 10000) in paragraph at lines 5111--5113
[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[839 [160]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5167--5167
 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5168--5168
 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[840]]
Underfull \hbox (badness 3954) in paragraph at lines 5269--5272
[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[841]) (Concept index)
Underfull \hbox (badness 10000) in paragraph at lines 5325--5329
\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[842
[161]] [843] (./R-exts.cps [844] [162 [845]]) [163] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb
Underfull \hbox (badness 10000) in paragraph at lines 5580--5584
[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g.,

Underfull \hbox (badness 1024) in paragraph at lines 5580--5584
\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[846></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb]><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmmi7.pfb [847></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi9.pfb]>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmr8.pfb> [848</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb>]</us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmss10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb
></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pfb> [849</usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmti10.pfb>]</usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmti9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pf
b>
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5850--5850
 []\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col.
axis = "red")[] 
[850</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.pfb]></usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmtt9.pfb></usr/share/texmf-texlive/fonts/type1
/bluesky/latex-fonts/lcircle1.pfb> [851
Output written on R-exts.pdf (169 pages, 1007794 bytes).
Transcript written on R-exts.log.
]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6002--6002
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
[852]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6008--6008
 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[853] [854] [855] [856] [857]
Underfull \hbox (badness 10000) in paragraph at lines 6378--6380
[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[858] [859]
Underfull \hbox (badness 1028) in paragraph at lines 6472--6474
[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of

</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf, id=15005, 36
1.35pt x 50.1875pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf>
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6515--6516
[][] 
[860 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf>]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6609--6609
 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[861]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6640--6640
 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [862]
[863]
Underfull \hbox (badness 10000) in paragraph at lines 6762--6764
[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr

Overfull \hbox (15.18042pt too wide) in paragraph at lines 6789--6789
 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 6795--6795
 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[864]
Underfull \hbox (badness 2600) in paragraph at lines 6855--6857
[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[865] [866] [867]
Underfull \hbox (badness 1881) in paragraph at lines 7044--7049
[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[868]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7087--7087
 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[869] [870] [871] [872] [873] [874]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7465--7465
 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 7476--7476
 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE))[] 
[875] [876] [877] [878] [879] [880]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7816--7816
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7819--7819
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 7823--7823
 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[881] [882] [883]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.

Overfull \hbox (30.78088pt too wide) in paragraph at lines 7994--7994
 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 7995--7995
 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[884]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts, [885] markup,
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8099--8099
 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 

Underfull \hbox (badness 2080) in paragraph at lines 8110--8115
[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[886 glyphs,
page headings, tables,] conditionals, indexing, sectioning, toc, environments,
defuns,
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8214--8214
 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
[887 macros, cross references,]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8229--8229
 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[888] insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, [889]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8360--8360
 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[890 formatting, and turning on texinfo input format.)]
(./R-intro.aux
Underfull \hbox (badness 7415) in paragraph at lines 8480--8487
[]\T1/ptm/m/n/10 The Euro sym-bol was in-tro-duced rel-a-tively re-cently and m
ay not be avail-able in

Underfull \hbox (badness 6808) in paragraph at lines 8480--8487
\T1/ptm/m/n/10 older fonts. In re-cent ver-sions of Adobe sym-bol fonts it is c
har-ac-ter 160, so
[891]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8532--8532
 []     \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: 
Règles, Liberté, Egalité, Fraternité...")[] 
[892]
Underfull \hbox (badness 6691) in paragraph at lines 8558--8561
[]\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex-
pan-sion)

Underfull \hbox (badness 1584) in paragraph at lines 8595--8601
[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[893]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8643 \HeaderA{units}{Graphical Units}{units}
                                               [894]
Underfull \hbox (badness 1205) in paragraph at lines 8708--8710
[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[895] [896]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8827--8827
 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[897]) (./grid-pkg.tex [898]
Chapter 6.
[899] [900] [901] [902] [903] [904]
Underfull \hbox (badness 10000) in paragraph at lines 383--389
\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,

Underfull \hbox (badness 1024) in paragraph at lines 383--389
\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[905] [906] [907] [908] [909] [910] [911]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [912)]
(./version.texi) [1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [913] [914This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 

Underfull \vbox (badness 10000) has occurred while \output is active [915}]]
[2] (./R-intro.tocentering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]: pdf, fonts,
Underfull \hbox (badness 1430) in paragraph at lines 1074--1079
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[916] [-1] [917 markup, glyphs,]
page headings, tables, conditionals, indexing, sectioning, [-2 toc, environments, [918
defuns,] macros,] cross references, insertions, (./epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,
Underfull \hbox (badness 3219) in paragraph at lines 1288--1291
[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
[919] [-3] [920 formatting,) and turning on texinfo input format.]) [-4 (./R-exts.aux
] (./R-intro.toc) (./R-intro.toc [921])
(Preface) Chapter 1 [922 [1]] [923] [924 [2]] [925] [3]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675
 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[926] [4 [927]] [928] [5
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[929]] Chapter 2 [6]
Underfull \hbox (badness 2961) in paragraph at lines 1926--1931
[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[930]
Underfull \hbox (badness 1430) in paragraph at lines 1985--1990
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-

Underfull \hbox (badness 4479) in paragraph at lines 2014--2017
[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
[931] [932 [7]] [933] [8
Underfull \hbox (badness 2894) in paragraph at lines 2221--2228
[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[934]] [935] [936 [9]]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377
 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 

Underfull \hbox (badness 1430) in paragraph at lines 2389--2394
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[937] [10] [938] [939 [11]]
Chapter 3 [12]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2582--2582
 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 2614--2614
 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[940] [941 [13]] [942] [14] [943 Chapter 4] [15]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2854--2854
 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[944] [16] [945]) Chapter 5 [17 (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)] [946]) (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [947] [18 [948]] [19]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3164--3164
 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[949]}] [2] (./R-exts.toc
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3260--3260
 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[950 [20]]
[-1
Underfull \hbox (badness 2799) in paragraph at lines 3294--3300
[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[951]]
[21
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3386--3386
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[952]] [-2
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3393--3393
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[953]] [22 [954 [-3]]] [955]) [-4
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3587--3587
 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 3602--3602
 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
[956 [23]] (./R-exts.toc]) (./R-exts.toc) (Acknowledgements) [957
Chapter 1] [1] [24] [958 Chapter 6 [25]] [2] [959 [26]] [3 [960]] [961 [27 [4]]] [5 [962 [28]]] Chapter 7 [29 [963] [6]] [30 [964]] [7]
Underfull \hbox (badness 1430) in paragraph at lines 4159--4164
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[965] [31]
Chapter 8 [8 [32]] [966] [9 [967] [33]]
Underfull \hbox (badness 1067) in paragraph at lines 4342--4345
[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[968 <./images/hist.pdf>] [34] [10 <./images/ecdf.pdf>] <./images/QQ.p
df> [35
Underfull \hbox (badness 1430) in paragraph at lines 4388--4393
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[969]] [36] [970 [11] <./images/ice.pdf>] [37] [38 [971] Chapter 9] [39] [12]
Underfull \hbox (badness 7256) in paragraph at lines 4585--4587
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[972] [973 [13] [40]] [974 Chapter 10]
[41] [14] [975] [42] [15 [976]] [977
[16] [43]] [17 [978]] [18 [44 [979]]] [45] [980] [19] [46] [47 [20]
Underfull \hbox (badness 10000) in paragraph at lines 5174--5176
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[981]] [21] [982 [48]] [49] [22 Chapter 11 [983 [50]]] [51
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2069--2069
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
[23 [984]]] [52]
Overfull \hbox (31.98314pt too wide) in paragraph at lines 2071--2071
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[24 [985]] [25] [986 [53]] [26] [987] [27 [988
[54]]] [28 [989]] [55 [29] [990]] [56
Underfull \hbox (badness 3449) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[991]] [30] [57 [992]] [31 [58]] [993] [59 [32 [994]]] [60] [995] [33]
Underfull \hbox (badness 1867) in paragraph at lines 6157--6159
[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[996] [34] [61
Underfull \hbox (badness 10000) in paragraph at lines 6194--6200
[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[997]] [35 Chapter 12 [62]] [998]
Underfull \hbox (badness 7649) in paragraph at lines 6326--6329
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[999 [36] [63]] [1000] [37 [64 [1001]]]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6530--6530
 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1002]) (./methods-pkg.tex [65] [38
Chapter 7.
[1003]] [66
[39] [1004]] [40
[67] [1005]] [68 [41
Underfull \hbox (badness 10000) in paragraph at lines 278--285
[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-

Underfull \hbox (badness 7704) in paragraph at lines 278--285
\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the

Underfull \hbox (badness 10000) in paragraph at lines 278--285
\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't

Underfull \hbox (badness 5817) in paragraph at lines 278--285
\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,

Overfull \hbox (0.78088pt too wide) in paragraph at lines 278--285
\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1006]]] [69 [42 [1007]]] [70] [43 [1008]] <./images/fig11.pdf> [71] [1009] <./images/fig12.pdf> [72 [44]
[73]] [1010] [45 [1011]] [74]
Underfull \hbox (badness 1281) in paragraph at lines 658--667
[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
thod is de-fined uniquely when
[1012] [46] [75] [1013 [47] Chapter 13 [76]] [48 [1014]] [1015 [49] [77]] Chapter 14 [78] [1016 [50]] [79] [1017 [51]
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and

Underfull \hbox (badness 7064) in paragraph at lines 6647--6652
 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they 
may work in
[80]] Appendix A [81] [1018 [52]] [82] [1019 [83]]
Chapter 2 [53 Appendix B [84]] [1020] [54 [85] [1021]] [86 [55] [1022]] [87] [56]
[1023 [88]] [57 [89] [1024]]
[90 [1025] [58 Appendix C] [91]] [1026] [92 [59]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1841--1841
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1843--1843
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 

Underfull \hbox (badness 10000) in paragraph at lines 1885--1887
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1027 Appendix D]] [93] (./R-intro.vrs [1028 [60]] [94
Underfull \hbox (badness 10000) in paragraph at lines 2028--2033
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1029]] [61 [1030]] [95 [1031] [62]] [1032]) Appendix E
[96 [63 [1033]] (./R-intro.cps]
Underfull \hbox (badness 10000) in paragraph at lines 2382--2386
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
[1034 [97] [64]) Appendix F [98] [1035]] [99] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb
Underfull \hbox (badness 10000) in paragraph at lines 5752--5759
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[65 [1036></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb]]><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx7.pfb></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmcsc10.pfb></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmex10.pfb
Underfull \hbox (badness 3792) in paragraph at lines 2628--2631
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1037></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pf
b]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1
/bluesky/cm/cmmi9.pfb [66
Underfull \hbox (badness 1194) in paragraph at lines 2659--2663
[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and

Overfull \hbox (24.78088pt too wide) in paragraph at lines 2715--2715
 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1038></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pf
b]]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmr9.pfb [1039>
Underfull \hbox (badness 10000) in paragraph at lines 5929--5935
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[67</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb]]><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl9.pfb></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmsy10.pfb [1040></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pf
b></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti10.pfb]> [68</usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmti9.pfb
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2951--2951
 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1041]></usr/share/texmf-texlive/fonts/type1
/bluesky/cm/cmtt10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.
pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.pfb> [1042</usr/share/texm
f-texlive/fonts/type1/bluesky/latex-fonts/lcircle1.pfb>] [69]
Output written on R-intro.pdf (105 pages, 673913 bytes).
Transcript written on R-intro.log.
 Chapter 3 [1043 [70]] [1044 [71]] [72] [1045] [1046 [73]] [1047] [1048 [74]] [75 [1049]] [76] [77
Underfull \hbox (badness 10000) in paragraph at lines 3531--3535
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1050]] Chapter 4
[78]
Underfull \hbox (badness 10000) in paragraph at lines 3637--3642
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

Overfull \hbox (28.78088pt too wide) in paragraph at lines 3645--3654
[]
[1051 [79]] [80
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3734--3734
 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1052]] [81]
Underfull \hbox (badness 1394) in paragraph at lines 3805--3810
\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class

[1053 [82]]
Underfull \hbox (badness 10000) in paragraph at lines 7180--7189
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[83 [1054]] [1055 [84]] [85
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4067--4067
 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1056]] [1057 [86]] [1058]
Underfull \hbox (badness 7379) in paragraph at lines 7588--7591
[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few 
files (e.g.
[87]
Underfull \hbox (badness 10000) in paragraph at lines 4252--4254
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1059]
Underfull \hbox (badness 10000) in paragraph at lines 7592--7594
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[88
Underfull \hbox (badness 1629) in paragraph at lines 4354--4363
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1060]]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4415--4415
 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 4416--4416
 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1061]
Overfull \hbox (50.80455pt too wide) in paragraph at lines 7713--7713
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[89] [90]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4473--4473
 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1062] [91] [92] Chapter 5 [93 [1063]] [1064] [1065 [94]] [95 [1066]] [96 [1067]] [97
Underfull \hbox (badness 10000) in paragraph at lines 4945--4954
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1068]] [98]
Underfull \vbox (badness 10000) has occurred while \output is active [1069]
[1070 [99]]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5138--5138
 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5167--5167
 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier
 fails here)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5181--5181
 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1071] [100
[1072]]
Underfull \hbox (badness 1033) in paragraph at lines 5251--5258
\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture

Underfull \hbox (badness 10000) in paragraph at lines 5325--5327
[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1073] [101 [1074]]
[102 [1075]] [103 [1076]] [1077] [104]
Underfull \hbox (badness 1087) in paragraph at lines 5619--5624
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing

Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1078]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 9020--9020
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[105
Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1079]] [1080 [106]]
Underfull \hbox (badness 10000) in paragraph at lines 5900--5916
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1081 [107]] [1082] [1083 [108]]
Underfull \hbox (badness 1248) in paragraph at lines 6186--6190
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,

Underfull \hbox (badness 1960) in paragraph at lines 6186--6190
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1084 [109]] [110]
Underfull \hbox (badness 4647) in paragraph at lines 6274--6276
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1085] [111]
Underfull \hbox (badness 1072) in paragraph at lines 6348--6355
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1086] [1087 [112]] [1088] [113 [1089]] [1090
Underfull \hbox (badness 10000) in paragraph at lines 9854--9856
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[114]]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6707 \aliasA{S4}{S3Part}{S4}
                               [1091] [115] [116 [1092]] [1093 [117]] [118]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6948--6948
 []\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
 the S3 part:[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6953--6953
 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6983 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.6985 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.6986 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored

<to be read again> 
                   \relax 
l.6988 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.6989 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1094] [119] [120] [121]
Underfull \hbox (badness 2050) in paragraph at lines 7050--7054
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing

Underfull \hbox (badness 6708) in paragraph at lines 7063--7075
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2012) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3209) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1095] [122] [1096 [123]] [124
Underfull \hbox (badness 1694) in paragraph at lines 7223--7225
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
[1097]] [125]
Underfull \hbox (badness 10000) in paragraph at lines 7247--7250
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1098
Overfull \hbox (22.06111pt too wide) in paragraph at lines 10865--10865
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[126]] [1099] Chapter 6 [127 [1100]] [1101] [128] [1102] [1103] [129]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7702--7702
 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[] 
[1104] [1105] [130
Underfull \hbox (badness 2277) in paragraph at lines 7838--7846
[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10 
in this form is not strictly nec-es-sary be-fore call-ing

Underfull \hbox (badness 3128) in paragraph at lines 7879--7884
[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
[1106]]
Underfull \hbox (badness 1052) in paragraph at lines 7916--7923
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1107] [131] [1108] [132 [1109]] [1110] [133]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8236--8236
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1111]
Underfull \hbox (badness 1755) in paragraph at lines 8270--8273
[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the 
method. For
[1112]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8413--8413
 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[] 
[1113] [134 [1114]] [1115] [135] [1116] [1117] [136
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8819--8819
 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date 
= "POSIXt"))[] 
[1118]]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8832--8832
 []\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 s class, then calls the S3 print method.[] 
[1119]
[137]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8930--8930
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 8941--8941
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1120]
Underfull \hbox (badness 10000) in paragraph at lines 12079--12083
 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
 R_orderVector(indx, n,
[138] [1121] [1122] [139 [1123]] [1124 [140]] [1125] [141] [1126] [142 [1127]] [143 [1128]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12517
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7] [144] [145
Underfull \hbox (badness 10000) in paragraph at lines 9634--9636
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class

Underfull \hbox (badness 1852) in paragraph at lines 9642--9646
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,

Underfull \hbox (badness 1681) in paragraph at lines 9642--9646
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1129]] Chapter 8 [146] [1130] [147] [1131] [148 [1132]]) (./parallel-pkg.tex
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12921--12921
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[149]
Chapter 8.

Underfull \hbox (badness 2418) in paragraph at lines 15--17
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1133]
Overfull \hbox (33.55849pt too wide) in paragraph at lines 12969--12969
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[150]
Underfull \hbox (badness 4242) in paragraph at lines 94--96
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1134] [151] [1135 [152]]
Underfull \hbox (badness 1024) in paragraph at lines 194--197
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1136] [153
Underfull \hbox (badness 5077) in paragraph at lines 281--284
[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, OS X, FreeBSD, So-laris, I
rix and Win-dows.
[1137]] [154 [1138]] [155]
Underfull \hbox (badness 10000) in paragraph at lines 13477--13484
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[156]
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1139] [157]
Underfull \hbox (badness 10000) in paragraph at lines 13600--13604
 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [158 [1140]] (./R-exts.vrs [1141] [1142] [159
Underfull \hbox (badness 1917) in paragraph at lines 702--711
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class

Underfull \hbox (badness 1178) in paragraph at lines 702--711
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1143]] [1144] [160
Underfull \hbox (badness 10000) in paragraph at lines 839--842
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1145]] [1146] [1147)] (Concept index)
[161
Underfull \hbox (badness 5388) in paragraph at lines 1028--1033
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1148]] (./R-exts.cps
Underfull \hbox (badness 10000) in paragraph at lines 1052--1060
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1088--1088
 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1149] [162 [1150])] [163] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk>
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1203--1203
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1217--1217
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 

Underfull \hbox (badness 1577) in paragraph at lines 1246--1249
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1151</usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb><
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb
Underfull \hbox (badness 3375) in paragraph at lines 1292--1294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1152></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi12.pfb]></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi9.pfb [1153>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb]) (./splines-pkg.tex [1154>]</usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb></us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb
Chapter 9.

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1155>]</usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmss10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb
></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pfb [1156]></usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmti10.pfb></usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmti9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pf
b></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.pfb [1157>]</usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmtt9.pfb></usr/share/texmf-texlive/fonts/type1
/bluesky/latex-fonts/lcircle1.pfb> [1158
Output written on R-exts.pdf (169 pages, 1007799 bytes).
Transcript written on R-exts.log.
] [1159] [1160] [1161]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 467--467
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1162] [1163] [1164]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 678--678
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1165] [1166] [1167]) (./stats-pkg.tex [1168]
Chapter 10.
[1169]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1170] [1171] [1172] [1173] [1174]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 416--416
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 437--437
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1175] [1176] [1177] [1178] [1179] [1180]
Underfull \hbox (badness 1024) in paragraph at lines 843--845
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189]
Underfull \hbox (badness 10000) in paragraph at lines 1387--1389
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1190]
Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class

Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class

Underfull \hbox (badness 1490) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199]
Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure

Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r

Underfull \hbox (badness 1371) in paragraph at lines 2076--2081
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous

Underfull \hbox (badness 1221) in paragraph at lines 2082--2088
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-

Underfull \hbox (badness 4608) in paragraph at lines 2082--2088
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1200]
Underfull \hbox (badness 3965) in paragraph at lines 2163--2165
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1201] [1202] [1203]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 file:line:error style messages enabled.
 %&-line parsing enabled.
 [1204]entering extended mode
(/usr/src/RPM/BUILD/R-3.1.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2015-06-24.23]:
Underfull \hbox (badness 1221) in paragraph at lines 2418--2423
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-

Underfull \hbox (badness 4608) in paragraph at lines 2418--2423
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1205 pdf, fonts,]
Underfull \hbox (badness 3965) in paragraph at lines 2495--2497
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1206] markup, glyphs,
page headings, tables, [1207 conditionals, indexing,] sectioning, toc, environments,
defuns, macros, cross references, insertions, (./epsf.tex
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2630--2630
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1208
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization,] [1209] formatting, and turning on texinfo input format.) (./R-exts.aux
 [1210] [1211]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2866--2866
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1212] [1213] [1214]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3059--3061
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 3106--3106
 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 3107--3107
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1215] [1216] [1217] [1218] [1219] [1220]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3485--3485
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1221] [1222] [1223] [1224]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3755--3755
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1225] [1226] [1227] [1228] [1229]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4040--4040
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 4041--4041
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1230] [1231] [1232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4276--4276
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1233]) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex) [1234)] (./version.texi)
[1{/var/cache/texmf/fonts/map/pdftex/updmap/pdftex.map [1235]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4439--4439
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1236]
Underfull \hbox (badness 3989) in paragraph at lines 4528--4535
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1237}]] [2] (./R-exts.toc [1238]
[-1] [1239] [-2 [1240]] [1241] [-3
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4876--4876
 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4878--4878
 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1242]]) [-4
Underfull \hbox (badness 7397) in paragraph at lines 4965--4969
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever

Underfull \hbox (badness 7326) in paragraph at lines 4965--4969
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1243] (./R-exts.toc]) (./R-exts.toc) (Acknowledgements) [1244
Chapter 1 [1]] [2
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5099--5099
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 5117--5117
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1245]]
Underfull \hbox (badness 2680) in paragraph at lines 5144--5146
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by

Underfull \hbox (badness 10000) in paragraph at lines 5149--5151
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1246] [3] [1247] [4] [1248] [5]
Underfull \hbox (badness 1436) in paragraph at lines 5327--5332
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances

Underfull \hbox (badness 1377) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)

Underfull \hbox (badness 1448) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1249 [6]] [1250]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5513--5513
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1251] [7]
Underfull \hbox (badness 1168) in paragraph at lines 5585--5590
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1252 [8]] [1253] [9]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5679--5679
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1254] [10 [1255]] [1256] [11]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5864--5864
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1257] [1258] [12 [1259]]
Underfull \hbox (badness 10000) in paragraph at lines 6027--6032
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When
[1260] [13] [1261] [14 [1262]] [15
Underfull \hbox (badness 5954) in paragraph at lines 6215--6217
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1263]]
[16]
Underfull \hbox (badness 2503) in paragraph at lines 6297--6300
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 5563) in paragraph at lines 6301--6303
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also

Underfull \hbox (badness 1655) in paragraph at lines 6304--6309
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,

Underfull \hbox (badness 7238) in paragraph at lines 6339--6342
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1264 [17]]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6374--6374
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6389--6389
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 6404--6404
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1265] [18]
[1266] [19] [1267] [20 [1268]] [21]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6645--6645
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1269] [22 [1270]] [1271]
Overfull \hbox (46.15797pt too wide) in paragraph at lines 2069--2069
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 
[23]
Overfull \hbox (31.98314pt too wide) in paragraph at lines 2071--2071
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[24 [1272]] [25] [1273] [26 [1274]] [27]
Underfull \hbox (badness 10000) in paragraph at lines 7012--7016
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1275] [28
Underfull \hbox (badness 6493) in paragraph at lines 7109--7112
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1276]] [29] [1277]
Underfull \hbox (badness 1430) in paragraph at lines 7246--7249
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tp : / / cran . r-[]project . org / web / views /
[1278 [30]] [1279] [31] [1280] [32 [1281]] [1282] [33] [1283] [34]
Underfull \hbox (badness 10000) in paragraph at lines 7656--7661
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1284] [35] [1285] [36]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7794--7796
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1286] [37] [1287] [38 [1288]]
[39]
Underfull \hbox (badness 1210) in paragraph at lines 8011--8013
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1289] [40] [1290] [41] [1291] [42] [1292] [43] [1293] [44] [1294] [45] [1295] [46
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8455--8455
 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8477--8477
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 8480--8480
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1296]] [47] [1297] [48]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8618--8618
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 

Underfull \hbox (badness 1859) in paragraph at lines 8655--8660
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1298] [49 [1299]] [1300 [50]] [1301 [51]] [1302] [52]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8987--8987
 []                \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[] 
[1303]
Chapter 2 [53] [1304] [54] [1305] [55]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9155--9157
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1306] [56] [1307 [57]] [1308] [58] [1309] [59] [1310] [1311] [60] [1312]
Underfull \hbox (badness 2443) in paragraph at lines 9607--9613
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1313 [61]] [1314] [62] [1315]
Underfull \hbox (badness 10000) in paragraph at lines 9821--9824
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org /
 wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1316 [63]] [1317] [64 [1318]] [1319]
Underfull \hbox (badness 10000) in paragraph at lines 5752--5759
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[65]
Underfull \hbox (badness 4518) in paragraph at lines 10081--10086
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1320]
Underfull \hbox (badness 4132) in paragraph at lines 10120--10124
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1321 [66]]
Underfull \hbox (badness 10000) in paragraph at lines 10223--10226
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1322
Underfull \hbox (badness 10000) in paragraph at lines 5929--5935
[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
-ally be used within the @textsl text[] @textrm part of
[67]] [1323] [68] [1324] [69
Underfull \hbox (badness 2142) in paragraph at lines 10423--10426
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1325]] Chapter 3 [70]
Underfull \hbox (badness 1708) in paragraph at lines 10504--10507
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1326] [71] [72
Underfull \hbox (badness 10000) in paragraph at lines 10545--10551
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,

Underfull \hbox (badness 1418) in paragraph at lines 10583--10588
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1327]] [1328 [73]]
Underfull \hbox (badness 2635) in paragraph at lines 10716--10719
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1329] [74] [1330] [75] [76]
Underfull \hbox (badness 1694) in paragraph at lines 10883--10886
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1331 [77]] Chapter 4
[78]
Underfull \hbox (badness 1337) in paragraph at lines 10902--10911
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-

Underfull \hbox (badness 3049) in paragraph at lines 10902--10911
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1332] [79]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10984--10984
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 11017--11017
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
[1333 [80]] [81
Underfull \hbox (badness 10000) in paragraph at lines 11030--11034
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1334]] [82] [1335]
Underfull \hbox (badness 10000) in paragraph at lines 7180--7189
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g.
[83] [1336] [84] [1337] [85] [1338]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11334--11334
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11349 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11401--11401
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1339 [86]]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11413--11413
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 

Underfull \hbox (badness 1062) in paragraph at lines 11460--11465
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-

Underfull \hbox (badness 1052) in paragraph at lines 11471--11473
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1340
Underfull \hbox (badness 7379) in paragraph at lines 7588--7591
[]@textrm Some ver-sions have greatly in-creased com-pi-la-tion times on a few 
files (e.g.
[87]] [1341]
Underfull \hbox (badness 10000) in paragraph at lines 7592--7594
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by
[88]
Underfull \hbox (badness 3623) in paragraph at lines 11600--11602
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1342] [1343
Overfull \hbox (50.80455pt too wide) in paragraph at lines 7713--7713
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[89]] [90]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11688--11688
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1344] [91]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11781--11781
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1345 [92]] Chapter 5 [93]
Underfull \hbox (badness 10000) in paragraph at lines 11829--11832
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1346] [94 [1347]] [95] [1348] [96
Underfull \hbox (badness 4441) in paragraph at lines 12024--12026
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

Underfull \hbox (badness 10000) in paragraph at lines 12031--12033
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1349]] [97] [1350] [98]
Underfull \hbox (badness 2753) in paragraph at lines 12121--12123
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1351] [99] [1352] [100]
Underfull \hbox (badness 1292) in paragraph at lines 12246--12250
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1353]
Underfull \hbox (badness 10000) in paragraph at lines 12359--12361
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of

Underfull \hbox (badness 2894) in paragraph at lines 12365--12369
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method

Underfull \hbox (badness 1038) in paragraph at lines 12365--12369
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1354] [101 [1355]]
[102 [1356]] [103 [1357]] [1358] [104] [1359]
Overfull \hbox (16.31242pt too wide) in paragraph at lines 9020--9020
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[105 [1360]] [1361] [106] [1362] [107] [1363] [108 [1364]] [109]
Underfull \hbox (badness 4518) in paragraph at lines 13059--13064
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1365 [110]] [111] [1366] [112] [1367] [113]
Underfull \hbox (badness 10000) in paragraph at lines 13253--13257
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1368]
Underfull \hbox (badness 10000) in paragraph at lines 9854--9856
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[114] [1369] [115] [116]
Underfull \hbox (badness 6995) in paragraph at lines 13438--13440
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1370] [117] [118 [1371]] [119] [1372 [120]] [121] [122]
Underfull \hbox (badness 1163) in paragraph at lines 13586--13594
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1373] [123]
Underfull \hbox (badness 4518) in paragraph at lines 13706--13711
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1374] [124] [1375 [125]]
Overfull \hbox (22.06111pt too wide) in paragraph at lines 10865--10865
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[126 [1376]]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13884--13884
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 13885--13885
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1377 Chapter 6] [127]
Underfull \hbox (badness 10000) in paragraph at lines 13940--13943
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,

Underfull \hbox (badness 1715) in paragraph at lines 13940--13943
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1378] [128 [1379]] [1380] [129] [1381]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14226--14226
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 14227--14227
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1382] [130]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14277--14279
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 14320--14320
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1383] [1384 [131]] [132] [1385] [133 [1386]] [1387] [1388] [134 [1389]]
Underfull \hbox (badness 2726) in paragraph at lines 14722--14725
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1390] [135] [1391] [1392] [136] [1393] [1394
[137]] [1395]
Underfull \hbox (badness 10000) in paragraph at lines 12079--12083
 @texttt <- order(x, y, na.last, decreasing)[] @textrm cor-re-sponds to @texttt
 R_orderVector(indx, n,
[138] [1396] [1397 [139]] [1398] [140] [1399] [1400 [141]]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15436--15436
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1401] [142] [1402] [143]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12517
[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [144] [1403 [145]] Chapter 8 [146]
Underfull \hbox (badness 1648) in paragraph at lines 15627--15629
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,

Underfull \hbox (badness 2591) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would

Underfull \hbox (badness 3930) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1404] [147
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15705--15705
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
[1405]] [148] [1406
Overfull \hbox (22.06111pt too wide) in paragraph at lines 12921--12921
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[149]] [1407
Overfull \hbox (33.55849pt too wide) in paragraph at lines 12969--12969
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[150]] [1408] [151] [1409 [152]] [1410 [153]] [1411] [154] [155] [1412
Underfull \hbox (badness 10000) in paragraph at lines 13477--13484
 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra-
tive in-stall and
[156]] [157]
Underfull \hbox (badness 10000) in paragraph at lines 13600--13604
 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index)
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16258--16258
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1413 [158]] (./R-exts.vrs [1414] [159 [1415]] [1416]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16486--16486
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1417] [160 [1418]] [1419]) (Concept index)
[161 [1420]] (./R-exts.cps [1421] [162 [1422]])
Underfull \hbox (badness 2772) in paragraph at lines 16922--16925
[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When

Underfull \hbox (badness 10000) in paragraph at lines 16922--16925
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1423 [163]] )
(see the transcript file for additional information) </usr/src/.texmf-var/fonts
/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmb10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx12.pfb> [1424<
/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmmi12.pfb]></usr/share/texmf-texlive/fonts/type1/b
luesky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi9.pfb>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb
Underfull \hbox (badness 2359) in paragraph at lines 17041--17043
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1425>]</usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmr8.pfb
Underfull \vbox (badness 10000) has occurred while \output is active [1426>]</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr9.pfb>
Underfull \vbox (badness 10000) has occurred while \output is active [1427</us
r/share/texmf-texlive/fonts/type1/bluesky/cm/cmsl10.pfb]></usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmsltt10.pfb></usr/share/texmf-texlive/fonts/type1/bl
uesky/cm/cmss10.pfb
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17213--17213
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1428></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb
]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pfb></usr/share/texmf-t
exlive/fonts/type1/bluesky/cm/cmti10.pfb></usr/share/texmf-texlive/fonts/type1/
bluesky/cm/cmti9.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt10.pf
b
Underfull \hbox (badness 10000) in paragraph at lines 17293--17297
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1429]></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt12.pfb></usr/share/texmf
-texlive/fonts/type1/bluesky/cm/cmtt9.pfb></usr/share/texmf-texlive/fonts/type1
/bluesky/latex-fonts/lcircle1.pfb> [1430]
Output written on R-exts.pdf (169 pages, 1007799 bytes).
Transcript written on R-exts.log.

Overfull \hbox (9.78043pt too wide) in paragraph at lines 17373--17373
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 17420--17420
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1431]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17467--17467
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439]
Underfull \hbox (badness 1248) in paragraph at lines 17957--17960
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on

Underfull \hbox (badness 1127) in paragraph at lines 17970--17974
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 1478) in paragraph at lines 17978--17982
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and

[1440]
Underfull \hbox (badness 2042) in paragraph at lines 18031--18033
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1441]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18127--18127
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1442]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18169--18169
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
[1443]
Underfull \hbox (badness 2564) in paragraph at lines 18240--18251
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1082) in paragraph at lines 18240--18251
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18303--18303
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1445] [1446] [1447]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18518--18518
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1448]
Underfull \hbox (badness 1337) in paragraph at lines 18594--18597
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1449] [1450] [1451] [1452] [1453] [1454]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18910--18910
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1455]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 18997--18997
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 19000--19000
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1456] [1457] [1458] [1459] [1460]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19313--19313
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 

Underfull \hbox (badness 4779) in paragraph at lines 19320--19322
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

Underfull \hbox (badness 1194) in paragraph at lines 19323--19326
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1461]
Underfull \hbox (badness 1107) in paragraph at lines 19381--19383
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1462]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19436--19436
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1463]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19443--19443
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 

Underfull \hbox (badness 10000) in paragraph at lines 19492--19495
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives

Underfull \hbox (badness 10000) in paragraph at lines 19492--19495
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for

[1464]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19536--19536
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1465] [1466]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19658--19658
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1467]
Underfull \hbox (badness 10000) in paragraph at lines 19716--19718
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478]
[1479] [1480] [1481]
Underfull \hbox (badness 6859) in paragraph at lines 20681--20688
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 20692--20698
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492]
[1493] [1494] [1495] [1496] [1497] [1498]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21684--21684
 []                          \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == 
"Pr(",[] 
[1499] [1500] [1501] [1502] [1503]
Underfull \hbox (badness 1337) in paragraph at lines 22007--22013
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 1028) in paragraph at lines 22690--22693
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1514] [1515]
Underfull \hbox (badness 10000) in paragraph at lines 22800--22803
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 5091) in paragraph at lines 22800--22803
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
[1516] [1517] [1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23011--23011
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1519] [1520] [1521]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23230--23230
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1522] [1523]
Underfull \hbox (badness 10000) in paragraph at lines 23375--23378
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1524]
Underfull \hbox (badness 2134) in paragraph at lines 23426--23430
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from

Overfull \hbox (9.78043pt too wide) in paragraph at lines 23439--23439
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1525] [1526] [1527] [1528]
Underfull \hbox (badness 7667) in paragraph at lines 23692--23694
[]\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je
ct which is co-ercible to one by
[1529] [1530] [1531]
Underfull \hbox (badness 2591) in paragraph at lines 23895--23901
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
[1532] [1533] [1534] [1535] [1536] [1537]
Underfull \hbox (badness 1412) in paragraph at lines 24301--24303
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1538] [1539]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 24388--24388
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 

Underfull \hbox (badness 10000) in paragraph at lines 24443--24448
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when

Underfull \hbox (badness 2435) in paragraph at lines 24443--24448
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1540] [1541]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 24600--24600
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
[1542] [1543] [1544]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24770--24770
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1545]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24837--24837
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1546] [1547] [1548] [1549] [1550] [1551]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 25213--25213
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 

Underfull \hbox (badness 6477) in paragraph at lines 25266--25269
[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1552] [1553]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25392--25392
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 25393--25393
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1554]
Underfull \hbox (badness 2922) in paragraph at lines 25459--25464
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1555]
Underfull \hbox (badness 2922) in paragraph at lines 25521--25526
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion

Underfull \hbox (badness 3240) in paragraph at lines 25533--25537
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1556]
Underfull \hbox (badness 2922) in paragraph at lines 25578--25583
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1557]
Underfull \hbox (badness 2922) in paragraph at lines 25639--25645
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1558]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25661--25661
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 25677--25677
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1559] [1560]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 25791--25791
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 25814--25814
 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response 
and gradient[] 
[1561]
Underfull \hbox (badness 2922) in paragraph at lines 25852--25857
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1562]
Underfull \hbox (badness 2922) in paragraph at lines 25908--25913
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion

Underfull \hbox (badness 2922) in paragraph at lines 25965--25970
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1563]
Underfull \hbox (badness 2922) in paragraph at lines 26020--26025
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26041--26041
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 

Underfull \hbox (badness 6493) in paragraph at lines 26089--26094
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1565]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26115--26115
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 26117--26117
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1566] [1567] [1568] [1569] [1570] [1571] [1572]
Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1573] [1574] [1575] [1576] [1577] [1578] [1579]
Underfull \hbox (badness 3396) in paragraph at lines 27040--27042
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1580] [1581] [1582]
Underfull \hbox (badness 2237) in paragraph at lines 27217--27219
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1583] [1584]
Underfull \hbox (badness 2591) in paragraph at lines 27381--27383
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1585]
Underfull \hbox (badness 2237) in paragraph at lines 27427--27430
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1586] [1587] [1588]
Underfull \hbox (badness 3407) in paragraph at lines 27606--27610
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1589] [1590]
Underfull \hbox (badness 1337) in paragraph at lines 27739--27743
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1591] [1592]
Underfull \hbox (badness 10000) in paragraph at lines 27856--27859
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1593] [1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27985--27985
 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 28013--28013
 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1595]
Underfull \hbox (badness 1616) in paragraph at lines 28039--28042
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1596]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 28118--28118
 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1597]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 28195--28195
 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1598]
Underfull \hbox (badness 5050) in paragraph at lines 28231--28236
[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
 is re-turned. The ob-ject it-self is the re-ordered (un-less
[1599]
Underfull \hbox (badness 2205) in paragraph at lines 28281--28286
[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 28875--28875
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1608]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 28876--28876
 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1609] [1610]
Underfull \hbox (badness 1178) in paragraph at lines 29008--29010
[]\T1/ptm/m/n/10 In \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2 and ear-lier the re-
sults were \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 for fits with \T1/pcr/m/n/10 na.act
ion \T1/ptm/m/n/10 meth-ods such as
[1611] [1612]
Underfull \hbox (badness 10000) in paragraph at lines 29161--29165
[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect

Underfull \hbox (badness 1596) in paragraph at lines 29161--29165
\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at

Overfull \hbox (30.78088pt too wide) in paragraph at lines 29172--29172
 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 29173--29173
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1613] [1614]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 29299--29299
 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 29308--29308
 []\T1/pcr/m/n/9 ## where as  \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 '  \T1/pcr/m/n/9 simply first enlarges the search interval:[] 
[1615] [1616] [1617] [1618]
Underfull \hbox (badness 1337) in paragraph at lines 29524--29528
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626]
Underfull \hbox (badness 1337) in paragraph at lines 30008--30012
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1627]
Underfull \hbox (badness 5161) in paragraph at lines 30101--30103
[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1628] [1629] [1630] [1631] [1632]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30426--30426
 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 30427--30427
 []      \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F
ALSE)[] 

Underfull \hbox (badness 6775) in paragraph at lines 30465--30470
[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1633] [1634]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30531--30531
 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1635]) (./stats4-pkg.tex [1636]
Chapter 11.
[1637] [1638] [1639]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192
 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1640] [1641] [1642]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1643]
Underfull \hbox (badness 10000) in paragraph at lines 440--443
[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1644] [1645]) (./tcltk-pkg.tex [1646]
Chapter 12.
[1647] [1648] [1649] [1650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 342--342
 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1651] [1652] [1653]
Underfull \vbox (badness 10000) has occurred while \output is active [1654]
Underfull \hbox (badness 1292) in paragraph at lines 649--656
[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665]
Underfull \hbox (badness 1490) in paragraph at lines 1390--1393
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1666]) (./tools-pkg.tex
Chapter 13.
[1667]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69
 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1668]
Underfull \hbox (badness 10000) in paragraph at lines 138--140
[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
 which will be eval-u-ated via

Underfull \hbox (badness 1253) in paragraph at lines 164--167
[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1669]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215
 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1670]
Underfull \hbox (badness 5147) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12

Underfull \hbox (badness 4792) in paragraph at lines 285--298
\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-

Underfull \hbox (badness 2237) in paragraph at lines 285--298
\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1671]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370
 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 

Underfull \hbox (badness 2460) in paragraph at lines 389--391
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1672] [1673] [1674]
Underfull \hbox (badness 10000) in paragraph at lines 538--539
[][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer / 
en / opentype / glyphlist .
[1675] [1676] [1677] [1678] [1679] [1680]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 900--900
 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
[1681]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 948--948
 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1682]
Underfull \hbox (badness 1635) in paragraph at lines 1048--1050
[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1683]
Underfull \hbox (badness 5431) in paragraph at lines 1114--1117
[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to

Underfull \hbox (badness 1112) in paragraph at lines 1117--1125
\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:

Underfull \hbox (badness 3724) in paragraph at lines 1117--1125
\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1684]
Underfull \hbox (badness 1014) in paragraph at lines 1137--1139
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 10000) in paragraph at lines 1166--1169
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-

Underfull \hbox (badness 10000) in paragraph at lines 1166--1169
\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1685] [1686]
Underfull \hbox (badness 10000) in paragraph at lines 1273--1276
[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and

Underfull \hbox (badness 10000) in paragraph at lines 1294--1296
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1687] [1688] [1689]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1454--1454
 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 

Underfull \hbox (badness 7981) in paragraph at lines 1464--1468
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 1464--1468
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1690] [1691] [1692]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1666 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1693] [1694]
Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList

Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if

Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1695] [1696] [1697] [1698]
Underfull \hbox (badness 1342) in paragraph at lines 2060--2066
\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1699] [1700]
Underfull \hbox (badness 7981) in paragraph at lines 2183--2189
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 2183--2189
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1701]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2218--2218
 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
[1702] [1703] [1704] [1705] [1706] [1707] [1708]
Underfull \hbox (badness 1072) in paragraph at lines 2679--2681
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1709] [1710] [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3349--3349
 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 

Underfull \hbox (badness 10000) in paragraph at lines 3369--3371
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,

Underfull \hbox (badness 2932) in paragraph at lines 3386--3392
[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1719] [1720] [1721] [1722] [1723]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3671--3671
 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 

Underfull \hbox (badness 10000) in paragraph at lines 3682--3685
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and

Underfull \hbox (badness 6859) in paragraph at lines 3698--3703
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from

Underfull \hbox (badness 1184) in paragraph at lines 3706--3712
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he

Underfull \hbox (badness 2941) in paragraph at lines 3706--3712
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1724]
Underfull \hbox (badness 3758) in paragraph at lines 3786--3791
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-

Underfull \hbox (badness 2865) in paragraph at lines 3786--3791
\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1725] [1726]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3916--3916
 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 

Underfull \hbox (badness 1742) in paragraph at lines 3928--3940
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
[1727]
Underfull \hbox (badness 1127) in paragraph at lines 3962--3966
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from

Underfull \hbox (badness 3623) in paragraph at lines 3989--3992
[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the 
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1728] [1729] [1730]) (./utils-pkg.tex
Chapter 14.

Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1731] [1732] [1733]
Underfull \hbox (badness 1038) in paragraph at lines 197--200
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1734]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 253--253
 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1735] [1736] [1737]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 493--493
 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
[1738]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 499--499
 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 500--500
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 501--501
 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 502--502
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

Underfull \hbox (badness 10000) in paragraph at lines 536--542
[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4416) in paragraph at lines 536--542
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1739] [1740]
Underfull \hbox (badness 4505) in paragraph at lines 647--653
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1741]
Underfull \hbox (badness 1603) in paragraph at lines 764--770
\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts

Underfull \hbox (badness 3029) in paragraph at lines 764--770
\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1742]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 817--817
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1743] [1744] [1745]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1746] [1747] [1748] [1749] [1750]
Underfull \hbox (badness 1859) in paragraph at lines 1379--1388
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1751] [1752]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1506--1506
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1753] [1754]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1652--1652
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1672--1672
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL) 
[1755]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1714--1714
 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL) 
[1756] [1757]
Underfull \hbox (badness 10000) in paragraph at lines 1841--1843
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1758]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1886--1886
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 

Underfull \hbox (badness 5189) in paragraph at lines 1931--1933
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1759]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2006--2006
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1760]
Underfull \hbox (badness 1082) in paragraph at lines 2080--2084
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;

[1761]
Underfull \hbox (badness 1057) in paragraph at lines 2146--2153
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1762]
Underfull \hbox (badness 10000) in paragraph at lines 2158--2160
[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1763] [1764] [1765]
Underfull \hbox (badness 10000) in paragraph at lines 2336--2338
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1766] [1767] [1768]
Underfull \hbox (badness 10000) in paragraph at lines 2568--2571
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing

Overfull \hbox (55.10922pt too wide) in paragraph at lines 2572--2575
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 ,
[1769]
Underfull \hbox (badness 10000) in paragraph at lines 2621--2624
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set
[1770]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2693--2693
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1771]
Underfull \hbox (badness 2452) in paragraph at lines 2769--2772
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1772] [1773] [1774] [1775] [1776]
Underfull \hbox (badness 1077) in paragraph at lines 3116--3118
[]\T1/ptm/m/n/10 character vec-tor of ad-di-tional command-line ar-gu-ments for
 the \T1/pcr/m/n/10 "wget"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1072) in paragraph at lines 3155--3161
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the

Underfull \hbox (badness 1377) in paragraph at lines 3155--3161
\T1/pcr/m/n/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on th
e plat-form and scheme, but set-ting
[1777]
Underfull \hbox (badness 1057) in paragraph at lines 3180--3194
[]\T1/ptm/m/n/10 Proxies can be spec-i-fied via en-vi-ron-ment vari-ables. Set-
ting \T1/pcr/m/n/10 "no_proxy" \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "*" \T1/ptm/m/n
/10 stops

Underfull \hbox (badness 1742) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 fail-ing that, the all upper-case ver-sion) is con-sulted and if
 non-empty used as a proxy

Underfull \hbox (badness 1360) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 site. For FTP trans-fers, the user-name and pass-word on the pro
xy can be spec-i-fied by

Underfull \hbox (badness 1231) in paragraph at lines 3195--3201
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[1778]
Underfull \hbox (badness 4660) in paragraph at lines 3266--3269
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
[1779] [1780] [1781]
Underfull \hbox (badness 1565) in paragraph at lines 3472--3476
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of

Underfull \hbox (badness 10000) in paragraph at lines 3493--3499
[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1782]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3555--3555
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 

Overfull \hbox (2.55087pt too wide) in paragraph at lines 3583--3590
\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1783] [1784] [1785] [1786] [1787]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3896--3896
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1788]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3967 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.3967 ...mat Unordered and Ordered Lists}{format}
                                                   [1789] [1790] [1791]
[1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802]
[1803]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4871--4871
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1804]
Underfull \hbox (badness 10000) in paragraph at lines 4955--4957
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 http : / / www . r-[]p
roject . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1805]
Underfull \hbox (badness 1502) in paragraph at lines 5004--5009
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-

Underfull \hbox (badness 2103) in paragraph at lines 5004--5009
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1806] [1807]
Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,

Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1808] [1809]
Underfull \hbox (badness 3118) in paragraph at lines 5283--5285
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for

Underfull \hbox (badness 2409) in paragraph at lines 5316--5320
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1810] [1811]
Underfull \hbox (badness 1348) in paragraph at lines 5434--5439
[]\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages 
which these pack-

Underfull \hbox (badness 3884) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively)
. Not

Underfull \hbox (badness 1776) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 used if \T1/pcr/m/n/10 repos = NULL\T1/ptm/m/n/10 . Can also be 
a char-ac-ter vec-tor, a sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 5434--5439
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 . 

Overfull \hbox (48.30977pt too wide) in paragraph at lines 5447--5454
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")

Underfull \hbox (badness 10000) in paragraph at lines 5460--5464
[]\T1/ptm/m/n/10 Possible val-ues are (cur-rently) \T1/pcr/m/n/10 "source"\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2073) in paragraph at lines 5460--5464
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the bi-nary types
[1812]
Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed

Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1813]
Underfull \hbox (badness 1314) in paragraph at lines 5628--5635
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1814]
Underfull \hbox (badness 10000) in paragraph at lines 5649--5654
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 5670--5670
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 

Underfull \hbox (badness 5133) in paragraph at lines 5706--5710
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's

Underfull \hbox (badness 1983) in paragraph at lines 5718--5721
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1815]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5765--5765
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1816]
Underfull \hbox (badness 4132) in paragraph at lines 5796--5798
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1817] [1818]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5954--5954
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1819] [1820] [1821]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6097--6097
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1822] [1823] [1824]
Underfull \hbox (badness 10000) in paragraph at lines 6270--6272
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
[1825] [1826] [1827] [1828]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6537--6537
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1829] [1830] [1831] [1832]
Underfull \hbox (badness 10000) in paragraph at lines 6810--6812
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like

Underfull \hbox (badness 1259) in paragraph at lines 6815--6820
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
[1833] [1834]
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by

Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1835] [1836]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7088--7088
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 7089--7089
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1837] [1838] [1839] [1840]
Underfull \hbox (badness 1789) in paragraph at lines 7353--7355
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1841]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1842]
Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1843] [1844]
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1845] [1846] [1847] [1848]
Underfull \hbox (badness 5203) in paragraph at lines 7914--7917
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[1849] [1850] [1851]
Underfull \hbox (badness 1776) in paragraph at lines 8136--8143
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set

Overfull \hbox (30.78088pt too wide) in paragraph at lines 8160--8160
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1852] [1853]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8316--8316
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1854] [1855] [1856]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8491--8491
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
[1857]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8577--8577
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 8580--8580
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 8585--8585
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1858]
Underfull \hbox (badness 1077) in paragraph at lines 8656--8659
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[1859] [1860] [1861] [1862] [1863] [1864]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1865] [1866]
Underfull \hbox (badness 10000) in paragraph at lines 9181--9183
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1867] [1868]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9317
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1869] [1870]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9454--9454
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1871] [1872] [1873] [1874]
Underfull \hbox (badness 6725) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,

Underfull \hbox (badness 6428) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-

Underfull \hbox (badness 10000) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,

Underfull \hbox (badness 1997) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1875] [1876]
Underfull \hbox (badness 10000) in paragraph at lines 9820--9822
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/pt
m/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / www . gnu . org / software /
[1877] [1878] [1879]
Underfull \hbox (badness 10000) in paragraph at lines 9998--10002
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 10029--10035
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1880]
Underfull \hbox (badness 2012) in paragraph at lines 10124--10130
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use

Underfull \hbox (badness 2096) in paragraph at lines 10137--10139
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 2698) in paragraph at lines 10140--10142
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1527) in paragraph at lines 10147--10150
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1067) in paragraph at lines 10151--10154
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
[1881]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10205--10205
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 

Underfull \hbox (badness 10000) in paragraph at lines 10212--10214
[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,

Underfull \hbox (badness 1009) in paragraph at lines 10217--10228
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[1882] [1883]
Underfull \hbox (badness 2846) in paragraph at lines 10304--10314
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1884] [1885]
Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. For re-cent v
er-

Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
\T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form

Underfull \hbox (badness 10000) in paragraph at lines 10451--10454
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1886]
Underfull \hbox (badness 10000) in paragraph at lines 10504--10508
\T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son
al copy in

Underfull \hbox (badness 2158) in paragraph at lines 10524--10527
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[1887] [1888]
Underfull \hbox (badness 3333) in paragraph at lines 10704--10706
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[1889] [1890] [1891]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10865--10865
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 

Underfull \hbox (badness 5970) in paragraph at lines 10893--10896
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive

Underfull \hbox (badness 2600) in paragraph at lines 10893--10896
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less

Underfull \hbox (badness 2401) in paragraph at lines 10904--10913
[]\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/pcr/m/n/10 width \T1/ptm/m/n/1
0 ar-gu-ment's spec-i-fi-ca-tion should be fol-

Underfull \hbox (badness 2735) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 to the \T1/pcr/m/n/10 strict.width \T1/ptm/m/n/10 com-po-nent of
 op-tion \T1/pcr/m/n/10 "str" \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][
][]\T1/ptm/m/n/10 )

Underfull \hbox (badness 1859) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 which de-faults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back c
om-pat-i-bil-ity rea-sons; \T1/pcr/m/n/10 "wrap" \T1/ptm/m/n/10 uses

Underfull \hbox (badness 10000) in paragraph at lines 10904--10913
[][]\T1/pcr/m/n/10 strwrap[][][](*, width = width) \T1/ptm/m/n/10 whereas \T1/p
cr/m/n/10 "cut" \T1/ptm/m/n/10 cuts di-rectly to

Underfull \hbox (badness 1661) in paragraph at lines 10904--10913
\T1/pcr/m/n/10 width\T1/ptm/m/n/10 . Note that a small \T1/pcr/m/n/10 vec.lengt
h \T1/ptm/m/n/10 may be bet-ter than set-ting
[1892]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10948--10948
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[1893] [1894]
Underfull \hbox (badness 10000) in paragraph at lines 11072--11074
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[1895] [1896]
Underfull \hbox (badness 4492) in paragraph at lines 11226--11233
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in

Underfull \hbox (badness 6252) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file

Underfull \hbox (badness 2452) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[1897] [1898] [1899]
Underfull \hbox (badness 2020) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),

Underfull \hbox (badness 1194) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1900]
Underfull \hbox (badness 10000) in paragraph at lines 11469--11472
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ fo
rmat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .

Underfull \hbox (badness 10000) in paragraph at lines 11469--11472
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1901] [1902] [1903] [1904] [1905] [1906] [1907]
Underfull \hbox (badness 4660) in paragraph at lines 11974--11977
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to

Overfull \hbox (36.87935pt too wide) in paragraph at lines 11987--11991
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .

Underfull \hbox (badness 3557) in paragraph at lines 11993--11995
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to

Underfull \hbox (badness 1052) in paragraph at lines 11996--11998
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[1908]
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see

Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to

Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 12047--12052
[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with

Underfull \hbox (badness 10000) in paragraph at lines 12055--12058
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[1909] [1910] [1911] [1912] [1913]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12331--12331
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 

Underfull \hbox (badness 1454) in paragraph at lines 12358--12362
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[1914]
Underfull \hbox (badness 1715) in paragraph at lines 12383--12386
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 12428--12430
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion

Underfull \hbox (badness 3271) in paragraph at lines 12440--12444
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if

[1915] [1916] [1917]) [1918] [1919] [1920] (./KernSmooth-pkg.tex
Chapter 15.
[1921]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[1922] [1923] [1924] [1925] [1926]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[1927] [1928] [1929] [1930]) (./MASS-pkg.tex
Chapter 16.
[1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952]
[1953]
Underfull \hbox (badness 7256) in paragraph at lines 1601--1603
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962] [1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2409--2409
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2413--2413
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[1965] [1966] [1967] [1968]
Underfull \hbox (badness 6559) in paragraph at lines 2691--2694
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[1969] [1970] [1971]
Underfull \hbox (badness 7362) in paragraph at lines 2861--2866
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3557) in paragraph at lines 2897--2905
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if

Underfull \hbox (badness 3118) in paragraph at lines 2897--2905
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[1972] [1973]
Underfull \hbox (badness 4686) in paragraph at lines 3029--3031
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds

Underfull \hbox (badness 1515) in paragraph at lines 3043--3047
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[1974] [1975] [1976]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3224--3224
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 

Underfull \hbox (badness 5817) in paragraph at lines 3231--3233
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[1977]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3354--3354
 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988]
[1989]
Underfull \hbox (badness 1845) in paragraph at lines 4160--4162
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[1990] [1991] [1992] [1993] [1994] [1995] [1996]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4656--4656
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[1997] [1998]
Underfull \hbox (badness 10000) in paragraph at lines 4808--4811
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[1999]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4878--4878
 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 

Underfull \hbox (badness 10000) in paragraph at lines 4886--4889
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2000] [2001] [2002] [2003] [2004]
Underfull \hbox (badness 5681) in paragraph at lines 5286--5288
[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if

Underfull \hbox (badness 5022) in paragraph at lines 5290--5293
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2005]
Underfull \hbox (badness 1975) in paragraph at lines 5339--5341
[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5925--5925
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2014]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5987--5987
 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2015] [2016]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6129 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6129 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2017]
Underfull \hbox (badness 1783) in paragraph at lines 6247--6251
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2018] [2019] [2020] [2021]
Underfull \vbox (badness 10000) has occurred while \output is active [2022]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6545--6545
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2023]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6633--6633
 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2024] [2025] [2026] [2027] [2028] [2029]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7072--7072
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 7089--7089
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 

Underfull \hbox (badness 10000) in paragraph at lines 7096--7103
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2030]
Underfull \hbox (badness 10000) in paragraph at lines 7112--7114
[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat

Underfull \hbox (badness 3138) in paragraph at lines 7167--7173
[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2031]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7237--7237
 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2032] [2033]
Underfull \hbox (badness 5091) in paragraph at lines 7346--7349
\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2034] [2035]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7476--7476
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2036]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7541--7541
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2037] [2038] [2039] [2040] [2041] [2042]
Underfull \hbox (badness 4686) in paragraph at lines 7979--7981
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds

Underfull \hbox (badness 1515) in paragraph at lines 7995--7999
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2043] [2044]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8098--8098
 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 

Underfull \hbox (badness 1590) in paragraph at lines 8122--8126
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055]
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9501--9501
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2065]
Underfull \hbox (badness 1158) in paragraph at lines 9628--9631
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2066]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9710--9710
 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 9712--9712
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 9715--9715
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077]
[2078] [2079]) (./Matrix-pkg.tex [2080]
Chapter 17.

Underfull \hbox (badness 10000) in paragraph at lines 42--45
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you

Underfull \hbox (badness 10000) in paragraph at lines 42--45
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2081]
Underfull \hbox (badness 1769) in paragraph at lines 96--99
[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2082]
Underfull \hbox (badness 2229) in paragraph at lines 160--163
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is

Underfull \hbox (badness 1147) in paragraph at lines 160--163
\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2083]
Underfull \hbox (badness 10000) in paragraph at lines 258--261
[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing

Underfull \hbox (badness 10000) in paragraph at lines 264--266
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2084] [2085]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 487--487
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 

Underfull \hbox (badness 5147) in paragraph at lines 494--496
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2086]
Underfull \hbox (badness 5119) in paragraph at lines 506--510
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class

Underfull \hbox (badness 4621) in paragraph at lines 510--514
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a

Overfull \hbox (4.38043pt too wide) in paragraph at lines 533--533
 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535
 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 544--544
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2087] [2088]
Underfull \hbox (badness 3189) in paragraph at lines 681--685
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2089]
Underfull \hbox (badness 10000) in paragraph at lines 735--738
[]\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (where
as
[2090] [2091]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 873--873
 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2092]
Underfull \hbox (badness 10000) in paragraph at lines 948--950
[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-

Underfull \hbox (badness 10000) in paragraph at lines 971--976
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-

Underfull \hbox (badness 10000) in paragraph at lines 971--976
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to

Underfull \hbox (badness 1092) in paragraph at lines 971--976
\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of

Underfull \hbox (badness 10000) in paragraph at lines 994--1001
[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2093]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2094pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate i
gnored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate i
gnored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        ] [2095]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1192--1192
 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2096]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1286--1286
 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
[2097]
Underfull \hbox (badness 2277) in paragraph at lines 1314--1317
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use

Underfull \hbox (badness 1609) in paragraph at lines 1361--1365
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2098]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1388--1388
 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1402--1402
 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 

Overfull \hbox (74.58035pt too wide) in paragraph at lines 1410--1410
 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1420--1420
 []\T1/pcr/m/n/9 ## each has a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' 
\T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n
/9 matrix %% FIXME !! --- "check" them  __unfinished__[] 
[2099]
Underfull \hbox (badness 6445) in paragraph at lines 1457--1464
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",    ...) \T1/ptm/m/n/10 or

Underfull \hbox (badness 3861) in paragraph at lines 1457--1464
\T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls
 of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or

Underfull \hbox (badness 1783) in paragraph at lines 1492--1496
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend

Underfull \hbox (badness 1221) in paragraph at lines 1508--1514
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2100]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1549 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1549 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1550 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1571 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1582 \aliasA{rowSums}{colSums}{rowSums}
                                          [2101] [2102]
Underfull \hbox (badness 3547) in paragraph at lines 1757--1760
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2103] [2104] [2105] [2106]
Underfull \hbox (badness 10000) in paragraph at lines 1994--1996
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2107]
Underfull \hbox (badness 10000) in paragraph at lines 2116--2118
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =

Underfull \hbox (badness 3068) in paragraph at lines 2177--2181
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2108]
Underfull \hbox (badness 4713) in paragraph at lines 2212--2214
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2109]
Underfull \hbox (badness 10000) in paragraph at lines 2327--2330
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 2429--2433
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix",    ...)\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2429--2433
\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or

Underfull \hbox (badness 2707) in paragraph at lines 2486--2490
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
[2112]
Underfull \hbox (badness 2689) in paragraph at lines 2546--2548
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
[2113]
Underfull \hbox (badness 1097) in paragraph at lines 2572--2575
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
[2114]
Underfull \hbox (badness 3646) in paragraph at lines 2818--2821
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally

Underfull \hbox (badness 10000) in paragraph at lines 2840--2841
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :

Underfull \hbox (badness 1810) in paragraph at lines 2847--2849
[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of

Underfull \hbox (badness 10000) in paragraph at lines 2850--2852
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2115]
Underfull \hbox (badness 1371) in paragraph at lines 2857--2863
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class

Underfull \hbox (badness 10000) in paragraph at lines 2864--2868
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class

Underfull \hbox (badness 2318) in paragraph at lines 2874--2878
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2116] [2117]
Underfull \hbox (badness 1859) in paragraph at lines 3054--3056
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains

Underfull \hbox (badness 10000) in paragraph at lines 3099--3101
[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2118]
Underfull \hbox (badness 1168) in paragraph at lines 3214--3217
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2119] [2120]
Underfull \hbox (badness 4967) in paragraph at lines 3376--3380
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",    ...) \T1/ptm/m/n/10 or

Overfull \hbox (2.39853pt too wide) in paragraph at lines 3381--3383
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
[2121]
Underfull \hbox (badness 6364) in paragraph at lines 3423--3426
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2122] [2123]
Underfull \hbox (badness 10000) in paragraph at lines 3573--3578
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by

Underfull \hbox (badness 6961) in paragraph at lines 3573--3578
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class

Underfull \hbox (badness 10000) in paragraph at lines 3583--3585
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial

Underfull \hbox (badness 10000) in paragraph at lines 3585--3588
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2124]
Underfull \hbox (badness 10000) in paragraph at lines 3693--3696
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or

Underfull \hbox (badness 1735) in paragraph at lines 3693--3696
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the

Underfull \hbox (badness 10000) in paragraph at lines 3696--3699
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or

Underfull \hbox (badness 2318) in paragraph at lines 3696--3699
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2125]
Underfull \hbox (badness 6364) in paragraph at lines 3700--3703
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2126]
Underfull \hbox (badness 4060) in paragraph at lines 3817--3820
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2127]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3857--3857
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 

Underfull \hbox (badness 3635) in paragraph at lines 3923--3927
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class

Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-

Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
[2128]
Underfull \hbox (badness 10000) in paragraph at lines 3937--3941
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2129] [2130] [2131] [2132]
Underfull \hbox (badness 10000) in paragraph at lines 4225--4230
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2133] [2134]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4359--4359
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

Overfull \hbox (139.38028pt too wide) in paragraph at lines 4362--4362
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
[2135] [2136] [2137] [2138]
Underfull \hbox (badness 10000) in paragraph at lines 4670--4675
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2139]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4751--4751
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4753--4753
 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4757--4757
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 4764--4764
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2140] [2141]
Underfull \hbox (badness 4120) in paragraph at lines 4892--4895
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4921--4921
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
[2142]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4926--4926
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 4933--4933
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 4936--4936
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2143]
Underfull \hbox (badness 1817) in paragraph at lines 5024--5033
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the

Underfull \hbox (badness 5637) in paragraph at lines 5065--5067
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2144]
Underfull \hbox (badness 3138) in paragraph at lines 5091--5093
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2145]
Underfull \hbox (badness 1603) in paragraph at lines 5175--5177
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2146] [2147] [2148]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5411--5411
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
[2149]
Underfull \hbox (badness 10000) in paragraph at lines 5487--5490
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and

Overfull \hbox (9.78043pt too wide) in paragraph at lines 5498--5498
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2150]
Underfull \hbox (badness 1622) in paragraph at lines 5535--5540
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),

Underfull \hbox (badness 1418) in paragraph at lines 5535--5540
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2151] [2152]
Underfull \hbox (badness 1062) in paragraph at lines 5720--5723
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2153]
Underfull \hbox (badness 2809) in paragraph at lines 5749--5752
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2154]
Underfull \hbox (badness 2635) in paragraph at lines 5861--5866
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .

Underfull \hbox (badness 4229) in paragraph at lines 5861--5866
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class

Underfull \hbox (badness 10000) in paragraph at lines 5869--5872
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2155]
Underfull \hbox (badness 1184) in paragraph at lines 6042--6045
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2156] [2157]
Underfull \hbox (badness 10000) in paragraph at lines 6140--6143
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2158]
Underfull \hbox (badness 10000) in paragraph at lines 6215--6218
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 6231--6231
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 

Underfull \hbox (badness 2443) in paragraph at lines 6269--6275
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see

Underfull \hbox (badness 1776) in paragraph at lines 6269--6275
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
[2159]
Underfull \hbox (badness 1675) in paragraph at lines 6286--6289
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2160] [2161]
Underfull \hbox (badness 6268) in paragraph at lines 6480--6483
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2162]
Underfull \hbox (badness 5036) in paragraph at lines 6504--6508
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,

Underfull \hbox (badness 10000) in paragraph at lines 6504--6508
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2163]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6596 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 1348) in paragraph at lines 6670--6673
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing

Underfull \hbox (badness 10000) in paragraph at lines 6675--6678
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is

Underfull \hbox (badness 10000) in paragraph at lines 6675--6678
\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when

Underfull \hbox (badness 10000) in paragraph at lines 6692--6695

[2164] [2165]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn..Rpcent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6761 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.6851 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.6933 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
Underfull \hbox (badness 1881) in paragraph at lines 7015--7021
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn

Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-

Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see

Underfull \hbox (badness 5637) in paragraph at lines 7071--7076
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2166pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7076 \item[crossprod]
                        \code{signature(x = "dgeMatrix", y = "dgeMatrix")}:pdfT
eX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rd
ash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7076 \item[crossprod]
                        \code{signature(x = "dgeMatrix", y = "dgeMatrix")}:]
Underfull \hbox (badness 10000) in paragraph at lines 7080--7082
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns

Underfull \hbox (badness 10000) in paragraph at lines 7082--7084
[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns

Underfull \hbox (badness 10000) in paragraph at lines 7086--7087
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
[2167]
Underfull \hbox (badness 1062) in paragraph at lines 7203--7206
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2168]
Underfull \hbox (badness 2809) in paragraph at lines 7237--7240
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion

Underfull \hbox (badness 10000) in paragraph at lines 7289--7291
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2169]
Underfull \hbox (badness 1406) in paragraph at lines 7329--7333
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not

Underfull \hbox (badness 1019) in paragraph at lines 7329--7333
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2170] [2171]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7427--7427
 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 

Underfull \hbox (badness 2635) in paragraph at lines 7492--7497
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .

Underfull \hbox (badness 4229) in paragraph at lines 7492--7497
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class

Underfull \hbox (badness 10000) in paragraph at lines 7500--7503
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2172] [2173]
Underfull \hbox (badness 10000) in paragraph at lines 7686--7688
[]\T1/ptm/m/n/10 fast
[2174]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2175] [2176]
Underfull \hbox (badness 1184) in paragraph at lines 7971--7974
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2177]
Underfull \hbox (badness 10000) in paragraph at lines 8061--8064
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2178]
Underfull \hbox (badness 10000) in paragraph at lines 8137--8140
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 8153--8153
 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2179] [2180]
Underfull \hbox (badness 10000) in paragraph at lines 8263--8265
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use

Underfull \hbox (badness 1596) in paragraph at lines 8279--8281
[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse

Underfull \hbox (badness 1721) in paragraph at lines 8285--8289
\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2181]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8369--8369
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 8374--8374
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
[2182]
Underfull \hbox (badness 3989) in paragraph at lines 8396--8406
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should

Underfull \hbox (badness 10000) in paragraph at lines 8396--8406
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2183]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8488 \aliasA{qr}{qr-methods}{qr}
                                   [2184]
Underfull \hbox (badness 5119) in paragraph at lines 8530--8533
[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with

Overfull \hbox (36.7804pt too wide) in paragraph at lines 8550--8550
 []                  \T1/pcr/m/n/9 c1=rep(c(1,0,0), 2), c2=rep(c(0,1,0), 2), c3
=rep(c(0,0,1),2)),[] 
[2185]
Underfull \hbox (badness 10000) in paragraph at lines 8599--8605
[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of

Underfull \hbox (badness 10000) in paragraph at lines 8616--8619
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2186]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 8687--8687
 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8708--8708
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                #  wa
rning +  ~1.5 sec[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8709--8709
 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8723 ... the Reciprocal Condition Number}{rcond}
                                                   [2187] [2188]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8836--8836
 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2189] [2190] [2191]
Underfull \hbox (badness 2126) in paragraph at lines 9014--9019
[]\T1/ptm/m/n/10 the ran-dom num-ber gen-er-a-tor for the \T1/pcr/m/n/10 x \T1/
ptm/m/n/10 slot, a [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 such that

Underfull \hbox (badness 10000) in paragraph at lines 9019--9021
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
[2192] [2193]
Underfull \hbox (badness 1558) in paragraph at lines 9164--9167
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2194]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9226--9226
 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 9230--9230
 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9292 \aliasA{solve}{solve-methods}{solve}
                                           
Overfull \hbox (54.78088pt too wide) in paragraph at lines 9389--9389
 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 

Overfull \hbox (60.78088pt too wide) in paragraph at lines 9394--9394
 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2196]
Underfull \hbox (badness 6047) in paragraph at lines 9429--9441
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods

Underfull \hbox (badness 10000) in paragraph at lines 9446--9449
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via

Underfull \hbox (badness 7203) in paragraph at lines 9451--9452
[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar

Underfull \hbox (badness 7851) in paragraph at lines 9455--9462
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list

Underfull \hbox (badness 10000) in paragraph at lines 9455--9462
\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse

Underfull \hbox (badness 10000) in paragraph at lines 9468--9478
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list

Underfull \hbox (badness 2165) in paragraph at lines 9468--9478
\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-

Underfull \hbox (badness 1194) in paragraph at lines 9502--9504
[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2197]
Underfull \hbox (badness 10000) in paragraph at lines 9516--9519
[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing

Underfull \hbox (badness 10000) in paragraph at lines 9525--9526
[]\T1/ptm/m/n/10 works via

Underfull \hbox (badness 10000) in paragraph at lines 9531--9533
[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use

Underfull \hbox (badness 10000) in paragraph at lines 9535--9536
[]\T1/ptm/m/n/10 all work via

Underfull \hbox (badness 10000) in paragraph at lines 9543--9546
[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9561--9561
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 9565--9565
 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2198]
Underfull \hbox (badness 10000) in paragraph at lines 9586--9589
[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame

Underfull \hbox (badness 1648) in paragraph at lines 9614--9616
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,

Underfull \hbox (badness 10000) in paragraph at lines 9622--9625
[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)

Underfull \hbox (badness 2591) in paragraph at lines 9622--9625
\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the

Underfull \hbox (badness 10000) in paragraph at lines 9633--9637
[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for


Underfull \hbox (badness 2828) in paragraph at lines 9633--9637
\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2199]
Underfull \hbox (badness 6592) in paragraph at lines 9644--9646
[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2200]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9721--9721
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9722--9722
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9723--9723
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2201]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9804--9804
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2202]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 9900--9900
 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2203]
Underfull \hbox (badness 4621) in paragraph at lines 9937--9941
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2204]
Underfull \hbox (badness 10000) in paragraph at lines 10008--10011
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10025--10025
 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 10028--10028
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 10051--10051
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 10052--10052
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2205]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10096--10096
 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10101--10101
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2206]
Underfull \hbox (badness 10000) in paragraph at lines 10193--10201
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class

Underfull \hbox (badness 1325) in paragraph at lines 10214--10218
[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a

Underfull \hbox (badness 10000) in paragraph at lines 10244--10248
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or
[2207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10284 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2208]
Underfull \hbox (badness 1430) in paragraph at lines 10394--10396
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2209]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10420--10420
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2210]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.toe
plitz}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10559 ...toeplitz}{sparseVector-class}{toeplitz}
                                                  
Underfull \hbox (badness 2970) in paragraph at lines 10571--10577
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-

Underfull \hbox (badness 3679) in paragraph at lines 10571--10577
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 10622--10625
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2211]
Underfull \hbox (badness 10000) in paragraph at lines 10644--10647
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list

Underfull \hbox (badness 10000) in paragraph at lines 10660--10665
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or

Underfull \hbox (badness 10000) in paragraph at lines 10671--10673
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2212] [2213]
Underfull \hbox (badness 3525) in paragraph at lines 10767--10771
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
[2214]
Underfull \hbox (badness 2591) in paragraph at lines 10868--10873
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2215]
Underfull \hbox (badness 2057) in paragraph at lines 10930--10932
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2216]
Underfull \hbox (badness 6641) in paragraph at lines 10999--11002
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h

Underfull \hbox (badness 5133) in paragraph at lines 11036--11040
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in

Underfull \hbox (badness 2818) in paragraph at lines 11036--11040
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2217] [2218] [2219]
Underfull \hbox (badness 7362) in paragraph at lines 11245--11247
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
[2220]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 11283--11283
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 11284--11284
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2221] [2222]
Underfull \hbox (badness 6910) in paragraph at lines 11533--11535
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2223] [2224]) (./boot-pkg.tex
Chapter 18.
[2225] [2226] [2227] [2228] [2229] [2230] [2231]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2232]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble

Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-

Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2233]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2234]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2235]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.

Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2236]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2237]
[2238]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-

Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2239]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the

Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it

Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to

Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2240] [2241] [2242] [2243] [2244]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2245] [2246] [2247] [2248]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2249] [2250] [2251] [2252]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2253]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2254] [2255] [2256] [2257]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set

Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
[2258]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.

Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2259]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple

Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2260] [2261] [2262] [2263] [2264]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2265] [2266] [2267]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2268]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2269] [2270] [2271]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2272] [2273] [2274] [2275] [2276] [2277] [2278]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2279] [2280]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2281] [2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2284]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f

Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to

Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] [2295]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2296] [2297] [2298] [2299]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap

Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2300]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2309]
Underfull \hbox (badness 1127) in paragraph at lines 5983--6001
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2310]
Underfull \hbox (badness 2837) in paragraph at lines 6016--6019
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2311] [2312] [2313] [2314]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6301--6301
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2315] [2316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6490--6490
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 6492--6492
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2317] [2318] [2319]
Underfull \hbox (badness 1596) in paragraph at lines 6737--6741
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2320] [2321]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6897--6897
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2322] [2323] [2324] [2325] [2326] [2327] [2328] [2329]) (./class-pkg.tex
[2330]
Chapter 19.
[2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346]) (./cluster-pkg.tex
Chapter 20.
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 133--140
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible"

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 par-tic-u-larly for the case when \T1/pcr/m/n/10 par.method \T1/
ptm/m/n/10 is spec-i-fied of longer length

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 than one. The \T1/ptm/m/it/10 weighted av-er-age \T1/ptm/m/n/10 
(\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n/10 . Fur-ther, \T
1/pcr/m/n/10 method= "single" \T1/ptm/m/n/10 is

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c
(.5,.5,0,-.5)\T1/ptm/m/n/10 , and

Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 165--167
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2349]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 250--250
 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 

Overfull \hbox (63.78036pt too wide) in paragraph at lines 251--251
 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 

Overfull \hbox (63.78036pt too wide) in paragraph at lines 252--252
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2350] [2351]
Underfull \vbox (badness 7685) has occurred while \output is active [2352]
[2353]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 516--516
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 520--520
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2354]
Underfull \hbox (badness 5374) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2355] [2356]
Underfull \hbox (badness 3078) in paragraph at lines 680--683
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2357]
Underfull \hbox (badness 2941) in paragraph at lines 761--764
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
[2358]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 799--799
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see

Overfull \hbox (12.78088pt too wide) in paragraph at lines 893--893
 []\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, verbose = interactive(
), ...) 
[2360]
Underfull \hbox (badness 4872) in paragraph at lines 934--936
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
[2361]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1036--1036
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2362] [2363]
Underfull \hbox (badness 4144) in paragraph at lines 1112--1116
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2364]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1188--1188
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 1194--1194
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2365] [2366]
Underfull \hbox (badness 10000) in paragraph at lines 1394--1398
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
[2367]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1412--1412
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 1421--1421
 []         \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
 green", labels=3)[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1429--1429
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2368]
Underfull \hbox (badness 5741) in paragraph at lines 1469--1472
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2369] [2370]
Underfull \hbox (badness 5008) in paragraph at lines 1645--1653
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1736--1736
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 1755--1755
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2372] [2373] [2374] [2375] [2376]
Underfull \hbox (badness 10000) in paragraph at lines 2057--2059
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as

Underfull \hbox (badness 3179) in paragraph at lines 2081--2087
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2377] [2378]
Underfull \hbox (badness 10000) in paragraph at lines 2239--2242
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2379]
Underfull \hbox (badness 1292) in paragraph at lines 2307--2310
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2380]
Underfull \hbox (badness 6675) in paragraph at lines 2316--2318
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see

Underfull \hbox (badness 10000) in paragraph at lines 2339--2342
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,

Overfull \vbox (12.60576pt too high) has occurred while \output is active
[2381] [2382] [2383]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2546--2546
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2384] [2385] [2386]
Underfull \hbox (badness 1067) in paragraph at lines 2734--2739
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2387] [2388]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2889--2889
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2389] [2390] [2391]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3085--3085
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3086--3086
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 3153--3156
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2393]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3203--3203
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3204--3204
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 3389--3392
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for

Underfull \hbox (badness 3471) in paragraph at lines 3389--3392
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2397]
Underfull \hbox (badness 10000) in paragraph at lines 3452--3457
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2398]
Underfull \hbox (badness 1735) in paragraph at lines 3521--3523
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "twins"\T1/ptm/m/n/10 , typ
-i-cally cre-ated by ei-ther [][]\T1/pcr/m/n/10 agnes[][][]() \T1/ptm/m/n/10 or


Underfull \hbox (badness 4621) in paragraph at lines 3538--3543
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1990) in paragraph at lines 3538--3543
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider

Underfull \hbox (badness 6268) in paragraph at lines 3550--3553
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2399]
Underfull \hbox (badness 10000) in paragraph at lines 3614--3615
[]\T1/ptm/m/n/10 currently [][]$\T1/pcr/m/n/10 http : / / www . agoras . ua . a
c . be / datasets / clusplot-[]examples . tar .
[2400] [2401]
Underfull \hbox (badness 10000) in paragraph at lines 3733--3736
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2402]
Underfull \hbox (badness 10000) in paragraph at lines 3764--3767
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2403]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3817--3817
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 

Underfull \hbox (badness 2035) in paragraph at lines 3828--3830
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2404] [2405] [2406]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4021--4021
 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 4023--4023
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2407]
Underfull \hbox (badness 1946) in paragraph at lines 4052--4057
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col

Underfull \hbox (badness 1062) in paragraph at lines 4107--4109
[]\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means
 \T1/ptm/m/n/10 of sil-hou-ette widths where
[2408]
Underfull \hbox (badness 10000) in paragraph at lines 4118--4126
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by

Overfull \hbox (31.3804pt too wide) in paragraph at lines 4160--4160
 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4169--4169
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4171--4171
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 4174--4174
 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4176--4176
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
[2409]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4190--4190
 []   \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[] 
[2410] [2411] [2412] [2413] [2414] [2415] [2416]) (./codetools-pkg.tex
Chapter 21.

Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2417]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2418]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2419] [2420] [2421]) (./foreign-pkg.tex [2422]
Chapter 22.
[2423]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a

Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2424] [2425]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2426]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 293--293
 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2427] [2428] [2429]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[] 
[2430]
Underfull \hbox (badness 10000) in paragraph at lines 515--523
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2431]
Underfull \hbox (badness 7613) in paragraph at lines 533--539
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2432] [2433] [2434]
Underfull \hbox (badness 10000) in paragraph at lines 730--731


Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2435]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 816--816
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2436]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 879--879
 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 

Underfull \hbox (badness 6708) in paragraph at lines 905--908
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2437] [2438]
Underfull \hbox (badness 10000) in paragraph at lines 989--990
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .

Overfull \hbox (24.78088pt too wide) in paragraph at lines 1025--1025
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2439]
Underfull \hbox (badness 1286) in paragraph at lines 1110--1114
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2440]
Underfull \hbox (badness 10000) in paragraph at lines 1183--1189
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2441] [2442]) (./lattice-pkg.tex
Chapter 23.
[2443] [2444] [2445]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 287--287
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 291--291
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2446]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 299--299
 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 

Overfull \hbox (54.78088pt too wide) in paragraph at lines 306--306
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 

Overfull \hbox (66.78088pt too wide) in paragraph at lines 314--314
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 335--335
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 339--339
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2447]
Underfull \hbox (badness 4060) in paragraph at lines 358--370
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the

Underfull \hbox (badness 10000) in paragraph at lines 358--370
\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |

Underfull \hbox (badness 1028) in paragraph at lines 398--413
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both

Underfull \hbox (badness 10000) in paragraph at lines 414--416
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2448]
Underfull \hbox (badness 7631) in paragraph at lines 480--485
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2449] [2450]
Underfull \hbox (badness 1221) in paragraph at lines 651--659
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2451] [2452] [2453] [2454]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be

Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2455]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2456] [2457]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a

Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2458] [2459] [2460]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2461]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2462]
Underfull \vbox (badness 10000) has occurred while \output is active [2463]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 

Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2464]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to

Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
[2465]
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2466] [2467] [2468]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 

Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form

Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2469]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of

Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2470] [2471] [2472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 

Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2473] [2474] [2475]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2476] [2477]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2478]
Underfull \hbox (badness 10000) in paragraph at lines 2763--2768
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2479]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.

Underfull \hbox (badness 3058) in paragraph at lines 2793--2798
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as

Underfull \hbox (badness 6758) in paragraph at lines 2879--2883
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be


Underfull \hbox (badness 7576) in paragraph at lines 2879--2883
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also

Underfull \hbox (badness 10000) in paragraph at lines 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2480]
Underfull \hbox (badness 1609) in paragraph at lines 2937--2943
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,

Underfull \hbox (badness 2772) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-

Underfull \hbox (badness 1400) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from

Underfull \hbox (badness 2486) in paragraph at lines 2961--2965
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2481] [2482]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 3063--3063
 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 3064--3064
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 3075--3075
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 

Overfull \hbox (66.78088pt too wide) in paragraph at lines 3087--3087
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2483]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x

Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.

Underfull \hbox (badness 3058) in paragraph at lines 3145--3152
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2484] [2485] [2486] [2487]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3475--3475
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2488]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3498--3498
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2489] [2490] [2491] [2492] [2493]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2494]
Underfull \hbox (badness 10000) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .

Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2495] [2496]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4054--4054
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 

Underfull \hbox (badness 1173) in paragraph at lines 4063--4067
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in

Underfull \hbox (badness 3219) in paragraph at lines 4090--4092
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when

Underfull \hbox (badness 1728) in paragraph at lines 4107--4111
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2497]
Underfull \hbox (badness 5161) in paragraph at lines 4172--4176
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,

Underfull \hbox (badness 4913) in paragraph at lines 4172--4176
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2498] [2499]
Underfull \hbox (badness 1067) in paragraph at lines 4286--4296
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1735) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points

Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and

Underfull \hbox (badness 5231) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for

Underfull \hbox (badness 1701) in paragraph at lines 4311--4314
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4314--4316
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2500] [2501] [2502] [2503] [2504] [2505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4718--4718
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2506] [2507]
Underfull \hbox (badness 10000) in paragraph at lines 4905--4908
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2508] [2509]
Underfull \hbox (badness 1442) in paragraph at lines 5037--5040
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2510] [2511] [2512] [2513] [2514] [2515]
Underfull \hbox (badness 3646) in paragraph at lines 5369--5372
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or

Overfull \hbox (36.78088pt too wide) in paragraph at lines 5399--5399
 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 5400--5400
 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2516]
Underfull \hbox (badness 10000) in paragraph at lines 5488--5491
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

Underfull \hbox (badness 2103) in paragraph at lines 5488--5491
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing

Underfull \hbox (badness 6412) in paragraph at lines 5505--5511
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2517]
Underfull \hbox (badness 1635) in paragraph at lines 5514--5519
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2518]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5663--5663
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2519]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5677--5677
 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 5678--5678
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 5681--5681
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 5684--5684
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 5686--5686
 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 5695--5695
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 5696--5696
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 

Underfull \hbox (badness 10000) in paragraph at lines 5712--5714
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of

[2520]
Underfull \hbox (badness 2376) in paragraph at lines 5723--5725
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2521]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and

Underfull \hbox (badness 4205) in paragraph at lines 5859--5866
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to

Underfull \hbox (badness 4792) in paragraph at lines 5859--5866
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2524] [2525]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2526] [2527]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round

Underfull \hbox (badness 2486) in paragraph at lines 6275--6280
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2528] [2529]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6362--6362
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2530]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2531]
Underfull \hbox (badness 10000) in paragraph at lines 6551--6554
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The

Underfull \hbox (badness 1558) in paragraph at lines 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2532]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to

Underfull \hbox (badness 1571) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2533] [2534] [2535] [2536] [2537]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-

Underfull \hbox (badness 1715) in paragraph at lines 6957--6964
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
[2538]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7027--7027
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 7057--7060
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to

Underfull \hbox (badness 1584) in paragraph at lines 7057--7060
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2540]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2541] [2542]
Underfull \hbox (badness 2012) in paragraph at lines 7327--7330
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7373--7373
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2544] [2545]
Underfull \hbox (badness 2644) in paragraph at lines 7514--7518
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to

Underfull \hbox (badness 2772) in paragraph at lines 7527--7530
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to

Underfull \hbox (badness 4242) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly

Underfull \hbox (badness 1147) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-

Underfull \hbox (badness 2351) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-

Underfull \hbox (badness 1675) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the

Underfull \hbox (badness 1769) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2546]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597
 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7607--7607
 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2547]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668
 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 7673--7673
 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2548] [2549] [2550]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7854--7854
 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2551]
Underfull \hbox (badness 1436) in paragraph at lines 7909--7915
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for

Underfull \hbox (badness 1231) in paragraph at lines 7909--7915
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2552] [2553] [2554] [2555] [2556] [2557] [2558] [2559]
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se

Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2560] [2561]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8642--8642
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 8643--8643
 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 8655--8655
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2562]
Underfull \hbox (badness 3118) in paragraph at lines 8674--8677
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2563]
Underfull \hbox (badness 1515) in paragraph at lines 8750--8754
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2564]
Underfull \hbox (badness 6316) in paragraph at lines 8856--8861
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2565] [2566]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8963--8963
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9102--9102
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2569]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9161--9165
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,    right, left.name, right.name, condition

Overfull \hbox (104.63074pt too wide) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,    right.x, right.y, left.name
, right.x.name, right.y.name, condition
[2570] [2571] [2572] [2573] [2574] [2575] [2576]
Underfull \hbox (badness 4205) in paragraph at lines 9619--9623
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4518) in paragraph at lines 9619--9623
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 6300) in paragraph at lines 9624--9627
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2577] [2578] [2579]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2580] [2581] [2582] [2583])
(./mgcv-pkg.tex [2584]
Chapter 24.

Underfull \hbox (badness 1052) in paragraph at lines 40--42
[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term 
p-values. See
[2585] [2586]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 150--150
 []    \T1/pcr/m/n/10 chunk.size=10000,rho=0,AR.start=NULL,sparse=FALSE,cluster
=NULL,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 151--151
 []    \T1/pcr/m/n/10 gc.level=1,use.chol=FALSE,samfrac=1,drop.unused.levels=TR
UE,...)[] 
[2587]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

Underfull \hbox (badness 1043) in paragraph at lines 193--198
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2588]
Underfull \hbox (badness 2626) in paragraph at lines 248--251
[]\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of 
the form
[2589] [2590]
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2591] [2592] [2593]
Underfull \hbox (badness 2922) in paragraph at lines 521--522
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and

Underfull \hbox (badness 1158) in paragraph at lines 563--565
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2594] [2595]
Underfull \vbox (badness 10000) has occurred while \output is active [2596]
[2597] [2598] [2599] [2600]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 956--956
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 957--957
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 982--982
 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
[2601] [2602] [2603] [2604] [2605] [2606] [2607]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1382--1382
 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2608] [2609] [2610] [2611] [2612] [2613]
Underfull \hbox (badness 1221) in paragraph at lines 1743--1749
\T1/ptm/m/n/10 de-grees of free-dom (mix-tures of the two are per-mit-ted). Mul
ti-dimensional smooths are

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1758--1758
 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 1762--1762
 []    \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[] 

Underfull \hbox (badness 1142) in paragraph at lines 1783--1787
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2614]
Underfull \hbox (badness 1043) in paragraph at lines 1806--1811
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2615] [2616]
Underfull \hbox (badness 1043) in paragraph at lines 1966--1972
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2619]
Underfull \vbox (badness 10000) has occurred while \output is active [2620]
Underfull \vbox (badness 10000) has occurred while \output is active [2621]
Underfull \vbox (badness 10000) has occurred while \output is active [2622]
[2623] [2624] [2625] [2626] [2627] [2628]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2720--2720
 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2629] [2630] [2631] [2632] [2633]
Underfull \hbox (badness 5189) in paragraph at lines 3038--3042
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2634] [2635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2636]
[2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3709--3709
 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2645] [2646]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3824--3824
 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 

Underfull \hbox (badness 1142) in paragraph at lines 3855--3859
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2647] [2648] [2649]
Underfull \hbox (badness 5970) in paragraph at lines 4035--4041
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
[2650]
Underfull \vbox (badness 10000) has occurred while \output is active [2651]
[2652] [2653]
Underfull \hbox (badness 1577) in paragraph at lines 4280--4283
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment

Underfull \hbox (badness 2181) in paragraph at lines 4287--4288
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] [2662] [2663] [2664]
[2665]
Underfull \vbox (badness 10000) has occurred while \output is active [2666]
[2667] [2668]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 5234--5234
 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 5261--5261
 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2669] [2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] [2679]
[2680] [2681] [2682] [2683] [2684] [2685] [2686] [2687] [2688] [2689] [2690]
[2691] [2692] [2693]
Underfull \vbox (badness 10000) has occurred while \output is active [2694]
[2695]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3118) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2696]
Underfull \hbox (badness 10000) in paragraph at lines 6979--6982
[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,

Underfull \hbox (badness 3108) in paragraph at lines 6979--6982
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
[2697] [2698] [2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7199--7199
 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 7200--7200
 []         \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 7203--7203
 []         \T1/pcr/m/n/10 shift=0,trans=I,seWithMean=FALSE,unconditional=FALSE
,by.resids=FALSE,[] 
[2700] [2701] [2702]
Underfull \hbox (badness 1629) in paragraph at lines 7355--7360
\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
[2703] [2704] [2705]
Overfull \hbox (114.78088pt too wide) in paragraph at lines 7554--7554
 []        \T1/pcr/m/n/10 block.size=50000,newdata.guaranteed=FALSE,na.action=n
a.pass,cluster=NULL,...)[] 
[2706] [2707]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 7704--7704
 []        \T1/pcr/m/n/10 block.size=NULL,newdata.guaranteed=FALSE,na.action=na
.pass,[] 
[2708] [2709] [2710]
Underfull \vbox (badness 10000) has occurred while \output is active [2711]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7945--7945
 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
[2712]
Underfull \hbox (badness 1205) in paragraph at lines 7983--7985
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 7983--7985
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

Underfull \hbox (badness 1975) in paragraph at lines 7989--7994
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2713]
Underfull \hbox (badness 1205) in paragraph at lines 8073--8075
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 8073--8075
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2714]
Underfull \hbox (badness 10000) in paragraph at lines 8142--8145
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from

Underfull \hbox (badness 2057) in paragraph at lines 8142--8145
[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2715] [2716]
Underfull \hbox (badness 1253) in paragraph at lines 8272--8274
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2717] [2718] [2719] [2720]
Underfull \hbox (badness 1946) in paragraph at lines 8450--8457
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same

Underfull \hbox (badness 2221) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method

Underfull \hbox (badness 2042) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee

Underfull \hbox (badness 2846) in paragraph at lines 8458--8461
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:

Underfull \hbox (badness 5862) in paragraph at lines 8458--8461
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2721]
Underfull \hbox (badness 10000) in paragraph at lines 8537--8540
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9044--9044
 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 

Underfull \hbox (badness 1975) in paragraph at lines 9055--9060
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2730] [2731]
Underfull \hbox (badness 1803) in paragraph at lines 9132--9136
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .

Underfull \hbox (badness 1502) in paragraph at lines 9144--9156
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec

Underfull \hbox (badness 2401) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be

Underfull \hbox (badness 2970) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2732] [2733] [2734]
Underfull \hbox (badness 6876) in paragraph at lines 9354--9360
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
[2735]
Underfull \hbox (badness 10000) in paragraph at lines 9395--9396
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2736] [2737]
Underfull \hbox (badness 10000) in paragraph at lines 9524--9526
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term

Underfull \hbox (badness 10000) in paragraph at lines 9524--9526
\T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs",
...) \T1/ptm/m/n/10 or
[2738] [2739]
Underfull \hbox (badness 10000) in paragraph at lines 9652--9653
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2740] [2741]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9733--9733
 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9734--9734
 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 

Underfull \hbox (badness 7613) in paragraph at lines 9772--9775
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2742] [2743] [2744] [2745]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9985--9985
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2746]
Underfull \hbox (badness 10000) in paragraph at lines 10030--10032
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2747] [2748]
Underfull \hbox (badness 10000) in paragraph at lines 10138--10141
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-

Underfull \hbox (badness 3312) in paragraph at lines 10138--10141
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the

Underfull \hbox (badness 7099) in paragraph at lines 10138--10141
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2749]
Underfull \hbox (badness 10000) in paragraph at lines 10237--10243
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a

Underfull \hbox (badness 2698) in paragraph at lines 10237--10243
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2750] [2751] [2752]
Underfull \vbox (badness 10000) has occurred while \output is active [2753]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10451--10451
 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 


Overfull \hbox (58.38037pt too wide) in paragraph at lines 10453--10453
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[] 

Overfull \hbox (52.98038pt too wide) in paragraph at lines 10454--10454
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2754]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 10535--10535
 []\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[] 

Overfull \hbox (85.38034pt too wide) in paragraph at lines 10541--10541
 []          \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[] 
[2755]
Underfull \hbox (badness 10000) in paragraph at lines 10555--10563
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like

Underfull \hbox (badness 10000) in paragraph at lines 10581--10582
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2756] [2757]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 10683--10683
 []\T1/pcr/m/n/9 bk <- gam(y~s(la,lo,bs="sos",k=60),knots=list(la=dat$la[ind],l
o=dat$lo[ind]),data=dat)[] 
[2758] [2759]
Underfull \hbox (badness 3396) in paragraph at lines 10841--10846
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
[2760]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10888
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2761] [2762] [2763] [2764]
Underfull \hbox (badness 10000) in paragraph at lines 11074--11077
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-

Underfull \hbox (badness 3068) in paragraph at lines 11074--11077
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see

Underfull \hbox (badness 10000) in paragraph at lines 11107--11111
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 5652) in paragraph at lines 11107--11111
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , code[][]soap[][][], code[][]Spheri
cal.Spline[][][], [][]\T1/pcr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 ,
[2765] [2766]
Underfull \hbox (badness 2158) in paragraph at lines 11259--11259
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2767] [2768]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 11334--11334
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2769] [2770]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11468--11468
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2771] [2772]
Underfull \hbox (badness 4846) in paragraph at lines 11604--11607
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783]
[2784] [2785] [2786] [2787]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12501--12501
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2788] [2789] [2790] [2791] [2792] [2793] [2794]) (./nlme-pkg.tex
Chapter 25.
[2795]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2796]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2797] [2798] [2799] [2800] [2801]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] [2811]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1094--1094
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
Underfull \hbox (badness 10000) in paragraph at lines 1633--1636
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[2820]
Underfull \hbox (badness 3780) in paragraph at lines 1650--1652
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 2042) in paragraph at lines 1997--2003
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[2826]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2059--2059
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[2827]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2828] [2829]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[2830]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2831] [2832] [2833] [2834] [2835] [2836] [2837] [2838]
Underfull \hbox (badness 10000) in paragraph at lines 2846--2850
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849]
[2850]
Underfull \hbox (badness 6493) in paragraph at lines 3582--3590
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4348--4348
 []\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3), 
minAbsPar=0) 
[2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] [2872]
[2873] [2874]
Underfull \hbox (badness 10000) in paragraph at lines 5158--5162
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879]
Underfull \hbox (badness 10000) in paragraph at lines 5475--5479
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if

Underfull \hbox (badness 2671) in paragraph at lines 5475--5479
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2880] [2881]
Underfull \hbox (badness 10000) in paragraph at lines 5590--5593
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
Underfull \hbox (badness 2799) in paragraph at lines 6096--6102
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[2891]
Underfull \hbox (badness 7133) in paragraph at lines 6157--6161
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2892]
Underfull \hbox (badness 2057) in paragraph at lines 6241--6252
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[2893]
Underfull \hbox (badness 10000) in paragraph at lines 6305--6307
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6334--6334
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2894] [2895] [2896] [2897]
Underfull \hbox (badness 7133) in paragraph at lines 6553--6557
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2898]
Underfull \hbox (badness 10000) in paragraph at lines 6652--6658
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
[2899]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6718
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2900]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6743--6743
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2901] [2902] [2903]
Underfull \hbox (badness 10000) in paragraph at lines 6986--6993
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,

Overfull \hbox (15.18042pt too wide) in paragraph at lines 7003--7003
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 7011--7011
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
[2904]
Underfull \hbox (badness 2875) in paragraph at lines 7033--7035
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[2905] [2906] [2907]
Underfull \hbox (badness 10000) in paragraph at lines 7248--7253
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[2908] [2909]
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-

Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 1817) in paragraph at lines 7400--7408
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 
20 EM it-er-a-

Underfull \hbox (badness 3118) in paragraph at lines 7423--7426
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[2910] [2911] [2912] [2913]
Underfull \hbox (badness 3354) in paragraph at lines 7638--7640
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[2914] [2915] [2916] [2917] [2918] [2919]
Underfull \hbox (badness 1642) in paragraph at lines 8030--8052
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2920] [2921]
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (12.78088pt too wide) in paragraph at lines 8193--8193
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 

Underfull \hbox (badness 1642) in paragraph at lines 8202--8224
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2922] [2923] [2924] [2925] [2926]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8466--8466
 []\T1/pcr/m/n/10 lmeControl(maxIter, msMaxIter, tolerance, niterEM, msMaxEval,
 msTol, 

Underfull \hbox (badness 10000) in paragraph at lines 8509--8511
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2927]
Underfull \hbox (badness 1320) in paragraph at lines 8522--8526
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][] \T1/ptm/m/n/10 (those from

Overfull \hbox (9.78043pt too wide) in paragraph at lines 8544--8544
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2928] [2929] [2930]
Underfull \hbox (badness 10000) in paragraph at lines 8707--8719
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[2931] [2932] [2933] [2934] [2935] [2936] [2937] [2938] [2939]
Underfull \hbox (badness 10000) in paragraph at lines 9297--9304
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9308--9308
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[2940]
Underfull \hbox (badness 6300) in paragraph at lines 9390--9393
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[2941] [2942] [2943] [2944]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [2945]
Underfull \hbox (badness 10000) in paragraph at lines 9679--9682
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
[2946]
Underfull \hbox (badness 3108) in paragraph at lines 9727--9730
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite

Underfull \hbox (badness 2521) in paragraph at lines 9727--9730
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[2947] [2948]
Underfull \hbox (badness 2435) in paragraph at lines 9900--9905
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[2949] [2950] [2951] [2952] [2953]
Underfull \hbox (badness 7291) in paragraph at lines 10190--10192
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[2954] [2955] [2956]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10406--10406
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[2957]
Underfull \hbox (badness 1596) in paragraph at lines 10435--10461
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[2958] [2959] [2960]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10611--10611
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 10808--10810
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

Underfull \hbox (badness 1092) in paragraph at lines 10818--10821
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10840--10840
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2964] [2965] [2966]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10996--10996
 []\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool) 
[2967]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11091--11091
 []\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)[] 
[2968] [2969] [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978]
Underfull \hbox (badness 6268) in paragraph at lines 11852--11862
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[2979] [2980] [2981] [2982]
Underfull \hbox (badness 10000) in paragraph at lines 12113--12119
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[2983] [2984] [2985] [2986] [2987] [2988] [2989]
Underfull \hbox (badness 2452) in paragraph at lines 12576--12583
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[2990]
Underfull \hbox (badness 10000) in paragraph at lines 12641--12647
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001]
[3002] [3003] [3004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13593--13593
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3005]
Underfull \hbox (badness 10000) in paragraph at lines 13620--13623
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 6016) in paragraph at lines 13648--13651
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.

Underfull \hbox (badness 2653) in paragraph at lines 13648--13651
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and

Underfull \hbox (badness 1975) in paragraph at lines 13655--13658
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot

Underfull \hbox (badness 1838) in paragraph at lines 13663--13670
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner

Underfull \hbox (badness 3713) in paragraph at lines 13663--13670
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
[3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13720--13720
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 

Underfull \hbox (badness 10000) in paragraph at lines 13727--13730
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 2469) in paragraph at lines 13727--13730
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
[3007]
Underfull \hbox (badness 4582) in paragraph at lines 13755--13758
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is

Underfull \hbox (badness 2418) in paragraph at lines 13755--13758
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and

Underfull \hbox (badness 2990) in paragraph at lines 13759--13762
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3008]
Underfull \hbox (badness 10000) in paragraph at lines 13835--13838
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 1472) in paragraph at lines 13860--13867
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3009]
Underfull \hbox (badness 10000) in paragraph at lines 13929--13931
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3010] [3011] [3012] [3013]
Underfull \hbox (badness 1540) in paragraph at lines 14144--14149
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an

Underfull \hbox (badness 1215) in paragraph at lines 14191--14193
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3014] [3015] [3016] [3017] [3018]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14434--14434
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15072 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15072 ...Extract Random Effects}{random.effects}
                                                   [3028] [3029] [3030]
[3031] [3032] [3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 1009) in paragraph at lines 15729--15738
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038] [3039] [3040]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15876--15876
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3041] [3042] [3043] [3044]
Underfull \hbox (badness 10000) in paragraph at lines 16154--16172
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form

Underfull \hbox (badness 1708) in paragraph at lines 16154--16172
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3045]
Underfull \hbox (badness 10000) in paragraph at lines 16211--16217
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 1728) in paragraph at lines 16731--16734
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3054] [3055] [3056] [3057] [3058]
Underfull \hbox (badness 1867) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3059]
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063]
Underfull \hbox (badness 10000) in paragraph at lines 17375--17382
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3064] [3065] [3066] [3067] [3068] [3069] [3070]
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3071]
Underfull \hbox (badness 3579) in paragraph at lines 17942--17947
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3072]
Underfull \hbox (badness 3579) in paragraph at lines 18006--18011
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3073]
Underfull \hbox (badness 3579) in paragraph at lines 18069--18074
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3074]
Underfull \hbox (badness 1577) in paragraph at lines 18130--18132
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal

Underfull \hbox (badness 3579) in paragraph at lines 18132--18137
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3075]
Underfull \hbox (badness 3579) in paragraph at lines 18195--18200
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3076]
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3579) in paragraph at lines 18267--18272
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3077] [3078]
Underfull \hbox (badness 1009) in paragraph at lines 18416--18425
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3079] [3080] [3081]
Underfull \hbox (badness 1009) in paragraph at lines 18550--18559
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089]) (./nnet-pkg.tex
[3090]
Chapter 26.
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 

Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3092] [3093] [3094] [3095]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 383--383
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 440--440
 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 443--443
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3096]
Underfull \hbox (badness 4013) in paragraph at lines 488--491
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3097]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 523--523
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3098]) (./rpart-pkg.tex
Chapter 27.
[3099] [3100] [3101] [3102]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3103]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3104] [3105] [3106]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3107] [3108]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3109]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3110]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3111]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3112] [3113] [3114]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 

Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method

Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y

Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3115]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3116]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286
 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 

Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3117] [3118] [3119] [3120] [3121] [3122]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3123] [3124]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3125] [3126] [3127]) (./spatial-pkg.tex [3128]
Chapter 28.
[3129] [3130] [3131] [3132] [3133] [3134]
Underfull \hbox (badness 10000) in paragraph at lines 423--427

[3135] [3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145]
[3146] [3147]) (./survival-pkg.tex [3148]
Chapter 29.
[3149] [3150]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3151]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 226--226
 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 227--227
 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.267 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.267 ... Myelogenous Leukemia survival data}{aml}
                                                   [3152] [3153]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 364--364
 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 366--366
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3154]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 403--403
 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3155] [3156]
Underfull \vbox (badness 10000) has occurred while \output is active [3157]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 597--597
 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 598--598
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3158] [3159]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 741--741
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3160] [3161]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 891--891
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3162]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.957 ...herapy for Stage B/C colon cancer}{colon}
                                                   [3163] [3164] [3165]
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1747--1747
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3174] [3175]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1877--1877
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3176] [3177] [3178] [3179]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2159--2159
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 

Underfull \hbox (badness 1389) in paragraph at lines 2172--2174
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3180] [3181]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2274--2274
 []\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24)    #darken the first curve
 and add marks[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 2280--2280
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2916--2916
 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3192] [3193]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3072--3072
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3194] [3195]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3163--3163
 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3196]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3253--3253
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3197] [3198]
Underfull \hbox (badness 1852) in paragraph at lines 3401--3403
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3199] [3200]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3534--3534
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
[3201] [3202]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3694--3694
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3203]
Underfull \hbox (badness 1540) in paragraph at lines 3749--3752
[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3204]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3792--3792
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 3813--3813
 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 3815--3815
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3205] [3206]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3960--3960
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3207] [3208] [3209] [3210] [3211]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4287--4287
 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3212] [3213]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4407--4407
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 4408--4408
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3214] [3215] [3216] [3217] [3218] [3219] [3220]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4910--4910
 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3221] [3222] [3223]
Underfull \hbox (badness 10000) in paragraph at lines 5170--5179
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
[3224] [3225]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5280--5280
 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 

Underfull \hbox (badness 1038) in paragraph at lines 5322--5328
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival

Underfull \hbox (badness 3000) in paragraph at lines 5341--5343
[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3226]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5371--5371
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3227]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5457--5457
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5595
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (18.78088pt too wide) in paragraph at lines 5611--5611
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3230] [3231] [3232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5813--5813
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3233]
Underfull \hbox (badness 6332) in paragraph at lines 5917--5922
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3234] [3235]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6086--6086
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3236] [3237]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6246--6246
 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3238]
Underfull \hbox (badness 1354) in paragraph at lines 6287--6291
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3239] [3240]
Underfull \hbox (badness 2035) in paragraph at lines 6463--6470
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 6463--6470
\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1297) in paragraph at lines 6463--6470
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6524--6524
 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3242] [3243] [3244]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6682--6682
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3245] [3246]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813
 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 6816--6816
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3247] [3248] [3249] [3250]
Underfull \vbox (badness 10000) has occurred while \output is active [3251]
[3252])
No file fullrefman.ind.
(./fullrefman.aux) )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.tree} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mem.limits} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced
 but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does 
not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.standardGeneric} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texlive
/fonts/type1/bluesky/ams/cmbsy7.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmbx10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmex10.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmmi5.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmib10.pfb>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmr5.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pfb></usr/share/texmf-texl
ive/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texmf-texlive/fonts/type1/ur
w/courier/ucrr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/courier/ucrro8a.
pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/t
exmf-texlive/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/t
ype1/urw/times/utmbi8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr
8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr8a.pfb></usr/share/t
exmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on fullrefman.pdf (3255 pages, 8151750 bytes).
Transcript written on fullrefman.log.
This is makeindex, version 2.15 [20-Nov-2007] (kpathsea + Thai support).
Scanning input file fullrefman.idx..........................done (22246 entries accepted, 72 rejected).
Sorting entries........................................................................................................................................................................................................................................................done (366915 comparisons).
Generating output file fullrefman.ind........................done (18310 lines written, 111 warnings).
Output written in fullrefman.ind.
Transcript written in fullrefman.ilg.
This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 %&-line parsing enabled.
entering extended mode
(./fullrefman.tex
LaTeX2e <2005/12/01>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa
n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded.
(/usr/share/texmf-texlive/tex/latex/base/book.cls
Document Class: book 2005/09/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/bm.sty)
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def))
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty)
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))
(/etc/texmf/tex/latex/config/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty)))
(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hpdftex*
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def)

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 366.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 366.

) (/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
(/usr/share/texmf-texlive/tex/latex/base/utf8.def
(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu)))
(/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty
(/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty
(/usr/share/texmf-texlive/tex/latex/graphics/trig.sty)
(/etc/texmf/tex/latex/config/graphics.cfg)))
(/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
(./fullrefman.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./fullrefman.out)
(./fullrefman.out) (/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd)
(./version.tex) (/usr/share/texmf-texlive/tex/latex/psnfss/ts1ptm.fd) [1{/var/c
ache/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc
(/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5]
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]
[37] [38] [39] [40] [41] [42] [43] [44] [45] [46]) [47] [48] [1] [2]
(./base-pkg.tex
Chapter 1.

Underfull \hbox (badness 4595) in paragraph at lines 40--43
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[3]
Underfull \hbox (badness 4168) in paragraph at lines 94--99
[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one 
char-ac-ter vec-tors. The first en-try is al-ways
[4]
Underfull \hbox (badness 10000) in paragraph at lines 131--137
[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
 x \T1/ptm/m/n/10 such that

Underfull \hbox (badness 10000) in paragraph at lines 131--137
\T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base 
^ ulp.digits \T1/ptm/m/n/10 if ei-

Underfull \hbox (badness 6236) in paragraph at lines 131--137
\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m
/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise,

Underfull \hbox (badness 10000) in paragraph at lines 131--137
\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally

Underfull \hbox (badness 10000) in paragraph at lines 137--145
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 137--145
\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if

Underfull \hbox (badness 4328) in paragraph at lines 137--145
\T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is

Underfull \hbox (badness 10000) in paragraph at lines 137--145
\T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma
lly

Underfull \hbox (badness 10000) in paragraph at lines 148--155
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-

Underfull \hbox (badness 10000) in paragraph at lines 148--155
\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5] [6]
Underfull \hbox (badness 4036) in paragraph at lines 291--295
\T1/ptm/m/n/10 ues \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.
binary"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 an
d
[7]
Underfull \hbox (badness 10000) in paragraph at lines 330--333
[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8]
Underfull \hbox (badness 2359) in paragraph at lines 375--378
[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
Underfull \hbox (badness 1072) in paragraph at lines 505--511
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [13] [14]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 807--807
 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[15] [16] [17] [18] [19]
Underfull \hbox (badness 1838) in paragraph at lines 1094--1097
[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[20] [21] [22]
Underfull \hbox (badness 5862) in paragraph at lines 1302--1308
[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[23] [24] [25] [26] [27]
Underfull \hbox (badness 2865) in paragraph at lines 1665--1669
[]\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/
m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then

Underfull \hbox (badness 10000) in paragraph at lines 1669--1671
[]\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by
[28] [29]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 1808--1808
 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 

Overfull \hbox (19.13934pt too wide) in paragraph at lines 1843--1845
[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x,      parent = emptyenv())

Underfull \hbox (badness 10000) in paragraph at lines 1846--1848
[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[30] [31]
Underfull \hbox (badness 10000) in paragraph at lines 1993--1995
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[32] [33]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2100--2100
 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[34] [35]
Underfull \hbox (badness 1107) in paragraph at lines 2233--2235
[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[36] [37] [38] [39] [40]
Underfull \hbox (badness 5878) in paragraph at lines 2562--2567
[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to 
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-

Underfull \hbox (badness 10000) in paragraph at lines 2562--2567
\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53]
Underfull \hbox (badness 10000) in paragraph at lines 3446--3448
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[54] [55] [56] [57] [58] [59] [60]
Underfull \hbox (badness 4927) in paragraph at lines 3896--3900
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject

Underfull \hbox (badness 2012) in paragraph at lines 3896--3900
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[61]
Underfull \hbox (badness 5260) in paragraph at lines 4004--4009
[]\T1/ptm/m/n/10 Are the \T1/pcr/m/n/10 R.app \T1/ptm/m/n/10 GUI com-po-nents a
nd the [][]\T1/pcr/m/n/10 quartz[][][] \T1/ptm/m/n/10 func-tion op-er-a-

Underfull \hbox (badness 1354) in paragraph at lines 4004--4009
\T1/ptm/m/n/10 tional? Only on some OS X builds. Note that this is dis-tinct fr
om
[62] [63] [64]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4172--4172
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
[65]
Underfull \hbox (badness 10000) in paragraph at lines 4273--4278
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for

Underfull \hbox (badness 10000) in paragraph at lines 4273--4278
[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-

Underfull \hbox (badness 2181) in paragraph at lines 4273--4278
\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
 columns to fac-tors un-less
[66]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4352--4352
 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[67] [68] [69] [70]
Underfull \hbox (badness 2521) in paragraph at lines 4589--4591
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[71] [72] [73] [74] [75]
Underfull \hbox (badness 10000) in paragraph at lines 4922--4930
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[76] [77] [78] [79] [80] [81] [82] [83]
Underfull \hbox (badness 2443) in paragraph at lines 5465--5472
[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 http : / /
[84] [85] [86] [87]
Underfull \hbox (badness 1635) in paragraph at lines 5777--5780
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class

Underfull \hbox (badness 3009) in paragraph at lines 5781--5784
[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing

Underfull \hbox (badness 1102) in paragraph at lines 5798--5811
[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in

Underfull \hbox (badness 1308) in paragraph at lines 5812--5820
[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[88] [89] [90] [91]
Underfull \hbox (badness 2158) in paragraph at lines 6032--6036
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 '). Prox-ies can be spe
c-i-fied for HTTP and FTP \T1/pcr/m/n/10 url \T1/ptm/m/n/10 con-nec-tions: see
[92]
Underfull \hbox (badness 10000) in paragraph at lines 6120--6123
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is

Underfull \hbox (badness 2057) in paragraph at lines 6120--6123
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[93] [94]
Underfull \hbox (badness 3815) in paragraph at lines 6284--6290
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-


Underfull \hbox (badness 2343) in paragraph at lines 6284--6290
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1147) in paragraph at lines 6284--6290
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If it is re-quired (it is n
ot rec-om-mended) when writ-ing

Underfull \hbox (badness 10000) in paragraph at lines 6303--6305
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[95]
Underfull \hbox (badness 1067) in paragraph at lines 6345--6352
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[96]
Underfull \vbox (badness 10000) has occurred while \output is active [97]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6518--6518
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[98] [99] [100] [101] [102]
Underfull \hbox (badness 10000) in paragraph at lines 6844--6846
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[103] [104]
Underfull \hbox (badness 4595) in paragraph at lines 6950--6953
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[105] [106] [107]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7143--7143
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[108]
Underfull \hbox (badness 8132) in paragraph at lines 7239--7243
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The

Underfull \hbox (badness 4543) in paragraph at lines 7239--7243
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
[109]
Underfull \hbox (badness 10000) in paragraph at lines 7258--7269
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing

Underfull \hbox (badness 1062) in paragraph at lines 7258--7269
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be

Overfull \hbox (4.63962pt too wide) in paragraph at lines 7291--7295
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[110] [111] [112] [113] [114] [115]
Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[116] [117]
Underfull \hbox (badness 5802) in paragraph at lines 7938--7942
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
[118] [119]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8053--8057
\T1/pcr/m/n/10 trace("plot", browser, exit = browser, signature = c("track", "m
issing")) 
[120]
Underfull \hbox (badness 10000) in paragraph at lines 8106--8110
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[121]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8187--8187
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO
! "); pi+2})[] 
[122] [123]
Underfull \hbox (badness 4254) in paragraph at lines 8340--8344
[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
[124]
Underfull \hbox (badness 1132) in paragraph at lines 8383--8390
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[125]
Underfull \hbox (badness 1603) in paragraph at lines 8492--8495
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[126] [127] [128] [129] [130] [131] [132] [133] [134]
Underfull \hbox (badness 1917) in paragraph at lines 9077--9080
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has

Overfull \hbox (36.7804pt too wide) in paragraph at lines 9130--9130
 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 9131--9131
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[135] [136]
Underfull \hbox (badness 1168) in paragraph at lines 9231--9236
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[137] [138]
Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]198
5$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / en . wikipedia .

Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 http : / / en . wikipedia . org / wiki / Double _
[139] [140] [141]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9588--9588
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[142]
Underfull \hbox (badness 1629) in paragraph at lines 9661--9665
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[143] [144]
Underfull \hbox (badness 2150) in paragraph at lines 9760--9763
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 3690) in paragraph at lines 9774--9782
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for

Underfull \hbox (badness 10000) in paragraph at lines 9783--9785
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
[145]
Underfull \hbox (badness 3735) in paragraph at lines 9815--9822
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[146] [147]
Underfull \hbox (badness 10000) in paragraph at lines 10010--10013
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[148] [149] [150] [151] [152] [153] [154] [155] [156]
Underfull \hbox (badness 5288) in paragraph at lines 10669--10671
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of

Underfull \hbox (badness 3039) in paragraph at lines 10679--10684
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
[157]
Underfull \hbox (badness 10000) in paragraph at lines 10737--10739
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[158] [159]
Underfull \hbox (badness 4569) in paragraph at lines 10854--10858
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 10854--10858
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[160]
Underfull \hbox (badness 10000) in paragraph at lines 10965--10967
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[161] [162] [163]
Underfull \hbox (badness 4048) in paragraph at lines 11151--11161
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is

Underfull \hbox (badness 3657) in paragraph at lines 11151--11161
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[164] [165] [166]
Underfull \hbox (badness 5460) in paragraph at lines 11398--11407
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-

Underfull \hbox (badness 2221) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those

Underfull \hbox (badness 2707) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL

Underfull \hbox (badness 2818) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,

Underfull \hbox (badness 6978) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[167] [168] [169] [170] [171]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11761--11761
 []\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[] 
[172] [173] [174] [175] [176]
Underfull \hbox (badness 2221) in paragraph at lines 12121--12127
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[177] [178] [179] [180]
Underfull \hbox (badness 2253) in paragraph at lines 12350--12352
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[181]
Underfull \hbox (badness 10000) in paragraph at lines 12454--12456
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[182] [183]
Underfull \hbox (badness 10000) in paragraph at lines 12602--12604
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See

[184] [185]
Underfull \hbox (badness 10000) in paragraph at lines 12700--12704
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (30.78088pt too wide) in paragraph at lines 12750--12750
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777") 
[186] [187]
Underfull \hbox (badness 10000) in paragraph at lines 12839--12842
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 12849--12849
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive  TRUE)[] 
[188]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12932--12932
 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE) 

Underfull \hbox (badness 7238) in paragraph at lines 12950--12957
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 12950--12957
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to

Underfull \hbox (badness 2126) in paragraph at lines 12950--12957
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-

Underfull \hbox (badness 3965) in paragraph at lines 12958--12962
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[189] [190]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13066--13066
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 13067--13067
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[191]
Underfull \hbox (badness 10000) in paragraph at lines 13148--13152
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a

Underfull \hbox (badness 1389) in paragraph at lines 13148--13152
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[192]
Underfull \hbox (badness 1314) in paragraph at lines 13208--13210
[]\T1/ptm/m/n/10 In re-cent ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 most u
n-nec-es-sary copy-ing is avoided: on the other hand us-ing
[193] [194] [195]
Underfull \hbox (badness 1168) in paragraph at lines 13402--13406
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-

Underfull \hbox (badness 2012) in paragraph at lines 13402--13406
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[196]
Underfull \hbox (badness 6944) in paragraph at lines 13496--13499
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 13521--13521
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[197] [198] [199]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13668--13668
 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 

Underfull \hbox (badness 2790) in paragraph at lines 13675--13678
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for

Underfull \hbox (badness 4254) in paragraph at lines 13691--13699
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,

Underfull \hbox (badness 1024) in paragraph at lines 13706--13710
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[200]
Underfull \hbox (badness 10000) in paragraph at lines 13761--13763
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point,

Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives

Underfull \hbox (badness 10000) in paragraph at lines 13772--13780
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[201]
Underfull \hbox (badness 1009) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 is
 not ap-pro-pri-ate for use within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/1
0 meth-ods: use
[202]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13869--13869
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
[203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214]
[215]
Underfull \hbox (badness 2418) in paragraph at lines 14776--14780
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,

Underfull \hbox (badness 6510) in paragraph at lines 14783--14786
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle

Underfull \hbox (badness 2326) in paragraph at lines 14811--14818
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[216] [217] [218] [219]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15057--15057
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 

Underfull \hbox (badness 1867) in paragraph at lines 15082--15089
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[220] [221] [222] [223]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15316--15316
 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 15343--15343
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 

Underfull \vbox (badness 10000) has occurred while \output is active [224]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15387--15387
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 

Underfull \hbox (badness 10000) in paragraph at lines 15393--15397
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for

Underfull \hbox (badness 1028) in paragraph at lines 15393--15397
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[225] [226] [227] [228] [229] [230] [231]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15921--15921
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[232] [233] [234] [235]
Underfull \hbox (badness 2435) in paragraph at lines 16174--16176
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /

Underfull \hbox (badness 2285) in paragraph at lines 16227--16229
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /

Overfull \hbox (9.78043pt too wide) in paragraph at lines 16235--16235
 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
[236]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16245--16245
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 16265--16265
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[237] [238] [239] [240] [241] [242] [243]
Underfull \hbox (badness 10000) in paragraph at lines 16701--16703
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[244]
Underfull \hbox (badness 4217) in paragraph at lines 16785--16794
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2057) in paragraph at lines 16800--16816
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[245] [246] [247] [248] [249] [250]
Underfull \hbox (badness 4699) in paragraph at lines 17207--17210
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the atomic types (\T1/pcr
/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[251] [252]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17329--17329
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[253] [254]
Underfull \hbox (badness 4739) in paragraph at lines 17460--17462
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[255] [256] [257] [258] [259] [260]
Underfull \hbox (badness 1430) in paragraph at lines 17858--17863
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .


Underfull \hbox (badness 10000) in paragraph at lines 17858--17863
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[261]
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher

Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would

Underfull \hbox (badness 5008) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to

Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[262]
Underfull \hbox (badness 10000) in paragraph at lines 17979--17986
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If

Underfull \hbox (badness 6364) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-

Underfull \hbox (badness 5064) in paragraph at lines 17979--17986
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with

Underfull \hbox (badness 5908) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with

Underfull \hbox (badness 10000) in paragraph at lines 17995--17997
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[263]
Underfull \hbox (badness 1975) in paragraph at lines 18067--18070
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[264] [265] [266] [267] [268]
Underfull \hbox (badness 10000) in paragraph at lines 18364--18368
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[269]
Underfull \hbox (badness 10000) in paragraph at lines 18494--18498
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use

Underfull \hbox (badness 1454) in paragraph at lines 18494--18498
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
[270] [271]
Underfull \hbox (badness 10000) in paragraph at lines 18589--18596
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[272] [273]
Underfull \hbox (badness 10000) in paragraph at lines 18710--18714
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use

Underfull \hbox (badness 5161) in paragraph at lines 18765--18770
[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the

Underfull \hbox (badness 6592) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of

Underfull \hbox (badness 5133) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed

Underfull \hbox (badness 10000) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[274] [275] [276]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 18927--18927
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 18931--18931
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[277]
Underfull \hbox (badness 3343) in paragraph at lines 18987--18991
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[278]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19073--19073
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 19084--19084
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[279] [280]
Underfull \hbox (badness 6380) in paragraph at lines 19229--19234
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[281]
Underfull \hbox (badness 10000) in paragraph at lines 19258--19261
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1337) in paragraph at lines 19287--19294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be

Underfull \hbox (badness 2229) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or

Underfull \hbox (badness 1043) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in

Underfull \hbox (badness 2564) in paragraph at lines 19306--19309
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[282]
Underfull \hbox (badness 1205) in paragraph at lines 19359--19364
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[283] [284] [285] [286]
Underfull \hbox (badness 2469) in paragraph at lines 19668--19674
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,

Underfull \hbox (badness 1939) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing names.

Underfull \hbox (badness 10000) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[287] [288] [289] [290] [291]
Underfull \hbox (badness 10000) in paragraph at lines 19977--19979
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[292] [293] [294] [295] [296] [297]
Underfull \hbox (badness 1655) in paragraph at lines 20374--20378
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[298] [299] [300] [301] [302] [303] [304] [305] [306]
Underfull \hbox (badness 4366) in paragraph at lines 20965--20971
\T1/pcr/m/n/10 www . bzip . org/$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http 
: / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n
/10 http : / / tukaani .
[307] [308]
Underfull \hbox (badness 10000) in paragraph at lines 21094--21100
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed

Underfull \hbox (badness 6316) in paragraph at lines 21094--21100
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[309] [310]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 21203--21203
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[311]
Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-

Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[312] [313] [314] [315] [316] [317] [318]
Underfull \hbox (badness 3849) in paragraph at lines 21797--21802
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[319]
Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
[320] [321] [322]
Underfull \hbox (badness 10000) in paragraph at lines 22025--22027
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[323] [324] [325] [326] [327] [328] [329] [330]
Underfull \hbox (badness 2197) in paragraph at lines 22624--22628
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by

Underfull \hbox (badness 4048) in paragraph at lines 22624--22628
\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[331]
Underfull \hbox (badness 2846) in paragraph at lines 22638--22642
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-

Underfull \hbox (badness 1990) in paragraph at lines 22638--22642
\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
[332]
Underfull \hbox (badness 10000) in paragraph at lines 22722--22728
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.

Underfull \hbox (badness 1168) in paragraph at lines 22722--22728
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
[333] [334] [335]
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of

Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,

Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[336]
Underfull \hbox (badness 4120) in paragraph at lines 22997--23004
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from

[337]
Underfull \hbox (badness 1694) in paragraph at lines 23107--23110
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[338] [339] [340]
Underfull \hbox (badness 1603) in paragraph at lines 23346--23348
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[341] [342]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 23464--23473
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[343]
Underfull \hbox (badness 5475) in paragraph at lines 23559--23569
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 3271) in paragraph at lines 23578--23581
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able

Underfull \hbox (badness 10000) in paragraph at lines 23593--23595
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[344] [345] [346]
Underfull \hbox (badness 3138) in paragraph at lines 23833--23839
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4132) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "http://www.bioconductor.org"\
T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror

Underfull \hbox (badness 4001) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T
1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 1194) in paragraph at lines 23845--23848
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 1389) in paragraph at lines 23869--23871
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[347]
Underfull \hbox (badness 10000) in paragraph at lines 23886--23892
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by

Underfull \hbox (badness 1009) in paragraph at lines 23897--23900
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 23907--23914
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see

Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 23916--23923
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Overfull \hbox (34.78088pt too wide) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";

Underfull \hbox (badness 1881) in paragraph at lines 23930--23935
[]\T1/ptm/m/n/10 a char-ac-ter string, the path of the com-mand used for un-zip
-ping help files, or
[348] [349] [350] [351]
Underfull \vbox (badness 10000) has occurred while \output is active [352]
Underfull \hbox (badness 10000) in paragraph at lines 24227--24231
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 24227--24231
\T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[353] [354] [355] [356]
Underfull \hbox (badness 4341) in paragraph at lines 24550--24552
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[357] [358] [359] [360] [361] [362] [363]
Underfull \hbox (badness 10000) in paragraph at lines 24977--24981
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[364]
Underfull \hbox (badness 1796) in paragraph at lines 25040--25043
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[365] [366] [367]
Underfull \hbox (badness 10000) in paragraph at lines 25235--25238
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[368] [369] [370] [371] [372] [373] [374] [375] [376]
Underfull \hbox (badness 1226) in paragraph at lines 25855--25860
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[377]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25900--25900
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[378] [379] [380] [381]
Underfull \hbox (badness 7415) in paragraph at lines 26181--26185
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use

Overfull \hbox (42.18039pt too wide) in paragraph at lines 26202--26202
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[382] [383]
Underfull \hbox (badness 2418) in paragraph at lines 26350--26361
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[384] [385] [386]
Underfull \hbox (badness 1533) in paragraph at lines 26583--26586
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[387]
Underfull \hbox (badness 1337) in paragraph at lines 26680--26683
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[388]
Underfull \hbox (badness 1038) in paragraph at lines 26745--26755
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[389]
Underfull \hbox (badness 10000) in paragraph at lines 26756--26759
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[390]
Underfull \hbox (badness 1117) in paragraph at lines 26840--26846
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[391] [392] [393] [394] [395] [396]
Underfull \hbox (badness 4048) in paragraph at lines 27210--27215
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to

Underfull \hbox (badness 4582) in paragraph at lines 27210--27215
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:

Underfull \hbox (badness 1824) in paragraph at lines 27210--27215
\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[397] [398] [399] [400] [401] [402] [403] [404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27743--27743
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[405] [406] [407] [408]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 28025--28027
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[409] [410]
Underfull \hbox (badness 7558) in paragraph at lines 28234--28238
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 5417) in paragraph at lines 28250--28253
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
[411]
Underfull \hbox (badness 10000) in paragraph at lines 28254--28256
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /

Underfull \hbox (badness 10000) in paragraph at lines 28257--28259
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[412] [413] [414] [415] [416] [417]
Underfull \hbox (badness 10000) in paragraph at lines 28664--28668
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[418] [419] [420] [421] [422] [423] [424] [425] [426] [427] [428] [429]
Underfull \hbox (badness 10000) in paragraph at lines 29470--29473
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,

Underfull \hbox (badness 1430) in paragraph at lines 29470--29473
\T1/pcr/m/n/10 save(list = ls(all = TRUE), file =     ".RData")\T1/ptm/m/n/10 .
 It is also what hap-
[430] [431] [432]
Underfull \hbox (badness 2302) in paragraph at lines 29681--29688
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3815) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[433]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29733--29733
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[434]
Underfull \hbox (badness 1158) in paragraph at lines 29834--29839
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 29861--29867
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1953) in paragraph at lines 29861--29867
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[435]
Underfull \hbox (badness 10000) in paragraph at lines 29937--29942
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by

Underfull \hbox (badness 6725) in paragraph at lines 29937--29942
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[436]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30019--30019
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[437] [438] [439] [440]
Underfull \hbox (badness 2809) in paragraph at lines 30282--30288
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment

Underfull \hbox (badness 7759) in paragraph at lines 30289--30292
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 1735) in paragraph at lines 31079--31085
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent

Underfull \hbox (badness 4303) in paragraph at lines 31095--31098
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[453] [454] [455] [456] [457] [458] [459] [460]
Underfull \hbox (badness 2512) in paragraph at lines 31636--31638
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[461] [462] [463] [464]
Underfull \vbox (badness 10000) has occurred while \output is active [465]
[466]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32030--32030
 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 32045--32045
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[467] [468] [469] [470] [471]
Underfull \hbox (badness 1087) in paragraph at lines 32416--32418
[]\T1/ptm/m/n/10 Markus Kuhn, ``ASCII and Uni-code quo-ta-tion marks''. [][]$\T
1/pcr/m/n/10 http : / / www . cl . cam . ac . uk /
[472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32480--32480
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 32481--32481
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[473] [474] [475]
Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want

Underfull \hbox (badness 8113) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call

Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,

Underfull \hbox (badness 6542) in paragraph at lines 32696--32706
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on

Underfull \hbox (badness 5189) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-

Underfull \hbox (badness 4193) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or

Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,

Underfull \hbox (badness 1496) in paragraph at lines 32740--32746
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
[476]
Underfull \hbox (badness 1728) in paragraph at lines 32753--32760
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 33049--33055
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[481] [482]
Underfull \hbox (badness 1163) in paragraph at lines 33224--33231
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6

Underfull \hbox (badness 8132) in paragraph at lines 33224--33231
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[483] [484] [485]
Underfull \hbox (badness 1142) in paragraph at lines 33440--33446
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
[486]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 33455--33455
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[487] [488] [489]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 33707--33707
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33751--33751
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[491] [492] [493] [494] [495] [496] [497]
Underfull \hbox (badness 10000) in paragraph at lines 34212--34215
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
[498]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34259--34259
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[499] [500] [501] [502]
Underfull \hbox (badness 2762) in paragraph at lines 34489--34498
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less

Underfull \hbox (badness 1466) in paragraph at lines 34489--34498
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple

Overfull \hbox (31.3804pt too wide) in paragraph at lines 34548--34548
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[503] [504] [505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34688--34688
 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[506]
Underfull \hbox (badness 3219) in paragraph at lines 34770--34775
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple

Underfull \hbox (badness 1107) in paragraph at lines 34770--34775
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[507]
Underfull \hbox (badness 2452) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes

Underfull \hbox (badness 10000) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[508] [509] [510]
Underfull \hbox (badness 10000) in paragraph at lines 35040--35044
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and

Underfull \hbox (badness 1584) in paragraph at lines 35055--35058
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[511] [512] [513]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 35248--35248
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[514] [515]
Underfull \hbox (badness 1082) in paragraph at lines 35377--35380
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[516] [517] [518]
Underfull \hbox (badness 1038) in paragraph at lines 35565--35568
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[519] [520] [521] [522] [523]
Underfull \hbox (badness 1515) in paragraph at lines 35904--35907
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[524]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36020--36020
 []\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c
("no", 
[525]
Underfull \hbox (badness 1924) in paragraph at lines 36039--36042
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[526]
Underfull \hbox (badness 4096) in paragraph at lines 36123--36126
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[527] [528] [529]
Underfull \hbox (badness 10000) in paragraph at lines 36363--36365
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[530]
Underfull \hbox (badness 10000) in paragraph at lines 36443--36446
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$http : / / developer .
[531] [532]
Underfull \hbox (badness 5475) in paragraph at lines 36564--36568
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http : / /
[533]
Underfull \hbox (badness 10000) in paragraph at lines 36626--36630
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http :
[534] [535] [536] [537] [538] [539]
Underfull \hbox (badness 5637) in paragraph at lines 37038--37047
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the Ol-son/IANA

Underfull \hbox (badness 1629) in paragraph at lines 37038--37047
\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
 in the file sys-tem varies,
[540]
Underfull \hbox (badness 3460) in paragraph at lines 37092--37094
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Time _ zone$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / www . twinsun . com /
[541] [542] [543]
Underfull \hbox (badness 10000) in paragraph at lines 37299--37301
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[544] [545] [546] [547] [548] [549]
Underfull \hbox (badness 6542) in paragraph at lines 37718--37720
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[550] [551]
Underfull \hbox (badness 1708) in paragraph at lines 37841--37849
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 3713) in paragraph at lines 37841--37849
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less

Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-

Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like

Underfull \hbox (badness 3281) in paragraph at lines 37850--37854
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-

Underfull \hbox (badness 4859) in paragraph at lines 37864--37869
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[552]
Underfull \hbox (badness 3895) in paragraph at lines 37926--37938
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in

Underfull \hbox (badness 1303) in paragraph at lines 37926--37938
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[553] [554] [555]
Underfull \hbox (badness 1515) in paragraph at lines 38113--38118
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[556] [557]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 38252--38252
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[558] [559] [560] [561] [562] [563]
Underfull \hbox (badness 1803) in paragraph at lines 38707--38710
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),

Underfull \hbox (badness 2334) in paragraph at lines 38711--38718
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and

Underfull \hbox (badness 4726) in paragraph at lines 38737--38741
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be

Underfull \hbox (badness 1122) in paragraph at lines 38737--38741
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[564] [565] [566]
Underfull \hbox (badness 3668) in paragraph at lines 38915--38917
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[567] [568] [569] [570]
Underfull \hbox (badness 6220) in paragraph at lines 39189--39194
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,

Underfull \hbox (badness 3098) in paragraph at lines 39189--39194
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,

Underfull \hbox (badness 1533) in paragraph at lines 39189--39194
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,

Underfull \hbox (badness 6592) in paragraph at lines 39205--39210
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[571]
Underfull \hbox (badness 1603) in paragraph at lines 39224--39228
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[572] [573] [574] [575] [576] [577]
Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to

Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[578]
Underfull \hbox (badness 2846) in paragraph at lines 39729--39733
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[579]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39769--39769
 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 

Underfull \hbox (badness 3209) in paragraph at lines 39790--39794
[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[580]) (./compiler-pkg.tex
Chapter 2.
[581] [582] [583]) (./datasets-pkg.tex [584]
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[585] [586] [587] [588] [589]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 294--294
 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[590]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368
 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
[591] [592] [593] [594] [595]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 691--694
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[596] [597]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 824--827
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[598] [599] [600] [601]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[602] [603] [604] [605] [606]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1432--1432
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[607] [608]
Underfull \hbox (badness 10000) in paragraph at lines 1517--1520
[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2903) in paragraph at lines 1517--1520
\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[609]
Underfull \hbox (badness 1325) in paragraph at lines 1598--1603
[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[610] [611]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1705--1708
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1799--1799
 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807
 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[613] [614]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1923--1923
 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1924--1924
 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[615] [616] [617] [618]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2127--2130
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[619] [620] [621] [622] [623] [624] [625] [626]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2666--2669
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[627]
Overfull \vbox (13.87083pt too high) has occurred while \output is active
[628]
Underfull \vbox (badness 1789) has occurred while \output is active [629]
[630]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[631] [632]
Overfull \vbox (17.12102pt too high) has occurred while \output is active
[633]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3083--3083
 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[634] [635] [636] [637] [638] [639] [640]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3540--3540
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[641]
Underfull \hbox (badness 5175) in paragraph at lines 3639--3642
[]\T1/ptm/m/n/10 Files for all 182 dis-tricts in 1888 and other years have been
 avail-able at [][]$\T1/pcr/m/n/10 http :

Underfull \hbox (badness 10000) in paragraph at lines 3639--3642
\T1/pcr/m/n/10 / / opr . princeton . edu / archive / eufert / switz . html$[][]
 \T1/ptm/m/n/10 or [][]$\T1/pcr/m/n/10 http : / / opr .
[642]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 3689--3692
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[643]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[644]
Overfull \vbox (27.49593pt too high) has occurred while \output is active
[645]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3891--3891
 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 

Underfull \hbox (badness 10000) in paragraph at lines 3920--3923
[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
[646] [647] [648] [649] [650] [651] [652] [653] [654] [655]
Underfull \vbox (badness 10000) has occurred while \output is active [656]
[657] [658]) (./grDevices-pkg.tex
Chapter 4.
[659] [660] [661] [662] [663]
Underfull \hbox (badness 10000) in paragraph at lines 366--374
[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to

Underfull \hbox (badness 10000) in paragraph at lines 366--374
[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[664] [665]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462
 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[666] [667] [668] [669] [670] [671] [672] [673] [674]
Underfull \hbox (badness 5175) in paragraph at lines 1058--1060
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[675]
Underfull \hbox (badness 1325) in paragraph at lines 1120--1126
\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[676]
Underfull \hbox (badness 10000) in paragraph at lines 1161--1163
[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /

Overfull \hbox (25.98041pt too wide) in paragraph at lines 1213--1213
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[677]
Underfull \hbox (badness 1173) in paragraph at lines 1255--1258
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[678] [679] [680]
Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on

Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of

Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
[681]
Underfull \hbox (badness 2221) in paragraph at lines 1515--1518
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[682]
Underfull \hbox (badness 10000) in paragraph at lines 1584--1588
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when

Underfull \hbox (badness 10000) in paragraph at lines 1584--1588
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[683] [684] [685]
Underfull \hbox (badness 1565) in paragraph at lines 1743--1748
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not

Underfull \hbox (badness 1354) in paragraph at lines 1743--1748
\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[686]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1826--1826
 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 

Underfull \hbox (badness 1184) in paragraph at lines 1867--1877
[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-

Underfull \hbox (badness 2057) in paragraph at lines 1867--1877
\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[687] [688]
Underfull \hbox (badness 10000) in paragraph at lines 1972--1974
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[689] [690]
Underfull \hbox (badness 6758) in paragraph at lines 2133--2136
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[691] [692]
Underfull \hbox (badness 2326) in paragraph at lines 2240--2250
\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place

Underfull \hbox (badness 2318) in paragraph at lines 2240--2250
\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0

Underfull \hbox (badness 2460) in paragraph at lines 2240--2250
\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing

Underfull \hbox (badness 1221) in paragraph at lines 2240--2250
\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[693]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2324--2324
 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
[694] [695] [696] [697] [698]
Underfull \hbox (badness 10000) in paragraph at lines 2650--2651

[699] [700] [701] [702] [703] [704]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3056--3056
 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 3057--3057
 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[705]
Underfull \hbox (badness 1210) in paragraph at lines 3088--3090
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[706] [707] [708]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3302--3302
 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[709] [710]
Underfull \hbox (badness 3525) in paragraph at lines 3409--3412
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

Underfull \hbox (badness 1968) in paragraph at lines 3423--3425
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[711] [712] [713] [714]
Underfull \hbox (badness 5939) in paragraph at lines 3717--3722
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[715] [716] [717] [718] [719] [720] [721]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4200--4200
 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[722]
Underfull \hbox (badness 1502) in paragraph at lines 4247--4252
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[723] [724]
Underfull \hbox (badness 4765) in paragraph at lines 4407--4409
[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if

Overfull \hbox (9.78043pt too wide) in paragraph at lines 4421--4421
 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[725]
Underfull \hbox (badness 5077) in paragraph at lines 4461--4467
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as

Underfull \hbox (badness 1342) in paragraph at lines 4477--4479
[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[726]
Underfull \hbox (badness 1874) in paragraph at lines 4554--4562
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[727]
Underfull \hbox (badness 1755) in paragraph at lines 4621--4623
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[728] [729]
Underfull \hbox (badness 7344) in paragraph at lines 4792--4794
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso

Underfull \hbox (badness 7397) in paragraph at lines 4803--4807
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[730] [731]
Underfull \hbox (badness 1552) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
[732]
Underfull \hbox (badness 4686) in paragraph at lines 4959--4965
\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for

Underfull \hbox (badness 10000) in paragraph at lines 4984--4992
[]\T1/pcr/m/n/10 Baekmuk-Batang \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m/n
/10 ftp : / / ftp . mizi . com / pub / baekmuk/$[][]\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 4984--4992
\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m
/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \vbox (badness 10000) has occurred while \output is active [733]
Underfull \hbox (badness 7344) in paragraph at lines 5003--5005
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[734] [735] [736]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5194--5194
 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 

Underfull \hbox (badness 1648) in paragraph at lines 5200--5204
[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[737]
Underfull \hbox (badness 10000) in paragraph at lines 5280--5282
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[738]
Underfull \hbox (badness 1072) in paragraph at lines 5316--5322
[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[739] [740] [741] [742]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5610--5610
 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 

Underfull \hbox (badness 10000) in paragraph at lines 5623--5626
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[743] [744] [745] [746] [747] [748]
Underfull \hbox (badness 1189) in paragraph at lines 6019--6021
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[749] [750]
Underfull \hbox (badness 10000) in paragraph at lines 6117--6119
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and

Underfull \hbox (badness 10000) in paragraph at lines 6156--6163
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and

Underfull \hbox (badness 1584) in paragraph at lines 6156--6163
\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[751]
Underfull \hbox (badness 3088) in paragraph at lines 6240--6244
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[752]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6285--6285
 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 

Underfull \hbox (badness 10000) in paragraph at lines 6317--6320
[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[753] [754]
Underfull \hbox (badness 5637) in paragraph at lines 6408--6414
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1721) in paragraph at lines 6441--6444
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[755] [756] [757]
Underfull \hbox (badness 6157) in paragraph at lines 6593--6596
\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via

Underfull \hbox (badness 1231) in paragraph at lines 6604--6606
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[758] [759] [760]) (./graphics-pkg.tex
Chapter 5.

Underfull \hbox (badness 10000) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[761] [762] [763] [764]
Underfull \hbox (badness 1412) in paragraph at lines 286--291
[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[765] [766] [767]
Underfull \hbox (badness 2726) in paragraph at lines 465--471
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[768] [769] [770]
Underfull \hbox (badness 10000) in paragraph at lines 655--659
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or

Underfull \hbox (badness 3250) in paragraph at lines 655--659
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if

Underfull \hbox (badness 2735) in paragraph at lines 683--690
[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[771]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[772] [773]
Underfull \hbox (badness 1062) in paragraph at lines 849--852
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[774] [775] [776] [777] [778] [779] [780]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1274--1274
 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 

Underfull \hbox (badness 1024) in paragraph at lines 1319--1327
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
[781]
Underfull \hbox (badness 1248) in paragraph at lines 1347--1353
\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground

Underfull \hbox (badness 6893) in paragraph at lines 1347--1353
\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and

Underfull \hbox (badness 3375) in paragraph at lines 1353--1355
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),

Overfull \hbox (19.3703pt too wide) in paragraph at lines 1375--1379
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[782]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1423--1423
 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1424--1424
 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1430--1430
 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 1431--1431
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[783] [784] [785] [786] [787]
Underfull \hbox (badness 10000) in paragraph at lines 1731--1737
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
[788]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1768--1768
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[789]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1860--1860
 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[790] [791]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1989--1989
 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1994--1994
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[792] [793] [794] [795] [796]
Underfull \hbox (badness 1009) in paragraph at lines 2277--2284
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[797] [798] [799] [800] [801]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2605--2605
 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[802] [803]
Underfull \hbox (badness 5878) in paragraph at lines 2763--2767
\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy

Underfull \hbox (badness 10000) in paragraph at lines 2791--2794
[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[804] [805]
Underfull \hbox (badness 10000) in paragraph at lines 2869--2872
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[806] [807] [808]
Underfull \hbox (badness 1755) in paragraph at lines 3121--3125
[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[809]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the

Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther

Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[810] [811] [812]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3379--3379
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 3398--3398
 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[813]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3402--3402
 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[814] [815]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3578--3578
 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 3579--3579
 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[816]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3616--3616
 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [817]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3668--3668
 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 3688--3688
 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[818]
Underfull \hbox (badness 10000) in paragraph at lines 3751--3755
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for
[819] [820]
Underfull \hbox (badness 1867) in paragraph at lines 3903--3907
[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[821] [822] [823]
Underfull \hbox (badness 3930) in paragraph at lines 4066--4068
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[824] [825] [826] [827]
Underfull \hbox (badness 1924) in paragraph at lines 4354--4359
[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[828]
Underfull \hbox (badness 1286) in paragraph at lines 4376--4379
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing

Underfull \hbox (badness 2529) in paragraph at lines 4383--4386
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used: see
[829]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4468--4468
 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 4472--4472
 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[830]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4516--4516
 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[831]
Underfull \hbox (badness 1264) in paragraph at lines 4590--4603
\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[832] [833]
Underfull \hbox (badness 7925) in paragraph at lines 4727--4733
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[834]
Underfull \hbox (badness 10000) in paragraph at lines 4857--4860


</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf, id=27858, 28
9.08pt x 289.08pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf> [835 </u
sr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf>]
Underfull \hbox (badness 10000) in paragraph at lines 4918--4920


</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf, id=27871, 25
9.97125pt x 332.24126pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>
Underfull \vbox (badness 10000) has occurred while \output is active [836]
[837 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>]
[838]
Underfull \hbox (badness 10000) in paragraph at lines 5111--5113
[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[839]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5167--5167
 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5168--5168
 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[840]
Underfull \hbox (badness 3954) in paragraph at lines 5269--5272
[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[841]
Underfull \hbox (badness 10000) in paragraph at lines 5325--5329
\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[842] [843] [844] [845]
Underfull \hbox (badness 10000) in paragraph at lines 5580--5584
[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g.,

Underfull \hbox (badness 1024) in paragraph at lines 5580--5584
\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[846] [847] [848] [849]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5850--5850
 []\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col.
axis = "red")[] 
[850] [851]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6002--6002
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
[852]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6008--6008
 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[853] [854] [855] [856] [857]
Underfull \hbox (badness 10000) in paragraph at lines 6378--6380
[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[858] [859]
Underfull \hbox (badness 1028) in paragraph at lines 6472--6474
[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of

</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf, id=28270, 36
1.35pt x 50.1875pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf>
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6515--6516
[][] 
[860 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf>]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6609--6609
 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[861]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6640--6640
 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [862]
[863]
Underfull \hbox (badness 10000) in paragraph at lines 6762--6764
[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr

Overfull \hbox (15.18042pt too wide) in paragraph at lines 6789--6789
 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 6795--6795
 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[864]
Underfull \hbox (badness 2600) in paragraph at lines 6855--6857
[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[865] [866] [867]
Underfull \hbox (badness 1881) in paragraph at lines 7044--7049
[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[868]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7087--7087
 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[869] [870] [871] [872] [873] [874]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7465--7465
 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 7476--7476
 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE))[] 
[875] [876] [877] [878] [879] [880]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7816--7816
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7819--7819
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 7823--7823
 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[881] [882] [883]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 7994--7994
 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 7995--7995
 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[884] [885]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8099--8099
 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 

Underfull \hbox (badness 2080) in paragraph at lines 8110--8115
[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[886]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8214--8214
 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
[887]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8229--8229
 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[888] [889]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8360--8360
 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[890]
Underfull \hbox (badness 7415) in paragraph at lines 8480--8487
[]\T1/ptm/m/n/10 The Euro sym-bol was in-tro-duced rel-a-tively re-cently and m
ay not be avail-able in

Underfull \hbox (badness 6808) in paragraph at lines 8480--8487
\T1/ptm/m/n/10 older fonts. In re-cent ver-sions of Adobe sym-bol fonts it is c
har-ac-ter 160, so
[891]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8532--8532
 []     \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: 
Règles, Liberté, Egalité, Fraternité...")[] 
[892]
Underfull \hbox (badness 6691) in paragraph at lines 8558--8561
[]\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex-
pan-sion)

Underfull \hbox (badness 1584) in paragraph at lines 8595--8601
[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[893]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8643 \HeaderA{units}{Graphical Units}{units}
                                               [894]
Underfull \hbox (badness 1205) in paragraph at lines 8708--8710
[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[895] [896]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8827--8827
 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[897]) (./grid-pkg.tex [898]
Chapter 6.
[899] [900] [901] [902] [903] [904]
Underfull \hbox (badness 10000) in paragraph at lines 383--389
\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,

Underfull \hbox (badness 1024) in paragraph at lines 383--389
\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[905] [906] [907] [908] [909] [910] [911] [912] [913] [914]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 

Underfull \vbox (badness 10000) has occurred while \output is active [915]
Underfull \hbox (badness 1430) in paragraph at lines 1074--1079
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[916] [917] [918]
Underfull \hbox (badness 3219) in paragraph at lines 1288--1291
[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
[919] [920] [921] [922] [923] [924] [925]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675
 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[926] [927] [928]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[929]
Underfull \hbox (badness 2961) in paragraph at lines 1926--1931
[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[930]
Underfull \hbox (badness 1430) in paragraph at lines 1985--1990
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-

Underfull \hbox (badness 4479) in paragraph at lines 2014--2017
[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
[931] [932] [933]
Underfull \hbox (badness 2894) in paragraph at lines 2221--2228
[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[934] [935] [936]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377
 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 

Underfull \hbox (badness 1430) in paragraph at lines 2389--2394
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[937] [938] [939]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2582--2582
 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 2614--2614
 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[940] [941] [942] [943]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2854--2854
 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[944] [945] [946] [947] [948]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3164--3164
 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[949]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3260--3260
 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[950]
Underfull \hbox (badness 2799) in paragraph at lines 3294--3300
[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[951]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3386--3386
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[952]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3393--3393
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[953] [954] [955]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3587--3587
 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 3602--3602
 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
[956] [957] [958] [959] [960] [961] [962] [963] [964]
Underfull \hbox (badness 1430) in paragraph at lines 4159--4164
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[965] [966] [967]
Underfull \hbox (badness 1067) in paragraph at lines 4342--4345
[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[968]
Underfull \hbox (badness 1430) in paragraph at lines 4388--4393
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[969] [970] [971]
Underfull \hbox (badness 7256) in paragraph at lines 4585--4587
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[972] [973] [974] [975] [976] [977] [978] [979] [980]
Underfull \hbox (badness 10000) in paragraph at lines 5174--5176
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[981] [982] [983] [984] [985] [986] [987] [988] [989] [990]
Underfull \hbox (badness 3449) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[991] [992] [993] [994] [995]
Underfull \hbox (badness 1867) in paragraph at lines 6157--6159
[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[996]
Underfull \hbox (badness 10000) in paragraph at lines 6194--6200
[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[997] [998]
Underfull \hbox (badness 7649) in paragraph at lines 6326--6329
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[999] [1000] [1001]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6530--6530
 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1002]) (./methods-pkg.tex
Chapter 7.
[1003] [1004] [1005]
Underfull \hbox (badness 10000) in paragraph at lines 278--285
[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-

Underfull \hbox (badness 7704) in paragraph at lines 278--285
\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the

Underfull \hbox (badness 10000) in paragraph at lines 278--285
\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't

Underfull \hbox (badness 5817) in paragraph at lines 278--285
\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,

Overfull \hbox (0.78088pt too wide) in paragraph at lines 278--285
\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1006] [1007] [1008] [1009] [1010] [1011]
Underfull \hbox (badness 1281) in paragraph at lines 658--667
[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
thod is de-fined uniquely when
[1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022]
[1023] [1024] [1025] [1026]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1841--1841
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1843--1843
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 

Underfull \hbox (badness 10000) in paragraph at lines 1885--1887
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1027] [1028]
Underfull \hbox (badness 10000) in paragraph at lines 2028--2033
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1029] [1030] [1031] [1032] [1033]
Underfull \hbox (badness 10000) in paragraph at lines 2382--2386
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
[1034] [1035] [1036]
Underfull \hbox (badness 3792) in paragraph at lines 2628--2631
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1037]
Underfull \hbox (badness 1194) in paragraph at lines 2659--2663
[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and

Overfull \hbox (24.78088pt too wide) in paragraph at lines 2715--2715
 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1038] [1039] [1040]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2951--2951
 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049]
Underfull \hbox (badness 10000) in paragraph at lines 3531--3535
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1050]
Underfull \hbox (badness 10000) in paragraph at lines 3637--3642
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

Overfull \hbox (28.78088pt too wide) in paragraph at lines 3645--3654
[]
[1051]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3734--3734
 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1052]
Underfull \hbox (badness 1394) in paragraph at lines 3805--3810
\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class

[1053] [1054] [1055]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4067--4067
 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1056] [1057] [1058]
Underfull \hbox (badness 10000) in paragraph at lines 4252--4254
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1059]
Underfull \hbox (badness 1629) in paragraph at lines 4354--4363
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1060]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4415--4415
 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 4416--4416
 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1061]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4473--4473
 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1062] [1063] [1064] [1065] [1066] [1067]
Underfull \hbox (badness 10000) in paragraph at lines 4945--4954
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1068]
Underfull \vbox (badness 10000) has occurred while \output is active [1069]
[1070]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5138--5138
 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5167--5167
 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier
 fails here)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5181--5181
 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1071]
[1072]
Underfull \hbox (badness 1033) in paragraph at lines 5251--5258
\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture

Underfull \hbox (badness 10000) in paragraph at lines 5325--5327
[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1073] [1074] [1075] [1076] [1077]
Underfull \hbox (badness 1087) in paragraph at lines 5619--5624
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing

Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1078]
Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1079] [1080]
Underfull \hbox (badness 10000) in paragraph at lines 5900--5916
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1081] [1082] [1083]
Underfull \hbox (badness 1248) in paragraph at lines 6186--6190
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,

Underfull \hbox (badness 1960) in paragraph at lines 6186--6190
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1084]
Underfull \hbox (badness 4647) in paragraph at lines 6274--6276
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1085]
Underfull \hbox (badness 1072) in paragraph at lines 6348--6355
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1086] [1087] [1088] [1089] [1090]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6707 \aliasA{S4}{S3Part}{S4}
                               [1091] [1092] [1093]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6948--6948
 []\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
 the S3 part:[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6953--6953
 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6983 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.6985 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.6986 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored

<to be read again> 
                   \relax 
l.6988 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.6989 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1094]
Underfull \hbox (badness 2050) in paragraph at lines 7050--7054
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing

Underfull \hbox (badness 6708) in paragraph at lines 7063--7075
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2012) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3209) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1095] [1096]
Underfull \hbox (badness 1694) in paragraph at lines 7223--7225
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
[1097]
Underfull \hbox (badness 10000) in paragraph at lines 7247--7250
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1098] [1099] [1100] [1101] [1102] [1103]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7702--7702
 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[] 
[1104] [1105]
Underfull \hbox (badness 2277) in paragraph at lines 7838--7846
[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10 
in this form is not strictly nec-es-sary be-fore call-ing

Underfull \hbox (badness 3128) in paragraph at lines 7879--7884
[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
[1106]
Underfull \hbox (badness 1052) in paragraph at lines 7916--7923
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1107] [1108] [1109] [1110]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8236--8236
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1111]
Underfull \hbox (badness 1755) in paragraph at lines 8270--8273
[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the 
method. For
[1112]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8413--8413
 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[] 
[1113] [1114] [1115] [1116] [1117]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8819--8819
 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date 
= "POSIXt"))[] 
[1118]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8832--8832
 []\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 s class, then calls the S3 print method.[] 
[1119]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8930--8930
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 8941--8941
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128]
Underfull \hbox (badness 10000) in paragraph at lines 9634--9636
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class

Underfull \hbox (badness 1852) in paragraph at lines 9642--9646
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,

Underfull \hbox (badness 1681) in paragraph at lines 9642--9646
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1129] [1130] [1131] [1132]) (./parallel-pkg.tex
Chapter 8.

Underfull \hbox (badness 2418) in paragraph at lines 15--17
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1133]
Underfull \hbox (badness 4242) in paragraph at lines 94--96
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1134] [1135]
Underfull \hbox (badness 1024) in paragraph at lines 194--197
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1136]
Underfull \hbox (badness 5077) in paragraph at lines 281--284
[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, OS X, FreeBSD, So-laris, I
rix and Win-dows.
[1137] [1138]
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1139] [1140] [1141] [1142]
Underfull \hbox (badness 1917) in paragraph at lines 702--711
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class

Underfull \hbox (badness 1178) in paragraph at lines 702--711
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1143] [1144]
Underfull \hbox (badness 10000) in paragraph at lines 839--842
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1145] [1146] [1147]
Underfull \hbox (badness 5388) in paragraph at lines 1028--1033
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1148]
Underfull \hbox (badness 10000) in paragraph at lines 1052--1060
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1088--1088
 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1149] [1150]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1203--1203
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1217--1217
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 

Underfull \hbox (badness 1577) in paragraph at lines 1246--1249
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1151]
Underfull \hbox (badness 3375) in paragraph at lines 1292--1294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1152] [1153]) (./splines-pkg.tex [1154]
Chapter 9.

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1155] [1156] [1157] [1158] [1159] [1160] [1161]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 467--467
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1162] [1163] [1164]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 678--678
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1165] [1166] [1167]) (./stats-pkg.tex [1168]
Chapter 10.
[1169]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1170] [1171] [1172] [1173] [1174]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 416--416
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 437--437
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1175] [1176] [1177] [1178] [1179] [1180]
Underfull \hbox (badness 1024) in paragraph at lines 843--845
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189]
Underfull \hbox (badness 10000) in paragraph at lines 1387--1389
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1190]
Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class

Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class

Underfull \hbox (badness 1490) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199]
Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure

Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r

Underfull \hbox (badness 1371) in paragraph at lines 2076--2081
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous

Underfull \hbox (badness 1221) in paragraph at lines 2082--2088
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-

Underfull \hbox (badness 4608) in paragraph at lines 2082--2088
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1200]
Underfull \hbox (badness 3965) in paragraph at lines 2163--2165
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1201] [1202] [1203] [1204]
Underfull \hbox (badness 1221) in paragraph at lines 2418--2423
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-

Underfull \hbox (badness 4608) in paragraph at lines 2418--2423
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1205]
Underfull \hbox (badness 3965) in paragraph at lines 2495--2497
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1206] [1207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2630--2630
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1208] [1209] [1210] [1211]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2866--2866
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1212] [1213] [1214]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3059--3061
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 3106--3106
 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 3107--3107
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1215] [1216] [1217] [1218] [1219] [1220]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3485--3485
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1221] [1222] [1223] [1224]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3755--3755
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1225] [1226] [1227] [1228] [1229]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4040--4040
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 4041--4041
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1230] [1231] [1232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4276--4276
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1233] [1234] [1235]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4439--4439
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1236]
Underfull \hbox (badness 3989) in paragraph at lines 4528--4535
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1237] [1238] [1239] [1240] [1241]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4876--4876
 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4878--4878
 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1242]
Underfull \hbox (badness 7397) in paragraph at lines 4965--4969
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever

Underfull \hbox (badness 7326) in paragraph at lines 4965--4969
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1243] [1244]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5099--5099
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 5117--5117
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1245]
Underfull \hbox (badness 2680) in paragraph at lines 5144--5146
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by

Underfull \hbox (badness 10000) in paragraph at lines 5149--5151
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1246] [1247] [1248]
Underfull \hbox (badness 1436) in paragraph at lines 5327--5332
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances

Underfull \hbox (badness 1377) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)

Underfull \hbox (badness 1448) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1249] [1250]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5513--5513
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1251]
Underfull \hbox (badness 1168) in paragraph at lines 5585--5590
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1252] [1253]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5679--5679
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1254] [1255] [1256]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5864--5864
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1257] [1258] [1259]
Underfull \hbox (badness 10000) in paragraph at lines 6027--6032
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When
[1260] [1261] [1262]
Underfull \hbox (badness 5954) in paragraph at lines 6215--6217
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1263]
Underfull \hbox (badness 2503) in paragraph at lines 6297--6300
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 5563) in paragraph at lines 6301--6303
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also

Underfull \hbox (badness 1655) in paragraph at lines 6304--6309
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,

Underfull \hbox (badness 7238) in paragraph at lines 6339--6342
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1264]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6374--6374
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6389--6389
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 6404--6404
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1265]
[1266] [1267] [1268]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6645--6645
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1269] [1270] [1271] [1272] [1273] [1274]
Underfull \hbox (badness 10000) in paragraph at lines 7012--7016
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1275]
Underfull \hbox (badness 6493) in paragraph at lines 7109--7112
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1276] [1277]
Underfull \hbox (badness 1430) in paragraph at lines 7246--7249
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tp : / / cran . r-[]project . org / web / views /
[1278] [1279] [1280] [1281] [1282] [1283]
Underfull \hbox (badness 10000) in paragraph at lines 7656--7661
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1284] [1285]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7794--7796
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1286] [1287] [1288]
Underfull \hbox (badness 1210) in paragraph at lines 8011--8013
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1289] [1290] [1291] [1292] [1293] [1294] [1295]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8455--8455
 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8477--8477
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 8480--8480
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1296] [1297]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8618--8618
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 

Underfull \hbox (badness 1859) in paragraph at lines 8655--8660
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1298] [1299] [1300] [1301] [1302]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8987--8987
 []                \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[] 
[1303] [1304] [1305]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9155--9157
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1306] [1307] [1308] [1309] [1310] [1311] [1312]
Underfull \hbox (badness 2443) in paragraph at lines 9607--9613
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1313] [1314] [1315]
Underfull \hbox (badness 10000) in paragraph at lines 9821--9824
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org /
 wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1316] [1317] [1318] [1319]
Underfull \hbox (badness 4518) in paragraph at lines 10081--10086
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1320]
Underfull \hbox (badness 4132) in paragraph at lines 10120--10124
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1321]
Underfull \hbox (badness 10000) in paragraph at lines 10223--10226
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1322] [1323] [1324]
Underfull \hbox (badness 2142) in paragraph at lines 10423--10426
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1325]
Underfull \hbox (badness 1708) in paragraph at lines 10504--10507
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1326]
Underfull \hbox (badness 10000) in paragraph at lines 10545--10551
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,

Underfull \hbox (badness 1418) in paragraph at lines 10583--10588
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1327] [1328]
Underfull \hbox (badness 2635) in paragraph at lines 10716--10719
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1329] [1330]
Underfull \hbox (badness 1694) in paragraph at lines 10883--10886
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1331]
Underfull \hbox (badness 1337) in paragraph at lines 10902--10911
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-

Underfull \hbox (badness 3049) in paragraph at lines 10902--10911
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1332]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10984--10984
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 11017--11017
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
[1333]
Underfull \hbox (badness 10000) in paragraph at lines 11030--11034
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1334] [1335] [1336] [1337] [1338]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11334--11334
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11349 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11401--11401
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1339]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11413--11413
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 

Underfull \hbox (badness 1062) in paragraph at lines 11460--11465
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-

Underfull \hbox (badness 1052) in paragraph at lines 11471--11473
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1340] [1341]
Underfull \hbox (badness 3623) in paragraph at lines 11600--11602
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1342] [1343]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11688--11688
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1344]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11781--11781
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1345]
Underfull \hbox (badness 10000) in paragraph at lines 11829--11832
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1346] [1347] [1348]
Underfull \hbox (badness 4441) in paragraph at lines 12024--12026
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

Underfull \hbox (badness 10000) in paragraph at lines 12031--12033
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1349] [1350]
Underfull \hbox (badness 2753) in paragraph at lines 12121--12123
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1351] [1352]
Underfull \hbox (badness 1292) in paragraph at lines 12246--12250
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1353]
Underfull \hbox (badness 10000) in paragraph at lines 12359--12361
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of

Underfull \hbox (badness 2894) in paragraph at lines 12365--12369
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method

Underfull \hbox (badness 1038) in paragraph at lines 12365--12369
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364]
Underfull \hbox (badness 4518) in paragraph at lines 13059--13064
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1365] [1366] [1367]
Underfull \hbox (badness 10000) in paragraph at lines 13253--13257
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1368] [1369]
Underfull \hbox (badness 6995) in paragraph at lines 13438--13440
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1370] [1371] [1372]
Underfull \hbox (badness 1163) in paragraph at lines 13586--13594
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1373]
Underfull \hbox (badness 4518) in paragraph at lines 13706--13711
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1374] [1375] [1376]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13884--13884
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 13885--13885
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1377]
Underfull \hbox (badness 10000) in paragraph at lines 13940--13943
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,

Underfull \hbox (badness 1715) in paragraph at lines 13940--13943
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1378] [1379] [1380] [1381]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14226--14226
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 14227--14227
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1382]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14277--14279
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 14320--14320
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1383] [1384] [1385] [1386] [1387] [1388] [1389]
Underfull \hbox (badness 2726) in paragraph at lines 14722--14725
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15436--15436
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1401] [1402] [1403]
Underfull \hbox (badness 1648) in paragraph at lines 15627--15629
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,

Underfull \hbox (badness 2591) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would

Underfull \hbox (badness 3930) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1404]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15705--15705
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
[1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16258--16258
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1413] [1414] [1415] [1416]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16486--16486
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1417] [1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 2772) in paragraph at lines 16922--16925
[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When

Underfull \hbox (badness 10000) in paragraph at lines 16922--16925
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1423] [1424]
Underfull \hbox (badness 2359) in paragraph at lines 17041--17043
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1425]
Underfull \vbox (badness 10000) has occurred while \output is active [1426]
Underfull \vbox (badness 10000) has occurred while \output is active [1427]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17213--17213
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1428]
Underfull \hbox (badness 10000) in paragraph at lines 17293--17297
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1429] [1430]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17373--17373
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 17420--17420
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1431]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17467--17467
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439]
Underfull \hbox (badness 1248) in paragraph at lines 17957--17960
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on

Underfull \hbox (badness 1127) in paragraph at lines 17970--17974
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 1478) in paragraph at lines 17978--17982
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and

[1440]
Underfull \hbox (badness 2042) in paragraph at lines 18031--18033
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1441]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18127--18127
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1442]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18169--18169
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
[1443]
Underfull \hbox (badness 2564) in paragraph at lines 18240--18251
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1082) in paragraph at lines 18240--18251
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18303--18303
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1445] [1446] [1447]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18518--18518
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1448]
Underfull \hbox (badness 1337) in paragraph at lines 18594--18597
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1449] [1450] [1451] [1452] [1453] [1454]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18910--18910
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1455]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 18997--18997
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 19000--19000
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1456] [1457] [1458] [1459] [1460]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19313--19313
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 

Underfull \hbox (badness 4779) in paragraph at lines 19320--19322
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

Underfull \hbox (badness 1194) in paragraph at lines 19323--19326
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1461]
Underfull \hbox (badness 1107) in paragraph at lines 19381--19383
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1462]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19436--19436
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1463]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19443--19443
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 

Underfull \hbox (badness 10000) in paragraph at lines 19492--19495
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives

Underfull \hbox (badness 10000) in paragraph at lines 19492--19495
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for

[1464]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19536--19536
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1465] [1466]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19658--19658
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1467]
Underfull \hbox (badness 10000) in paragraph at lines 19716--19718
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478]
[1479] [1480] [1481]
Underfull \hbox (badness 6859) in paragraph at lines 20681--20688
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 20692--20698
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492]
[1493] [1494] [1495] [1496] [1497] [1498]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21684--21684
 []                          \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == 
"Pr(",[] 
[1499] [1500] [1501] [1502] [1503]
Underfull \hbox (badness 1337) in paragraph at lines 22007--22013
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 1028) in paragraph at lines 22690--22693
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1514] [1515]
Underfull \hbox (badness 10000) in paragraph at lines 22800--22803
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 5091) in paragraph at lines 22800--22803
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
[1516] [1517] [1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23011--23011
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1519] [1520] [1521]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23230--23230
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1522] [1523]
Underfull \hbox (badness 10000) in paragraph at lines 23375--23378
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1524]
Underfull \hbox (badness 2134) in paragraph at lines 23426--23430
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from

Overfull \hbox (9.78043pt too wide) in paragraph at lines 23439--23439
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1525] [1526] [1527] [1528]
Underfull \hbox (badness 7667) in paragraph at lines 23692--23694
[]\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je
ct which is co-ercible to one by
[1529] [1530] [1531]
Underfull \hbox (badness 2591) in paragraph at lines 23895--23901
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
[1532] [1533] [1534] [1535] [1536] [1537]
Underfull \hbox (badness 1412) in paragraph at lines 24301--24303
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1538] [1539]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 24388--24388
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 

Underfull \hbox (badness 10000) in paragraph at lines 24443--24448
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when

Underfull \hbox (badness 2435) in paragraph at lines 24443--24448
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1540] [1541]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 24600--24600
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
[1542] [1543] [1544]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24770--24770
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1545]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24837--24837
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1546] [1547] [1548] [1549] [1550] [1551]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 25213--25213
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 

Underfull \hbox (badness 6477) in paragraph at lines 25266--25269
[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1552] [1553]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25392--25392
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 25393--25393
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1554]
Underfull \hbox (badness 2922) in paragraph at lines 25459--25464
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1555]
Underfull \hbox (badness 2922) in paragraph at lines 25521--25526
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion

Underfull \hbox (badness 3240) in paragraph at lines 25533--25537
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1556]
Underfull \hbox (badness 2922) in paragraph at lines 25578--25583
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1557]
Underfull \hbox (badness 2922) in paragraph at lines 25639--25645
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1558]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25661--25661
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 25677--25677
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1559] [1560]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 25791--25791
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 25814--25814
 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response 
and gradient[] 
[1561]
Underfull \hbox (badness 2922) in paragraph at lines 25852--25857
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1562]
Underfull \hbox (badness 2922) in paragraph at lines 25908--25913
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion

Underfull \hbox (badness 2922) in paragraph at lines 25965--25970
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1563]
Underfull \hbox (badness 2922) in paragraph at lines 26020--26025
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26041--26041
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 

Underfull \hbox (badness 6493) in paragraph at lines 26089--26094
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1565]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26115--26115
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 26117--26117
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1566] [1567] [1568] [1569] [1570] [1571] [1572]
Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1573] [1574] [1575] [1576] [1577] [1578] [1579]
Underfull \hbox (badness 3396) in paragraph at lines 27040--27042
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1580] [1581] [1582]
Underfull \hbox (badness 2237) in paragraph at lines 27217--27219
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1583] [1584]
Underfull \hbox (badness 2591) in paragraph at lines 27381--27383
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1585]
Underfull \hbox (badness 2237) in paragraph at lines 27427--27430
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1586] [1587] [1588]
Underfull \hbox (badness 3407) in paragraph at lines 27606--27610
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1589] [1590]
Underfull \hbox (badness 1337) in paragraph at lines 27739--27743
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1591] [1592]
Underfull \hbox (badness 10000) in paragraph at lines 27856--27859
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1593] [1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27985--27985
 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 28013--28013
 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1595]
Underfull \hbox (badness 1616) in paragraph at lines 28039--28042
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1596]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 28118--28118
 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1597]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 28195--28195
 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1598]
Underfull \hbox (badness 5050) in paragraph at lines 28231--28236
[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
 is re-turned. The ob-ject it-self is the re-ordered (un-less
[1599]
Underfull \hbox (badness 2205) in paragraph at lines 28281--28286
[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 28875--28875
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1608]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 28876--28876
 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1609] [1610]
Underfull \hbox (badness 1178) in paragraph at lines 29008--29010
[]\T1/ptm/m/n/10 In \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2 and ear-lier the re-
sults were \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 for fits with \T1/pcr/m/n/10 na.act
ion \T1/ptm/m/n/10 meth-ods such as
[1611] [1612]
Underfull \hbox (badness 10000) in paragraph at lines 29161--29165
[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect

Underfull \hbox (badness 1596) in paragraph at lines 29161--29165
\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at

Overfull \hbox (30.78088pt too wide) in paragraph at lines 29172--29172
 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 29173--29173
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1613] [1614]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 29299--29299
 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 29308--29308
 []\T1/pcr/m/n/9 ## where as  \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 '  \T1/pcr/m/n/9 simply first enlarges the search interval:[] 
[1615] [1616] [1617] [1618]
Underfull \hbox (badness 1337) in paragraph at lines 29524--29528
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626]
Underfull \hbox (badness 1337) in paragraph at lines 30008--30012
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1627]
Underfull \hbox (badness 5161) in paragraph at lines 30101--30103
[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1628] [1629] [1630] [1631] [1632]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30426--30426
 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 30427--30427
 []      \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F
ALSE)[] 

Underfull \hbox (badness 6775) in paragraph at lines 30465--30470
[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1633] [1634]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30531--30531
 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1635]) (./stats4-pkg.tex [1636]
Chapter 11.
[1637] [1638] [1639]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192
 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1640] [1641] [1642]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1643]
Underfull \hbox (badness 10000) in paragraph at lines 440--443
[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1644] [1645]) (./tcltk-pkg.tex [1646]
Chapter 12.
[1647] [1648] [1649] [1650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 342--342
 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1651] [1652] [1653]
Underfull \vbox (badness 10000) has occurred while \output is active [1654]
Underfull \hbox (badness 1292) in paragraph at lines 649--656
[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665]
Underfull \hbox (badness 1490) in paragraph at lines 1390--1393
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1666]) (./tools-pkg.tex
Chapter 13.
[1667]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69
 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1668]
Underfull \hbox (badness 10000) in paragraph at lines 138--140
[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
 which will be eval-u-ated via

Underfull \hbox (badness 1253) in paragraph at lines 164--167
[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1669]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215
 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1670]
Underfull \hbox (badness 5147) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12

Underfull \hbox (badness 4792) in paragraph at lines 285--298
\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-

Underfull \hbox (badness 2237) in paragraph at lines 285--298
\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1671]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370
 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 

Underfull \hbox (badness 2460) in paragraph at lines 389--391
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1672] [1673] [1674]
Underfull \hbox (badness 10000) in paragraph at lines 538--539
[][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer / 
en / opentype / glyphlist .
[1675] [1676] [1677] [1678] [1679] [1680]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 900--900
 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
[1681]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 948--948
 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1682]
Underfull \hbox (badness 1635) in paragraph at lines 1048--1050
[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1683]
Underfull \hbox (badness 5431) in paragraph at lines 1114--1117
[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to

Underfull \hbox (badness 1112) in paragraph at lines 1117--1125
\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:

Underfull \hbox (badness 3724) in paragraph at lines 1117--1125
\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1684]
Underfull \hbox (badness 1014) in paragraph at lines 1137--1139
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 10000) in paragraph at lines 1166--1169
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-

Underfull \hbox (badness 10000) in paragraph at lines 1166--1169
\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1685] [1686]
Underfull \hbox (badness 10000) in paragraph at lines 1273--1276
[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and

Underfull \hbox (badness 10000) in paragraph at lines 1294--1296
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1687] [1688] [1689]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1454--1454
 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 

Underfull \hbox (badness 7981) in paragraph at lines 1464--1468
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 1464--1468
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1690] [1691] [1692]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1666 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1693] [1694]
Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList

Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if

Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1695] [1696] [1697] [1698]
Underfull \hbox (badness 1342) in paragraph at lines 2060--2066
\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1699] [1700]
Underfull \hbox (badness 7981) in paragraph at lines 2183--2189
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 2183--2189
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1701]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2218--2218
 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
[1702] [1703] [1704] [1705] [1706] [1707] [1708]
Underfull \hbox (badness 1072) in paragraph at lines 2679--2681
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1709] [1710] [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3349--3349
 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 

Underfull \hbox (badness 10000) in paragraph at lines 3369--3371
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,

Underfull \hbox (badness 2932) in paragraph at lines 3386--3392
[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1719] [1720] [1721] [1722] [1723]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3671--3671
 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 

Underfull \hbox (badness 10000) in paragraph at lines 3682--3685
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and

Underfull \hbox (badness 6859) in paragraph at lines 3698--3703
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from

Underfull \hbox (badness 1184) in paragraph at lines 3706--3712
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he

Underfull \hbox (badness 2941) in paragraph at lines 3706--3712
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1724]
Underfull \hbox (badness 3758) in paragraph at lines 3786--3791
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-

Underfull \hbox (badness 2865) in paragraph at lines 3786--3791
\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1725] [1726]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3916--3916
 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 

Underfull \hbox (badness 1742) in paragraph at lines 3928--3940
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
[1727]
Underfull \hbox (badness 1127) in paragraph at lines 3962--3966
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from

Underfull \hbox (badness 3623) in paragraph at lines 3989--3992
[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the 
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1728] [1729] [1730]) (./utils-pkg.tex
Chapter 14.

Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1731] [1732] [1733]
Underfull \hbox (badness 1038) in paragraph at lines 197--200
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1734]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 253--253
 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1735] [1736] [1737]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 493--493
 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
[1738]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 499--499
 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 500--500
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 501--501
 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 502--502
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

Underfull \hbox (badness 10000) in paragraph at lines 536--542
[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4416) in paragraph at lines 536--542
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1739] [1740]
Underfull \hbox (badness 4505) in paragraph at lines 647--653
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1741]
Underfull \hbox (badness 1603) in paragraph at lines 764--770
\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts

Underfull \hbox (badness 3029) in paragraph at lines 764--770
\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1742]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 817--817
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1743] [1744] [1745]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1746] [1747] [1748] [1749] [1750]
Underfull \hbox (badness 1859) in paragraph at lines 1379--1388
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1751] [1752]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1506--1506
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1753] [1754]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1652--1652
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1672--1672
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL) 
[1755]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1714--1714
 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL) 
[1756] [1757]
Underfull \hbox (badness 10000) in paragraph at lines 1841--1843
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1758]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1886--1886
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 

Underfull \hbox (badness 5189) in paragraph at lines 1931--1933
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1759]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2006--2006
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1760]
Underfull \hbox (badness 1082) in paragraph at lines 2080--2084
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;

[1761]
Underfull \hbox (badness 1057) in paragraph at lines 2146--2153
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1762]
Underfull \hbox (badness 10000) in paragraph at lines 2158--2160
[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1763] [1764] [1765]
Underfull \hbox (badness 10000) in paragraph at lines 2336--2338
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1766] [1767] [1768]
Underfull \hbox (badness 10000) in paragraph at lines 2568--2571
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing

Overfull \hbox (55.10922pt too wide) in paragraph at lines 2572--2575
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 ,
[1769]
Underfull \hbox (badness 10000) in paragraph at lines 2621--2624
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set
[1770]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2693--2693
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1771]
Underfull \hbox (badness 2452) in paragraph at lines 2769--2772
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1772] [1773] [1774] [1775] [1776]
Underfull \hbox (badness 1077) in paragraph at lines 3116--3118
[]\T1/ptm/m/n/10 character vec-tor of ad-di-tional command-line ar-gu-ments for
 the \T1/pcr/m/n/10 "wget"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1072) in paragraph at lines 3155--3161
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the

Underfull \hbox (badness 1377) in paragraph at lines 3155--3161
\T1/pcr/m/n/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on th
e plat-form and scheme, but set-ting
[1777]
Underfull \hbox (badness 1057) in paragraph at lines 3180--3194
[]\T1/ptm/m/n/10 Proxies can be spec-i-fied via en-vi-ron-ment vari-ables. Set-
ting \T1/pcr/m/n/10 "no_proxy" \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "*" \T1/ptm/m/n
/10 stops

Underfull \hbox (badness 1742) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 fail-ing that, the all upper-case ver-sion) is con-sulted and if
 non-empty used as a proxy

Underfull \hbox (badness 1360) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 site. For FTP trans-fers, the user-name and pass-word on the pro
xy can be spec-i-fied by

Underfull \hbox (badness 1231) in paragraph at lines 3195--3201
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[1778]
Underfull \hbox (badness 4660) in paragraph at lines 3266--3269
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
[1779] [1780] [1781]
Underfull \hbox (badness 1565) in paragraph at lines 3472--3476
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of

Underfull \hbox (badness 10000) in paragraph at lines 3493--3499
[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1782]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3555--3555
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 

Overfull \hbox (2.55087pt too wide) in paragraph at lines 3583--3590
\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1783] [1784] [1785] [1786] [1787]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3896--3896
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1788]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3967 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.3967 ...mat Unordered and Ordered Lists}{format}
                                                   [1789] [1790] [1791]
[1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802]
[1803]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4871--4871
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1804]
Underfull \hbox (badness 10000) in paragraph at lines 4955--4957
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 http : / / www . r-[]p
roject . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1805]
Underfull \hbox (badness 1502) in paragraph at lines 5004--5009
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-

Underfull \hbox (badness 2103) in paragraph at lines 5004--5009
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1806] [1807]
Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,

Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1808] [1809]
Underfull \hbox (badness 3118) in paragraph at lines 5283--5285
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for

Underfull \hbox (badness 2409) in paragraph at lines 5316--5320
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1810] [1811]
Underfull \hbox (badness 1348) in paragraph at lines 5434--5439
[]\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages 
which these pack-

Underfull \hbox (badness 3884) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively)
. Not

Underfull \hbox (badness 1776) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 used if \T1/pcr/m/n/10 repos = NULL\T1/ptm/m/n/10 . Can also be 
a char-ac-ter vec-tor, a sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 5434--5439
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 . 

Overfull \hbox (48.30977pt too wide) in paragraph at lines 5447--5454
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")

Underfull \hbox (badness 10000) in paragraph at lines 5460--5464
[]\T1/ptm/m/n/10 Possible val-ues are (cur-rently) \T1/pcr/m/n/10 "source"\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2073) in paragraph at lines 5460--5464
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the bi-nary types
[1812]
Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed

Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1813]
Underfull \hbox (badness 1314) in paragraph at lines 5628--5635
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1814]
Underfull \hbox (badness 10000) in paragraph at lines 5649--5654
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 5670--5670
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 

Underfull \hbox (badness 5133) in paragraph at lines 5706--5710
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's

Underfull \hbox (badness 1983) in paragraph at lines 5718--5721
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1815]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5765--5765
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1816]
Underfull \hbox (badness 4132) in paragraph at lines 5796--5798
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1817] [1818]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5954--5954
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1819] [1820] [1821]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6097--6097
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1822] [1823] [1824]
Underfull \hbox (badness 10000) in paragraph at lines 6270--6272
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
[1825] [1826] [1827] [1828]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6537--6537
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1829] [1830] [1831] [1832]
Underfull \hbox (badness 10000) in paragraph at lines 6810--6812
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like

Underfull \hbox (badness 1259) in paragraph at lines 6815--6820
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
[1833] [1834]
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by

Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1835] [1836]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7088--7088
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 7089--7089
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1837] [1838] [1839] [1840]
Underfull \hbox (badness 1789) in paragraph at lines 7353--7355
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1841]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1842]
Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1843] [1844]
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1845] [1846] [1847] [1848]
Underfull \hbox (badness 5203) in paragraph at lines 7914--7917
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[1849] [1850] [1851]
Underfull \hbox (badness 1776) in paragraph at lines 8136--8143
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set

Overfull \hbox (30.78088pt too wide) in paragraph at lines 8160--8160
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1852] [1853]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8316--8316
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1854] [1855] [1856]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8491--8491
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
[1857]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8577--8577
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 8580--8580
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 8585--8585
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1858]
Underfull \hbox (badness 1077) in paragraph at lines 8656--8659
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[1859] [1860] [1861] [1862] [1863] [1864]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1865] [1866]
Underfull \hbox (badness 10000) in paragraph at lines 9181--9183
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1867] [1868]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9317
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1869] [1870]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9454--9454
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1871] [1872] [1873] [1874]
Underfull \hbox (badness 6725) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,

Underfull \hbox (badness 6428) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-

Underfull \hbox (badness 10000) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,

Underfull \hbox (badness 1997) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1875] [1876]
Underfull \hbox (badness 10000) in paragraph at lines 9820--9822
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/pt
m/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / www . gnu . org / software /
[1877] [1878] [1879]
Underfull \hbox (badness 10000) in paragraph at lines 9998--10002
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 10029--10035
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1880]
Underfull \hbox (badness 2012) in paragraph at lines 10124--10130
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use

Underfull \hbox (badness 2096) in paragraph at lines 10137--10139
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 2698) in paragraph at lines 10140--10142
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1527) in paragraph at lines 10147--10150
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1067) in paragraph at lines 10151--10154
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
[1881]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10205--10205
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 

Underfull \hbox (badness 10000) in paragraph at lines 10212--10214
[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,

Underfull \hbox (badness 1009) in paragraph at lines 10217--10228
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[1882] [1883]
Underfull \hbox (badness 2846) in paragraph at lines 10304--10314
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1884] [1885]
Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. For re-cent v
er-

Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
\T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form

Underfull \hbox (badness 10000) in paragraph at lines 10451--10454
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1886]
Underfull \hbox (badness 10000) in paragraph at lines 10504--10508
\T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son
al copy in

Underfull \hbox (badness 2158) in paragraph at lines 10524--10527
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[1887] [1888]
Underfull \hbox (badness 3333) in paragraph at lines 10704--10706
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[1889] [1890] [1891]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10865--10865
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 

Underfull \hbox (badness 5970) in paragraph at lines 10893--10896
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive

Underfull \hbox (badness 2600) in paragraph at lines 10893--10896
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less

Underfull \hbox (badness 2401) in paragraph at lines 10904--10913
[]\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/pcr/m/n/10 width \T1/ptm/m/n/1
0 ar-gu-ment's spec-i-fi-ca-tion should be fol-

Underfull \hbox (badness 2735) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 to the \T1/pcr/m/n/10 strict.width \T1/ptm/m/n/10 com-po-nent of
 op-tion \T1/pcr/m/n/10 "str" \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][
][]\T1/ptm/m/n/10 )

Underfull \hbox (badness 1859) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 which de-faults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back c
om-pat-i-bil-ity rea-sons; \T1/pcr/m/n/10 "wrap" \T1/ptm/m/n/10 uses

Underfull \hbox (badness 10000) in paragraph at lines 10904--10913
[][]\T1/pcr/m/n/10 strwrap[][][](*, width = width) \T1/ptm/m/n/10 whereas \T1/p
cr/m/n/10 "cut" \T1/ptm/m/n/10 cuts di-rectly to

Underfull \hbox (badness 1661) in paragraph at lines 10904--10913
\T1/pcr/m/n/10 width\T1/ptm/m/n/10 . Note that a small \T1/pcr/m/n/10 vec.lengt
h \T1/ptm/m/n/10 may be bet-ter than set-ting
[1892]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10948--10948
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[1893] [1894]
Underfull \hbox (badness 10000) in paragraph at lines 11072--11074
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[1895] [1896]
Underfull \hbox (badness 4492) in paragraph at lines 11226--11233
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in

Underfull \hbox (badness 6252) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file

Underfull \hbox (badness 2452) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[1897] [1898] [1899]
Underfull \hbox (badness 2020) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),

Underfull \hbox (badness 1194) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1900]
Underfull \hbox (badness 10000) in paragraph at lines 11469--11472
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ fo
rmat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .

Underfull \hbox (badness 10000) in paragraph at lines 11469--11472
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1901] [1902] [1903] [1904] [1905] [1906] [1907]
Underfull \hbox (badness 4660) in paragraph at lines 11974--11977
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to

Overfull \hbox (36.87935pt too wide) in paragraph at lines 11987--11991
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .

Underfull \hbox (badness 3557) in paragraph at lines 11993--11995
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to

Underfull \hbox (badness 1052) in paragraph at lines 11996--11998
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[1908]
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see

Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to

Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 12047--12052
[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with

Underfull \hbox (badness 10000) in paragraph at lines 12055--12058
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[1909] [1910] [1911] [1912] [1913]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12331--12331
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 

Underfull \hbox (badness 1454) in paragraph at lines 12358--12362
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[1914]
Underfull \hbox (badness 1715) in paragraph at lines 12383--12386
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 12428--12430
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion

Underfull \hbox (badness 3271) in paragraph at lines 12440--12444
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if

[1915] [1916] [1917]) [1918] [1919] [1920] (./KernSmooth-pkg.tex
Chapter 15.
[1921]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[1922] [1923] [1924] [1925] [1926]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[1927] [1928] [1929] [1930]) (./MASS-pkg.tex
Chapter 16.
[1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952]
[1953]
Underfull \hbox (badness 7256) in paragraph at lines 1601--1603
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962] [1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2409--2409
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2413--2413
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[1965] [1966] [1967] [1968]
Underfull \hbox (badness 6559) in paragraph at lines 2691--2694
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[1969] [1970] [1971]
Underfull \hbox (badness 7362) in paragraph at lines 2861--2866
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3557) in paragraph at lines 2897--2905
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if

Underfull \hbox (badness 3118) in paragraph at lines 2897--2905
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[1972] [1973]
Underfull \hbox (badness 4686) in paragraph at lines 3029--3031
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds

Underfull \hbox (badness 1515) in paragraph at lines 3043--3047
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[1974] [1975] [1976]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3224--3224
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 

Underfull \hbox (badness 5817) in paragraph at lines 3231--3233
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[1977]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3354--3354
 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988]
[1989]
Underfull \hbox (badness 1845) in paragraph at lines 4160--4162
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[1990] [1991] [1992] [1993] [1994] [1995] [1996]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4656--4656
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[1997] [1998]
Underfull \hbox (badness 10000) in paragraph at lines 4808--4811
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[1999]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4878--4878
 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 

Underfull \hbox (badness 10000) in paragraph at lines 4886--4889
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2000] [2001] [2002] [2003] [2004]
Underfull \hbox (badness 5681) in paragraph at lines 5286--5288
[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if

Underfull \hbox (badness 5022) in paragraph at lines 5290--5293
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2005]
Underfull \hbox (badness 1975) in paragraph at lines 5339--5341
[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5925--5925
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2014]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5987--5987
 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2015] [2016]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6129 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6129 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2017]
Underfull \hbox (badness 1783) in paragraph at lines 6247--6251
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2018] [2019] [2020] [2021]
Underfull \vbox (badness 10000) has occurred while \output is active [2022]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6545--6545
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2023]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6633--6633
 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2024] [2025] [2026] [2027] [2028] [2029]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7072--7072
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 7089--7089
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 

Underfull \hbox (badness 10000) in paragraph at lines 7096--7103
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2030]
Underfull \hbox (badness 10000) in paragraph at lines 7112--7114
[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat

Underfull \hbox (badness 3138) in paragraph at lines 7167--7173
[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2031]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7237--7237
 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2032] [2033]
Underfull \hbox (badness 5091) in paragraph at lines 7346--7349
\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2034] [2035]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7476--7476
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2036]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7541--7541
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2037] [2038] [2039] [2040] [2041] [2042]
Underfull \hbox (badness 4686) in paragraph at lines 7979--7981
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds

Underfull \hbox (badness 1515) in paragraph at lines 7995--7999
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2043] [2044]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8098--8098
 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 

Underfull \hbox (badness 1590) in paragraph at lines 8122--8126
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055]
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9501--9501
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2065]
Underfull \hbox (badness 1158) in paragraph at lines 9628--9631
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2066]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9710--9710
 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 9712--9712
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 9715--9715
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077]
[2078] [2079]) (./Matrix-pkg.tex [2080]
Chapter 17.

Underfull \hbox (badness 10000) in paragraph at lines 42--45
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you

Underfull \hbox (badness 10000) in paragraph at lines 42--45
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2081]
Underfull \hbox (badness 1769) in paragraph at lines 96--99
[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2082]
Underfull \hbox (badness 2229) in paragraph at lines 160--163
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is

Underfull \hbox (badness 1147) in paragraph at lines 160--163
\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2083]
Underfull \hbox (badness 10000) in paragraph at lines 258--261
[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing

Underfull \hbox (badness 10000) in paragraph at lines 264--266
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2084] [2085]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 487--487
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 

Underfull \hbox (badness 5147) in paragraph at lines 494--496
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2086]
Underfull \hbox (badness 5119) in paragraph at lines 506--510
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class

Underfull \hbox (badness 4621) in paragraph at lines 510--514
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a

Overfull \hbox (4.38043pt too wide) in paragraph at lines 533--533
 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535
 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 544--544
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2087] [2088]
Underfull \hbox (badness 3189) in paragraph at lines 681--685
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2089]
Underfull \hbox (badness 10000) in paragraph at lines 735--738
[]\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (where
as
[2090] [2091]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 873--873
 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2092]
Underfull \hbox (badness 10000) in paragraph at lines 948--950
[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-

Underfull \hbox (badness 10000) in paragraph at lines 971--976
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-

Underfull \hbox (badness 10000) in paragraph at lines 971--976
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to

Underfull \hbox (badness 1092) in paragraph at lines 971--976
\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of

Underfull \hbox (badness 10000) in paragraph at lines 994--1001
[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2093]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2094pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate i
gnored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate i
gnored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        ] [2095]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1192--1192
 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2096]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1286--1286
 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
[2097]
Underfull \hbox (badness 2277) in paragraph at lines 1314--1317
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use

Underfull \hbox (badness 1609) in paragraph at lines 1361--1365
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2098]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1388--1388
 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1402--1402
 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 

Overfull \hbox (74.58035pt too wide) in paragraph at lines 1410--1410
 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1420--1420
 []\T1/pcr/m/n/9 ## each has a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' 
\T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n
/9 matrix %% FIXME !! --- "check" them  __unfinished__[] 
[2099]
Underfull \hbox (badness 6445) in paragraph at lines 1457--1464
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",    ...) \T1/ptm/m/n/10 or

Underfull \hbox (badness 3861) in paragraph at lines 1457--1464
\T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls
 of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or

Underfull \hbox (badness 1783) in paragraph at lines 1492--1496
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend

Underfull \hbox (badness 1221) in paragraph at lines 1508--1514
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2100]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1549 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1549 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1550 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1571 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1582 \aliasA{rowSums}{colSums}{rowSums}
                                          [2101] [2102]
Underfull \hbox (badness 3547) in paragraph at lines 1757--1760
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2103] [2104] [2105] [2106]
Underfull \hbox (badness 10000) in paragraph at lines 1994--1996
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2107]
Underfull \hbox (badness 10000) in paragraph at lines 2116--2118
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =

Underfull \hbox (badness 3068) in paragraph at lines 2177--2181
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2108]
Underfull \hbox (badness 4713) in paragraph at lines 2212--2214
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2109]
Underfull \hbox (badness 10000) in paragraph at lines 2327--2330
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 2429--2433
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix",    ...)\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2429--2433
\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or

Underfull \hbox (badness 2707) in paragraph at lines 2486--2490
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
[2112]
Underfull \hbox (badness 2689) in paragraph at lines 2546--2548
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
[2113]
Underfull \hbox (badness 1097) in paragraph at lines 2572--2575
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
[2114]
Underfull \hbox (badness 3646) in paragraph at lines 2818--2821
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally

Underfull \hbox (badness 10000) in paragraph at lines 2840--2841
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :

Underfull \hbox (badness 1810) in paragraph at lines 2847--2849
[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of

Underfull \hbox (badness 10000) in paragraph at lines 2850--2852
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2115]
Underfull \hbox (badness 1371) in paragraph at lines 2857--2863
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class

Underfull \hbox (badness 10000) in paragraph at lines 2864--2868
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class

Underfull \hbox (badness 2318) in paragraph at lines 2874--2878
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2116] [2117]
Underfull \hbox (badness 1859) in paragraph at lines 3054--3056
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains

Underfull \hbox (badness 10000) in paragraph at lines 3099--3101
[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2118]
Underfull \hbox (badness 1168) in paragraph at lines 3214--3217
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2119] [2120]
Underfull \hbox (badness 4967) in paragraph at lines 3376--3380
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",    ...) \T1/ptm/m/n/10 or

Overfull \hbox (2.39853pt too wide) in paragraph at lines 3381--3383
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
[2121]
Underfull \hbox (badness 6364) in paragraph at lines 3423--3426
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2122] [2123]
Underfull \hbox (badness 10000) in paragraph at lines 3573--3578
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by

Underfull \hbox (badness 6961) in paragraph at lines 3573--3578
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class

Underfull \hbox (badness 10000) in paragraph at lines 3583--3585
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial

Underfull \hbox (badness 10000) in paragraph at lines 3585--3588
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2124]
Underfull \hbox (badness 10000) in paragraph at lines 3693--3696
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or

Underfull \hbox (badness 1735) in paragraph at lines 3693--3696
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the

Underfull \hbox (badness 10000) in paragraph at lines 3696--3699
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or

Underfull \hbox (badness 2318) in paragraph at lines 3696--3699
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2125]
Underfull \hbox (badness 6364) in paragraph at lines 3700--3703
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2126]
Underfull \hbox (badness 4060) in paragraph at lines 3817--3820
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2127]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3857--3857
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 

Underfull \hbox (badness 3635) in paragraph at lines 3923--3927
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class

Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-

Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
[2128]
Underfull \hbox (badness 10000) in paragraph at lines 3937--3941
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2129] [2130] [2131] [2132]
Underfull \hbox (badness 10000) in paragraph at lines 4225--4230
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2133] [2134]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4359--4359
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

Overfull \hbox (139.38028pt too wide) in paragraph at lines 4362--4362
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
[2135] [2136] [2137] [2138]
Underfull \hbox (badness 10000) in paragraph at lines 4670--4675
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2139]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4751--4751
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4753--4753
 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4757--4757
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 4764--4764
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2140] [2141]
Underfull \hbox (badness 4120) in paragraph at lines 4892--4895
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4921--4921
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
[2142]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4926--4926
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 4933--4933
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 4936--4936
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2143]
Underfull \hbox (badness 1817) in paragraph at lines 5024--5033
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the

Underfull \hbox (badness 5637) in paragraph at lines 5065--5067
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2144]
Underfull \hbox (badness 3138) in paragraph at lines 5091--5093
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2145]
Underfull \hbox (badness 1603) in paragraph at lines 5175--5177
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2146] [2147] [2148]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5411--5411
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
[2149]
Underfull \hbox (badness 10000) in paragraph at lines 5487--5490
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and

Overfull \hbox (9.78043pt too wide) in paragraph at lines 5498--5498
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2150]
Underfull \hbox (badness 1622) in paragraph at lines 5535--5540
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),

Underfull \hbox (badness 1418) in paragraph at lines 5535--5540
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2151] [2152]
Underfull \hbox (badness 1062) in paragraph at lines 5720--5723
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2153]
Underfull \hbox (badness 2809) in paragraph at lines 5749--5752
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2154]
Underfull \hbox (badness 2635) in paragraph at lines 5861--5866
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .

Underfull \hbox (badness 4229) in paragraph at lines 5861--5866
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class

Underfull \hbox (badness 10000) in paragraph at lines 5869--5872
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2155]
Underfull \hbox (badness 1184) in paragraph at lines 6042--6045
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2156] [2157]
Underfull \hbox (badness 10000) in paragraph at lines 6140--6143
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2158]
Underfull \hbox (badness 10000) in paragraph at lines 6215--6218
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 6231--6231
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 

Underfull \hbox (badness 2443) in paragraph at lines 6269--6275
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see

Underfull \hbox (badness 1776) in paragraph at lines 6269--6275
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
[2159]
Underfull \hbox (badness 1675) in paragraph at lines 6286--6289
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2160] [2161]
Underfull \hbox (badness 6268) in paragraph at lines 6480--6483
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2162]
Underfull \hbox (badness 5036) in paragraph at lines 6504--6508
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,

Underfull \hbox (badness 10000) in paragraph at lines 6504--6508
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2163]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6596 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 1348) in paragraph at lines 6670--6673
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing

Underfull \hbox (badness 10000) in paragraph at lines 6675--6678
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is

Underfull \hbox (badness 10000) in paragraph at lines 6675--6678
\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when

Underfull \hbox (badness 10000) in paragraph at lines 6692--6695

[2164] [2165]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn..Rpcent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6761 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.6851 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.6933 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
Underfull \hbox (badness 1881) in paragraph at lines 7015--7021
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn

Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-

Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see

Underfull \hbox (badness 5637) in paragraph at lines 7071--7076
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2166pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7076 \item[crossprod]
                        \code{signature(x = "dgeMatrix", y = "dgeMatrix")}:pdfT
eX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rd
ash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7076 \item[crossprod]
                        \code{signature(x = "dgeMatrix", y = "dgeMatrix")}:]
Underfull \hbox (badness 10000) in paragraph at lines 7080--7082
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns

Underfull \hbox (badness 10000) in paragraph at lines 7082--7084
[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns

Underfull \hbox (badness 10000) in paragraph at lines 7086--7087
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
[2167]
Underfull \hbox (badness 1062) in paragraph at lines 7203--7206
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2168]
Underfull \hbox (badness 2809) in paragraph at lines 7237--7240
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion

Underfull \hbox (badness 10000) in paragraph at lines 7289--7291
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2169]
Underfull \hbox (badness 1406) in paragraph at lines 7329--7333
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not

Underfull \hbox (badness 1019) in paragraph at lines 7329--7333
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2170] [2171]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7427--7427
 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 

Underfull \hbox (badness 2635) in paragraph at lines 7492--7497
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .

Underfull \hbox (badness 4229) in paragraph at lines 7492--7497
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class

Underfull \hbox (badness 10000) in paragraph at lines 7500--7503
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2172] [2173]
Underfull \hbox (badness 10000) in paragraph at lines 7686--7688
[]\T1/ptm/m/n/10 fast
[2174]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2175] [2176]
Underfull \hbox (badness 1184) in paragraph at lines 7971--7974
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2177]
Underfull \hbox (badness 10000) in paragraph at lines 8061--8064
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2178]
Underfull \hbox (badness 10000) in paragraph at lines 8137--8140
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 8153--8153
 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2179] [2180]
Underfull \hbox (badness 10000) in paragraph at lines 8263--8265
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use

Underfull \hbox (badness 1596) in paragraph at lines 8279--8281
[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse

Underfull \hbox (badness 1721) in paragraph at lines 8285--8289
\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2181]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8369--8369
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 8374--8374
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
[2182]
Underfull \hbox (badness 3989) in paragraph at lines 8396--8406
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should

Underfull \hbox (badness 10000) in paragraph at lines 8396--8406
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2183]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8488 \aliasA{qr}{qr-methods}{qr}
                                   [2184]
Underfull \hbox (badness 5119) in paragraph at lines 8530--8533
[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with

Overfull \hbox (36.7804pt too wide) in paragraph at lines 8550--8550
 []                  \T1/pcr/m/n/9 c1=rep(c(1,0,0), 2), c2=rep(c(0,1,0), 2), c3
=rep(c(0,0,1),2)),[] 
[2185]
Underfull \hbox (badness 10000) in paragraph at lines 8599--8605
[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of

Underfull \hbox (badness 10000) in paragraph at lines 8616--8619
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2186]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 8687--8687
 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8708--8708
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                #  wa
rning +  ~1.5 sec[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8709--8709
 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8723 ... the Reciprocal Condition Number}{rcond}
                                                   [2187] [2188]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8836--8836
 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2189] [2190] [2191]
Underfull \hbox (badness 2126) in paragraph at lines 9014--9019
[]\T1/ptm/m/n/10 the ran-dom num-ber gen-er-a-tor for the \T1/pcr/m/n/10 x \T1/
ptm/m/n/10 slot, a [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 such that

Underfull \hbox (badness 10000) in paragraph at lines 9019--9021
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
[2192] [2193]
Underfull \hbox (badness 1558) in paragraph at lines 9164--9167
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2194]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9226--9226
 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 9230--9230
 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9292 \aliasA{solve}{solve-methods}{solve}
                                           
Overfull \hbox (54.78088pt too wide) in paragraph at lines 9389--9389
 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 

Overfull \hbox (60.78088pt too wide) in paragraph at lines 9394--9394
 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2196]
Underfull \hbox (badness 6047) in paragraph at lines 9429--9441
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods

Underfull \hbox (badness 10000) in paragraph at lines 9446--9449
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via

Underfull \hbox (badness 7203) in paragraph at lines 9451--9452
[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar

Underfull \hbox (badness 7851) in paragraph at lines 9455--9462
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list

Underfull \hbox (badness 10000) in paragraph at lines 9455--9462
\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse

Underfull \hbox (badness 10000) in paragraph at lines 9468--9478
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list

Underfull \hbox (badness 2165) in paragraph at lines 9468--9478
\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-

Underfull \hbox (badness 1194) in paragraph at lines 9502--9504
[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2197]
Underfull \hbox (badness 10000) in paragraph at lines 9516--9519
[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing

Underfull \hbox (badness 10000) in paragraph at lines 9525--9526
[]\T1/ptm/m/n/10 works via

Underfull \hbox (badness 10000) in paragraph at lines 9531--9533
[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use

Underfull \hbox (badness 10000) in paragraph at lines 9535--9536
[]\T1/ptm/m/n/10 all work via

Underfull \hbox (badness 10000) in paragraph at lines 9543--9546
[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9561--9561
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 9565--9565
 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2198]
Underfull \hbox (badness 10000) in paragraph at lines 9586--9589
[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame

Underfull \hbox (badness 1648) in paragraph at lines 9614--9616
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,

Underfull \hbox (badness 10000) in paragraph at lines 9622--9625
[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)

Underfull \hbox (badness 2591) in paragraph at lines 9622--9625
\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the

Underfull \hbox (badness 10000) in paragraph at lines 9633--9637
[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for


Underfull \hbox (badness 2828) in paragraph at lines 9633--9637
\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2199]
Underfull \hbox (badness 6592) in paragraph at lines 9644--9646
[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2200]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9721--9721
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9722--9722
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9723--9723
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2201]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9804--9804
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2202]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 9900--9900
 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2203]
Underfull \hbox (badness 4621) in paragraph at lines 9937--9941
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2204]
Underfull \hbox (badness 10000) in paragraph at lines 10008--10011
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10025--10025
 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 10028--10028
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 10051--10051
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 10052--10052
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2205]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10096--10096
 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10101--10101
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2206]
Underfull \hbox (badness 10000) in paragraph at lines 10193--10201
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class

Underfull \hbox (badness 1325) in paragraph at lines 10214--10218
[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a

Underfull \hbox (badness 10000) in paragraph at lines 10244--10248
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or
[2207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10284 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2208]
Underfull \hbox (badness 1430) in paragraph at lines 10394--10396
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2209]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10420--10420
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2210]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.toe
plitz}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10559 ...toeplitz}{sparseVector-class}{toeplitz}
                                                  
Underfull \hbox (badness 2970) in paragraph at lines 10571--10577
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-

Underfull \hbox (badness 3679) in paragraph at lines 10571--10577
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 10622--10625
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2211]
Underfull \hbox (badness 10000) in paragraph at lines 10644--10647
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list

Underfull \hbox (badness 10000) in paragraph at lines 10660--10665
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or

Underfull \hbox (badness 10000) in paragraph at lines 10671--10673
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2212] [2213]
Underfull \hbox (badness 3525) in paragraph at lines 10767--10771
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
[2214]
Underfull \hbox (badness 2591) in paragraph at lines 10868--10873
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2215]
Underfull \hbox (badness 2057) in paragraph at lines 10930--10932
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2216]
Underfull \hbox (badness 6641) in paragraph at lines 10999--11002
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h

Underfull \hbox (badness 5133) in paragraph at lines 11036--11040
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in

Underfull \hbox (badness 2818) in paragraph at lines 11036--11040
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2217] [2218] [2219]
Underfull \hbox (badness 7362) in paragraph at lines 11245--11247
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
[2220]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 11283--11283
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 11284--11284
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2221] [2222]
Underfull \hbox (badness 6910) in paragraph at lines 11533--11535
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2223] [2224]) (./boot-pkg.tex
Chapter 18.
[2225] [2226] [2227] [2228] [2229] [2230] [2231]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2232]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble

Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-

Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2233]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2234]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2235]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.

Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2236]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2237]
[2238]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-

Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2239]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the

Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it

Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to

Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2240] [2241] [2242] [2243] [2244]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2245] [2246] [2247] [2248]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2249] [2250] [2251] [2252]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2253]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2254] [2255] [2256] [2257]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set

Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
[2258]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.

Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2259]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple

Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2260] [2261] [2262] [2263] [2264]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2265] [2266] [2267]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2268]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2269] [2270] [2271]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2272] [2273] [2274] [2275] [2276] [2277] [2278]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2279] [2280]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2281] [2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2284]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f

Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to

Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] [2295]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2296] [2297] [2298] [2299]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap

Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2300]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2309]
Underfull \hbox (badness 1127) in paragraph at lines 5983--6001
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2310]
Underfull \hbox (badness 2837) in paragraph at lines 6016--6019
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2311] [2312] [2313] [2314]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6301--6301
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2315] [2316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6490--6490
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 6492--6492
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2317] [2318] [2319]
Underfull \hbox (badness 1596) in paragraph at lines 6737--6741
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2320] [2321]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6897--6897
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2322] [2323] [2324] [2325] [2326] [2327] [2328] [2329]) (./class-pkg.tex
[2330]
Chapter 19.
[2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346]) (./cluster-pkg.tex
Chapter 20.
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 133--140
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible"

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 par-tic-u-larly for the case when \T1/pcr/m/n/10 par.method \T1/
ptm/m/n/10 is spec-i-fied of longer length

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 than one. The \T1/ptm/m/it/10 weighted av-er-age \T1/ptm/m/n/10 
(\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n/10 . Fur-ther, \T
1/pcr/m/n/10 method= "single" \T1/ptm/m/n/10 is

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c
(.5,.5,0,-.5)\T1/ptm/m/n/10 , and

Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 165--167
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2349]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 250--250
 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 

Overfull \hbox (63.78036pt too wide) in paragraph at lines 251--251
 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 

Overfull \hbox (63.78036pt too wide) in paragraph at lines 252--252
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2350] [2351]
Underfull \vbox (badness 7685) has occurred while \output is active [2352]
[2353]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 516--516
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 520--520
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2354]
Underfull \hbox (badness 5374) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2355] [2356]
Underfull \hbox (badness 3078) in paragraph at lines 680--683
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2357]
Underfull \hbox (badness 2941) in paragraph at lines 761--764
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
[2358]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 799--799
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see

Overfull \hbox (12.78088pt too wide) in paragraph at lines 893--893
 []\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, verbose = interactive(
), ...) 
[2360]
Underfull \hbox (badness 4872) in paragraph at lines 934--936
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
[2361]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1036--1036
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2362] [2363]
Underfull \hbox (badness 4144) in paragraph at lines 1112--1116
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2364]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1188--1188
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 1194--1194
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2365] [2366]
Underfull \hbox (badness 10000) in paragraph at lines 1394--1398
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
[2367]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1412--1412
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 1421--1421
 []         \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
 green", labels=3)[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1429--1429
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2368]
Underfull \hbox (badness 5741) in paragraph at lines 1469--1472
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2369] [2370]
Underfull \hbox (badness 5008) in paragraph at lines 1645--1653
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1736--1736
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 1755--1755
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2372] [2373] [2374] [2375] [2376]
Underfull \hbox (badness 10000) in paragraph at lines 2057--2059
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as

Underfull \hbox (badness 3179) in paragraph at lines 2081--2087
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2377] [2378]
Underfull \hbox (badness 10000) in paragraph at lines 2239--2242
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2379]
Underfull \hbox (badness 1292) in paragraph at lines 2307--2310
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2380]
Underfull \hbox (badness 6675) in paragraph at lines 2316--2318
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see

Underfull \hbox (badness 10000) in paragraph at lines 2339--2342
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,

Overfull \vbox (12.60576pt too high) has occurred while \output is active
[2381] [2382] [2383]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2546--2546
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2384] [2385] [2386]
Underfull \hbox (badness 1067) in paragraph at lines 2734--2739
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2387] [2388]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2889--2889
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2389] [2390] [2391]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3085--3085
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3086--3086
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 3153--3156
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2393]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3203--3203
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3204--3204
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 3389--3392
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for

Underfull \hbox (badness 3471) in paragraph at lines 3389--3392
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2397]
Underfull \hbox (badness 10000) in paragraph at lines 3452--3457
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2398]
Underfull \hbox (badness 1735) in paragraph at lines 3521--3523
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "twins"\T1/ptm/m/n/10 , typ
-i-cally cre-ated by ei-ther [][]\T1/pcr/m/n/10 agnes[][][]() \T1/ptm/m/n/10 or


Underfull \hbox (badness 4621) in paragraph at lines 3538--3543
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1990) in paragraph at lines 3538--3543
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider

Underfull \hbox (badness 6268) in paragraph at lines 3550--3553
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2399]
Underfull \hbox (badness 10000) in paragraph at lines 3614--3615
[]\T1/ptm/m/n/10 currently [][]$\T1/pcr/m/n/10 http : / / www . agoras . ua . a
c . be / datasets / clusplot-[]examples . tar .
[2400] [2401]
Underfull \hbox (badness 10000) in paragraph at lines 3733--3736
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2402]
Underfull \hbox (badness 10000) in paragraph at lines 3764--3767
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2403]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3817--3817
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 

Underfull \hbox (badness 2035) in paragraph at lines 3828--3830
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2404] [2405] [2406]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4021--4021
 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 4023--4023
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2407]
Underfull \hbox (badness 1946) in paragraph at lines 4052--4057
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col

Underfull \hbox (badness 1062) in paragraph at lines 4107--4109
[]\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means
 \T1/ptm/m/n/10 of sil-hou-ette widths where
[2408]
Underfull \hbox (badness 10000) in paragraph at lines 4118--4126
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by

Overfull \hbox (31.3804pt too wide) in paragraph at lines 4160--4160
 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4169--4169
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4171--4171
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 4174--4174
 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4176--4176
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
[2409]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4190--4190
 []   \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[] 
[2410] [2411] [2412] [2413] [2414] [2415] [2416]) (./codetools-pkg.tex
Chapter 21.

Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2417]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2418]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2419] [2420] [2421]) (./foreign-pkg.tex [2422]
Chapter 22.
[2423]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a

Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2424] [2425]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2426]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 293--293
 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2427] [2428] [2429]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[] 
[2430]
Underfull \hbox (badness 10000) in paragraph at lines 515--523
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2431]
Underfull \hbox (badness 7613) in paragraph at lines 533--539
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2432] [2433] [2434]
Underfull \hbox (badness 10000) in paragraph at lines 730--731


Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2435]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 816--816
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2436]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 879--879
 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 

Underfull \hbox (badness 6708) in paragraph at lines 905--908
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2437] [2438]
Underfull \hbox (badness 10000) in paragraph at lines 989--990
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .

Overfull \hbox (24.78088pt too wide) in paragraph at lines 1025--1025
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2439]
Underfull \hbox (badness 1286) in paragraph at lines 1110--1114
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2440]
Underfull \hbox (badness 10000) in paragraph at lines 1183--1189
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2441] [2442]) (./lattice-pkg.tex
Chapter 23.
[2443] [2444] [2445]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 287--287
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 291--291
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2446]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 299--299
 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 

Overfull \hbox (54.78088pt too wide) in paragraph at lines 306--306
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 

Overfull \hbox (66.78088pt too wide) in paragraph at lines 314--314
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 335--335
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 339--339
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2447]
Underfull \hbox (badness 4060) in paragraph at lines 358--370
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the

Underfull \hbox (badness 10000) in paragraph at lines 358--370
\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |

Underfull \hbox (badness 1028) in paragraph at lines 398--413
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both

Underfull \hbox (badness 10000) in paragraph at lines 414--416
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2448]
Underfull \hbox (badness 7631) in paragraph at lines 480--485
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2449] [2450]
Underfull \hbox (badness 1221) in paragraph at lines 651--659
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2451] [2452] [2453] [2454]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be

Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2455]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2456] [2457]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a

Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2458] [2459] [2460]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2461]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2462]
Underfull \vbox (badness 10000) has occurred while \output is active [2463]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 

Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2464]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to

Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
[2465]
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2466] [2467] [2468]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 

Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form

Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2469]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of

Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2470] [2471] [2472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 

Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2473] [2474] [2475]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2476] [2477]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2478]
Underfull \hbox (badness 10000) in paragraph at lines 2763--2768
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2479]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.

Underfull \hbox (badness 3058) in paragraph at lines 2793--2798
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as

Underfull \hbox (badness 6758) in paragraph at lines 2879--2883
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be


Underfull \hbox (badness 7576) in paragraph at lines 2879--2883
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also

Underfull \hbox (badness 10000) in paragraph at lines 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2480]
Underfull \hbox (badness 1609) in paragraph at lines 2937--2943
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,

Underfull \hbox (badness 2772) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-

Underfull \hbox (badness 1400) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from

Underfull \hbox (badness 2486) in paragraph at lines 2961--2965
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2481] [2482]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 3063--3063
 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 3064--3064
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 3075--3075
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 

Overfull \hbox (66.78088pt too wide) in paragraph at lines 3087--3087
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2483]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x

Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.

Underfull \hbox (badness 3058) in paragraph at lines 3145--3152
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2484] [2485] [2486] [2487]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3475--3475
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2488]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3498--3498
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2489] [2490] [2491] [2492] [2493]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2494]
Underfull \hbox (badness 10000) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .

Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2495] [2496]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4054--4054
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 

Underfull \hbox (badness 1173) in paragraph at lines 4063--4067
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in

Underfull \hbox (badness 3219) in paragraph at lines 4090--4092
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when

Underfull \hbox (badness 1728) in paragraph at lines 4107--4111
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2497]
Underfull \hbox (badness 5161) in paragraph at lines 4172--4176
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,

Underfull \hbox (badness 4913) in paragraph at lines 4172--4176
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2498] [2499]
Underfull \hbox (badness 1067) in paragraph at lines 4286--4296
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1735) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points

Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and

Underfull \hbox (badness 5231) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for

Underfull \hbox (badness 1701) in paragraph at lines 4311--4314
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4314--4316
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2500] [2501] [2502] [2503] [2504] [2505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4718--4718
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2506] [2507]
Underfull \hbox (badness 10000) in paragraph at lines 4905--4908
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2508] [2509]
Underfull \hbox (badness 1442) in paragraph at lines 5037--5040
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2510] [2511] [2512] [2513] [2514] [2515]
Underfull \hbox (badness 3646) in paragraph at lines 5369--5372
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or

Overfull \hbox (36.78088pt too wide) in paragraph at lines 5399--5399
 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 5400--5400
 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2516]
Underfull \hbox (badness 10000) in paragraph at lines 5488--5491
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

Underfull \hbox (badness 2103) in paragraph at lines 5488--5491
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing

Underfull \hbox (badness 6412) in paragraph at lines 5505--5511
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2517]
Underfull \hbox (badness 1635) in paragraph at lines 5514--5519
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2518]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5663--5663
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2519]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5677--5677
 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 5678--5678
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 5681--5681
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 5684--5684
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 5686--5686
 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 5695--5695
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 5696--5696
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 

Underfull \hbox (badness 10000) in paragraph at lines 5712--5714
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of

[2520]
Underfull \hbox (badness 2376) in paragraph at lines 5723--5725
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2521]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and

Underfull \hbox (badness 4205) in paragraph at lines 5859--5866
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to

Underfull \hbox (badness 4792) in paragraph at lines 5859--5866
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2524] [2525]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2526] [2527]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round

Underfull \hbox (badness 2486) in paragraph at lines 6275--6280
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2528] [2529]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6362--6362
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2530]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2531]
Underfull \hbox (badness 10000) in paragraph at lines 6551--6554
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The

Underfull \hbox (badness 1558) in paragraph at lines 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2532]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to

Underfull \hbox (badness 1571) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2533] [2534] [2535] [2536] [2537]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-

Underfull \hbox (badness 1715) in paragraph at lines 6957--6964
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
[2538]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7027--7027
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 7057--7060
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to

Underfull \hbox (badness 1584) in paragraph at lines 7057--7060
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2540]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2541] [2542]
Underfull \hbox (badness 2012) in paragraph at lines 7327--7330
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7373--7373
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2544] [2545]
Underfull \hbox (badness 2644) in paragraph at lines 7514--7518
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to

Underfull \hbox (badness 2772) in paragraph at lines 7527--7530
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to

Underfull \hbox (badness 4242) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly

Underfull \hbox (badness 1147) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-

Underfull \hbox (badness 2351) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-

Underfull \hbox (badness 1675) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the

Underfull \hbox (badness 1769) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2546]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597
 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7607--7607
 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2547]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668
 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 7673--7673
 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2548] [2549] [2550]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7854--7854
 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2551]
Underfull \hbox (badness 1436) in paragraph at lines 7909--7915
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for

Underfull \hbox (badness 1231) in paragraph at lines 7909--7915
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2552] [2553] [2554] [2555] [2556] [2557] [2558] [2559]
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se

Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2560] [2561]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8642--8642
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 8643--8643
 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 8655--8655
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2562]
Underfull \hbox (badness 3118) in paragraph at lines 8674--8677
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2563]
Underfull \hbox (badness 1515) in paragraph at lines 8750--8754
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2564]
Underfull \hbox (badness 6316) in paragraph at lines 8856--8861
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2565] [2566]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8963--8963
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9102--9102
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2569]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9161--9165
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,    right, left.name, right.name, condition

Overfull \hbox (104.63074pt too wide) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,    right.x, right.y, left.name
, right.x.name, right.y.name, condition
[2570] [2571] [2572] [2573] [2574] [2575] [2576]
Underfull \hbox (badness 4205) in paragraph at lines 9619--9623
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4518) in paragraph at lines 9619--9623
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 6300) in paragraph at lines 9624--9627
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2577] [2578] [2579]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2580] [2581] [2582] [2583])
(./mgcv-pkg.tex [2584]
Chapter 24.

Underfull \hbox (badness 1052) in paragraph at lines 40--42
[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term 
p-values. See
[2585] [2586]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 150--150
 []    \T1/pcr/m/n/10 chunk.size=10000,rho=0,AR.start=NULL,sparse=FALSE,cluster
=NULL,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 151--151
 []    \T1/pcr/m/n/10 gc.level=1,use.chol=FALSE,samfrac=1,drop.unused.levels=TR
UE,...)[] 
[2587]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

Underfull \hbox (badness 1043) in paragraph at lines 193--198
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2588]
Underfull \hbox (badness 2626) in paragraph at lines 248--251
[]\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of 
the form
[2589] [2590]
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2591] [2592] [2593]
Underfull \hbox (badness 2922) in paragraph at lines 521--522
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and

Underfull \hbox (badness 1158) in paragraph at lines 563--565
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2594] [2595]
Underfull \vbox (badness 10000) has occurred while \output is active [2596]
[2597] [2598] [2599] [2600]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 956--956
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 957--957
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 982--982
 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
[2601] [2602] [2603] [2604] [2605] [2606] [2607]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1382--1382
 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2608] [2609] [2610] [2611] [2612] [2613]
Underfull \hbox (badness 1221) in paragraph at lines 1743--1749
\T1/ptm/m/n/10 de-grees of free-dom (mix-tures of the two are per-mit-ted). Mul
ti-dimensional smooths are

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1758--1758
 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 1762--1762
 []    \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[] 

Underfull \hbox (badness 1142) in paragraph at lines 1783--1787
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2614]
Underfull \hbox (badness 1043) in paragraph at lines 1806--1811
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2615] [2616]
Underfull \hbox (badness 1043) in paragraph at lines 1966--1972
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2619]
Underfull \vbox (badness 10000) has occurred while \output is active [2620]
Underfull \vbox (badness 10000) has occurred while \output is active [2621]
Underfull \vbox (badness 10000) has occurred while \output is active [2622]
[2623] [2624] [2625] [2626] [2627] [2628]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2720--2720
 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2629] [2630] [2631] [2632] [2633]
Underfull \hbox (badness 5189) in paragraph at lines 3038--3042
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2634] [2635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2636]
[2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3709--3709
 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2645] [2646]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3824--3824
 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 

Underfull \hbox (badness 1142) in paragraph at lines 3855--3859
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2647] [2648] [2649]
Underfull \hbox (badness 5970) in paragraph at lines 4035--4041
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
[2650]
Underfull \vbox (badness 10000) has occurred while \output is active [2651]
[2652] [2653]
Underfull \hbox (badness 1577) in paragraph at lines 4280--4283
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment

Underfull \hbox (badness 2181) in paragraph at lines 4287--4288
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] [2662] [2663] [2664]
[2665]
Underfull \vbox (badness 10000) has occurred while \output is active [2666]
[2667] [2668]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 5234--5234
 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 5261--5261
 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2669] [2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] [2679]
[2680] [2681] [2682] [2683] [2684] [2685] [2686] [2687] [2688] [2689] [2690]
[2691] [2692] [2693]
Underfull \vbox (badness 10000) has occurred while \output is active [2694]
[2695]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3118) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2696]
Underfull \hbox (badness 10000) in paragraph at lines 6979--6982
[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,

Underfull \hbox (badness 3108) in paragraph at lines 6979--6982
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
[2697] [2698] [2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7199--7199
 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 7200--7200
 []         \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 7203--7203
 []         \T1/pcr/m/n/10 shift=0,trans=I,seWithMean=FALSE,unconditional=FALSE
,by.resids=FALSE,[] 
[2700] [2701] [2702]
Underfull \hbox (badness 1629) in paragraph at lines 7355--7360
\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
[2703] [2704] [2705]
Overfull \hbox (114.78088pt too wide) in paragraph at lines 7554--7554
 []        \T1/pcr/m/n/10 block.size=50000,newdata.guaranteed=FALSE,na.action=n
a.pass,cluster=NULL,...)[] 
[2706] [2707]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 7704--7704
 []        \T1/pcr/m/n/10 block.size=NULL,newdata.guaranteed=FALSE,na.action=na
.pass,[] 
[2708] [2709] [2710]
Underfull \vbox (badness 10000) has occurred while \output is active [2711]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7945--7945
 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
[2712]
Underfull \hbox (badness 1205) in paragraph at lines 7983--7985
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 7983--7985
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

Underfull \hbox (badness 1975) in paragraph at lines 7989--7994
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2713]
Underfull \hbox (badness 1205) in paragraph at lines 8073--8075
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 8073--8075
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2714]
Underfull \hbox (badness 10000) in paragraph at lines 8142--8145
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from

Underfull \hbox (badness 2057) in paragraph at lines 8142--8145
[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2715] [2716]
Underfull \hbox (badness 1253) in paragraph at lines 8272--8274
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2717] [2718] [2719] [2720]
Underfull \hbox (badness 1946) in paragraph at lines 8450--8457
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same

Underfull \hbox (badness 2221) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method

Underfull \hbox (badness 2042) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee

Underfull \hbox (badness 2846) in paragraph at lines 8458--8461
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:

Underfull \hbox (badness 5862) in paragraph at lines 8458--8461
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2721]
Underfull \hbox (badness 10000) in paragraph at lines 8537--8540
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9044--9044
 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 

Underfull \hbox (badness 1975) in paragraph at lines 9055--9060
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2730] [2731]
Underfull \hbox (badness 1803) in paragraph at lines 9132--9136
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .

Underfull \hbox (badness 1502) in paragraph at lines 9144--9156
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec

Underfull \hbox (badness 2401) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be

Underfull \hbox (badness 2970) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2732] [2733] [2734]
Underfull \hbox (badness 6876) in paragraph at lines 9354--9360
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
[2735]
Underfull \hbox (badness 10000) in paragraph at lines 9395--9396
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2736] [2737]
Underfull \hbox (badness 10000) in paragraph at lines 9524--9526
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term

Underfull \hbox (badness 10000) in paragraph at lines 9524--9526
\T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs",
...) \T1/ptm/m/n/10 or
[2738] [2739]
Underfull \hbox (badness 10000) in paragraph at lines 9652--9653
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2740] [2741]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9733--9733
 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9734--9734
 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 

Underfull \hbox (badness 7613) in paragraph at lines 9772--9775
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2742] [2743] [2744] [2745]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9985--9985
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2746]
Underfull \hbox (badness 10000) in paragraph at lines 10030--10032
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2747] [2748]
Underfull \hbox (badness 10000) in paragraph at lines 10138--10141
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-

Underfull \hbox (badness 3312) in paragraph at lines 10138--10141
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the

Underfull \hbox (badness 7099) in paragraph at lines 10138--10141
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2749]
Underfull \hbox (badness 10000) in paragraph at lines 10237--10243
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a

Underfull \hbox (badness 2698) in paragraph at lines 10237--10243
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2750] [2751] [2752]
Underfull \vbox (badness 10000) has occurred while \output is active [2753]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10451--10451
 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 


Overfull \hbox (58.38037pt too wide) in paragraph at lines 10453--10453
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[] 

Overfull \hbox (52.98038pt too wide) in paragraph at lines 10454--10454
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2754]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 10535--10535
 []\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[] 

Overfull \hbox (85.38034pt too wide) in paragraph at lines 10541--10541
 []          \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[] 
[2755]
Underfull \hbox (badness 10000) in paragraph at lines 10555--10563
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like

Underfull \hbox (badness 10000) in paragraph at lines 10581--10582
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2756] [2757]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 10683--10683
 []\T1/pcr/m/n/9 bk <- gam(y~s(la,lo,bs="sos",k=60),knots=list(la=dat$la[ind],l
o=dat$lo[ind]),data=dat)[] 
[2758] [2759]
Underfull \hbox (badness 3396) in paragraph at lines 10841--10846
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
[2760]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10888
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2761] [2762] [2763] [2764]
Underfull \hbox (badness 10000) in paragraph at lines 11074--11077
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-

Underfull \hbox (badness 3068) in paragraph at lines 11074--11077
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see

Underfull \hbox (badness 10000) in paragraph at lines 11107--11111
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 5652) in paragraph at lines 11107--11111
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , code[][]soap[][][], code[][]Spheri
cal.Spline[][][], [][]\T1/pcr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 ,
[2765] [2766]
Underfull \hbox (badness 2158) in paragraph at lines 11259--11259
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2767] [2768]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 11334--11334
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2769] [2770]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11468--11468
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2771] [2772]
Underfull \hbox (badness 4846) in paragraph at lines 11604--11607
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783]
[2784] [2785] [2786] [2787]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12501--12501
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2788] [2789] [2790] [2791] [2792] [2793] [2794]) (./nlme-pkg.tex
Chapter 25.
[2795]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2796]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2797] [2798] [2799] [2800] [2801]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] [2811]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1094--1094
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
Underfull \hbox (badness 10000) in paragraph at lines 1633--1636
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[2820]
Underfull \hbox (badness 3780) in paragraph at lines 1650--1652
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 2042) in paragraph at lines 1997--2003
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[2826]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2059--2059
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[2827]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2828] [2829]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[2830]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2831] [2832] [2833] [2834] [2835] [2836] [2837] [2838]
Underfull \hbox (badness 10000) in paragraph at lines 2846--2850
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849]
[2850]
Underfull \hbox (badness 6493) in paragraph at lines 3582--3590
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4348--4348
 []\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3), 
minAbsPar=0) 
[2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] [2872]
[2873] [2874]
Underfull \hbox (badness 10000) in paragraph at lines 5158--5162
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879]
Underfull \hbox (badness 10000) in paragraph at lines 5475--5479
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if

Underfull \hbox (badness 2671) in paragraph at lines 5475--5479
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2880] [2881]
Underfull \hbox (badness 10000) in paragraph at lines 5590--5593
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
Underfull \hbox (badness 2799) in paragraph at lines 6096--6102
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[2891]
Underfull \hbox (badness 7133) in paragraph at lines 6157--6161
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2892]
Underfull \hbox (badness 2057) in paragraph at lines 6241--6252
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[2893]
Underfull \hbox (badness 10000) in paragraph at lines 6305--6307
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6334--6334
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2894] [2895] [2896] [2897]
Underfull \hbox (badness 7133) in paragraph at lines 6553--6557
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2898]
Underfull \hbox (badness 10000) in paragraph at lines 6652--6658
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
[2899]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6718
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2900]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6743--6743
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2901] [2902] [2903]
Underfull \hbox (badness 10000) in paragraph at lines 6986--6993
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,

Overfull \hbox (15.18042pt too wide) in paragraph at lines 7003--7003
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 7011--7011
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
[2904]
Underfull \hbox (badness 2875) in paragraph at lines 7033--7035
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[2905] [2906] [2907]
Underfull \hbox (badness 10000) in paragraph at lines 7248--7253
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[2908] [2909]
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-

Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 1817) in paragraph at lines 7400--7408
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 
20 EM it-er-a-

Underfull \hbox (badness 3118) in paragraph at lines 7423--7426
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[2910] [2911] [2912] [2913]
Underfull \hbox (badness 3354) in paragraph at lines 7638--7640
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[2914] [2915] [2916] [2917] [2918] [2919]
Underfull \hbox (badness 1642) in paragraph at lines 8030--8052
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2920] [2921]
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (12.78088pt too wide) in paragraph at lines 8193--8193
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 

Underfull \hbox (badness 1642) in paragraph at lines 8202--8224
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2922] [2923] [2924] [2925] [2926]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8466--8466
 []\T1/pcr/m/n/10 lmeControl(maxIter, msMaxIter, tolerance, niterEM, msMaxEval,
 msTol, 

Underfull \hbox (badness 10000) in paragraph at lines 8509--8511
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2927]
Underfull \hbox (badness 1320) in paragraph at lines 8522--8526
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][] \T1/ptm/m/n/10 (those from

Overfull \hbox (9.78043pt too wide) in paragraph at lines 8544--8544
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2928] [2929] [2930]
Underfull \hbox (badness 10000) in paragraph at lines 8707--8719
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[2931] [2932] [2933] [2934] [2935] [2936] [2937] [2938] [2939]
Underfull \hbox (badness 10000) in paragraph at lines 9297--9304
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9308--9308
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[2940]
Underfull \hbox (badness 6300) in paragraph at lines 9390--9393
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[2941] [2942] [2943] [2944]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [2945]
Underfull \hbox (badness 10000) in paragraph at lines 9679--9682
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
[2946]
Underfull \hbox (badness 3108) in paragraph at lines 9727--9730
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite

Underfull \hbox (badness 2521) in paragraph at lines 9727--9730
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[2947] [2948]
Underfull \hbox (badness 2435) in paragraph at lines 9900--9905
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[2949] [2950] [2951] [2952] [2953]
Underfull \hbox (badness 7291) in paragraph at lines 10190--10192
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[2954] [2955] [2956]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10406--10406
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[2957]
Underfull \hbox (badness 1596) in paragraph at lines 10435--10461
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[2958] [2959] [2960]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10611--10611
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 10808--10810
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

Underfull \hbox (badness 1092) in paragraph at lines 10818--10821
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10840--10840
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2964] [2965] [2966]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10996--10996
 []\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool) 
[2967]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11091--11091
 []\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)[] 
[2968] [2969] [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978]
Underfull \hbox (badness 6268) in paragraph at lines 11852--11862
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[2979] [2980] [2981] [2982]
Underfull \hbox (badness 10000) in paragraph at lines 12113--12119
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[2983] [2984] [2985] [2986] [2987] [2988] [2989]
Underfull \hbox (badness 2452) in paragraph at lines 12576--12583
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[2990]
Underfull \hbox (badness 10000) in paragraph at lines 12641--12647
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001]
[3002] [3003] [3004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13593--13593
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3005]
Underfull \hbox (badness 10000) in paragraph at lines 13620--13623
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 6016) in paragraph at lines 13648--13651
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.

Underfull \hbox (badness 2653) in paragraph at lines 13648--13651
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and

Underfull \hbox (badness 1975) in paragraph at lines 13655--13658
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot

Underfull \hbox (badness 1838) in paragraph at lines 13663--13670
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner

Underfull \hbox (badness 3713) in paragraph at lines 13663--13670
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
[3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13720--13720
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 

Underfull \hbox (badness 10000) in paragraph at lines 13727--13730
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 2469) in paragraph at lines 13727--13730
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
[3007]
Underfull \hbox (badness 4582) in paragraph at lines 13755--13758
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is

Underfull \hbox (badness 2418) in paragraph at lines 13755--13758
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and

Underfull \hbox (badness 2990) in paragraph at lines 13759--13762
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3008]
Underfull \hbox (badness 10000) in paragraph at lines 13835--13838
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 1472) in paragraph at lines 13860--13867
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3009]
Underfull \hbox (badness 10000) in paragraph at lines 13929--13931
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3010] [3011] [3012] [3013]
Underfull \hbox (badness 1540) in paragraph at lines 14144--14149
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an

Underfull \hbox (badness 1215) in paragraph at lines 14191--14193
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3014] [3015] [3016] [3017] [3018]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14434--14434
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15072 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15072 ...Extract Random Effects}{random.effects}
                                                   [3028] [3029] [3030]
[3031] [3032] [3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 1009) in paragraph at lines 15729--15738
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038] [3039] [3040]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15876--15876
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3041] [3042] [3043] [3044]
Underfull \hbox (badness 10000) in paragraph at lines 16154--16172
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form

Underfull \hbox (badness 1708) in paragraph at lines 16154--16172
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3045]
Underfull \hbox (badness 10000) in paragraph at lines 16211--16217
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 1728) in paragraph at lines 16731--16734
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3054] [3055] [3056] [3057] [3058]
Underfull \hbox (badness 1867) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3059]
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063]
Underfull \hbox (badness 10000) in paragraph at lines 17375--17382
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3064] [3065] [3066] [3067] [3068] [3069] [3070]
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3071]
Underfull \hbox (badness 3579) in paragraph at lines 17942--17947
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3072]
Underfull \hbox (badness 3579) in paragraph at lines 18006--18011
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3073]
Underfull \hbox (badness 3579) in paragraph at lines 18069--18074
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3074]
Underfull \hbox (badness 1577) in paragraph at lines 18130--18132
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal

Underfull \hbox (badness 3579) in paragraph at lines 18132--18137
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3075]
Underfull \hbox (badness 3579) in paragraph at lines 18195--18200
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3076]
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3579) in paragraph at lines 18267--18272
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3077] [3078]
Underfull \hbox (badness 1009) in paragraph at lines 18416--18425
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3079] [3080] [3081]
Underfull \hbox (badness 1009) in paragraph at lines 18550--18559
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089]) (./nnet-pkg.tex
[3090]
Chapter 26.
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 

Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3092] [3093] [3094] [3095]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 383--383
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 440--440
 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 443--443
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3096]
Underfull \hbox (badness 4013) in paragraph at lines 488--491
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3097]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 523--523
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3098]) (./rpart-pkg.tex
Chapter 27.
[3099] [3100] [3101] [3102]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3103]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3104] [3105] [3106]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3107] [3108]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3109]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3110]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3111]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3112] [3113] [3114]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 

Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method

Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y

Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3115]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3116]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286
 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 

Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3117] [3118] [3119] [3120] [3121] [3122]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3123] [3124]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3125] [3126] [3127]) (./spatial-pkg.tex [3128]
Chapter 28.
[3129] [3130] [3131] [3132] [3133] [3134]
Underfull \hbox (badness 10000) in paragraph at lines 423--427

[3135] [3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145]
[3146] [3147]) (./survival-pkg.tex [3148]
Chapter 29.
[3149] [3150]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3151]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 226--226
 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 227--227
 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.267 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.267 ... Myelogenous Leukemia survival data}{aml}
                                                   [3152] [3153]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 364--364
 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 366--366
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3154]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 403--403
 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3155] [3156]
Underfull \vbox (badness 10000) has occurred while \output is active [3157]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 597--597
 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 598--598
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3158] [3159]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 741--741
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3160] [3161]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 891--891
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3162]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.957 ...herapy for Stage B/C colon cancer}{colon}
                                                   [3163] [3164] [3165]
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1747--1747
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3174] [3175]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1877--1877
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3176] [3177] [3178] [3179]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2159--2159
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 

Underfull \hbox (badness 1389) in paragraph at lines 2172--2174
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3180] [3181]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2274--2274
 []\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24)    #darken the first curve
 and add marks[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 2280--2280
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2916--2916
 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3192] [3193]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3072--3072
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3194] [3195]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3163--3163
 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3196]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3253--3253
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3197] [3198]
Underfull \hbox (badness 1852) in paragraph at lines 3401--3403
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3199] [3200]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3534--3534
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
[3201] [3202]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3694--3694
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3203]
Underfull \hbox (badness 1540) in paragraph at lines 3749--3752
[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3204]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3792--3792
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 3813--3813
 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 3815--3815
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3205] [3206]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3960--3960
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3207] [3208] [3209] [3210] [3211]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4287--4287
 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3212] [3213]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4407--4407
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 4408--4408
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3214] [3215] [3216] [3217] [3218] [3219] [3220]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4910--4910
 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3221] [3222] [3223]
Underfull \hbox (badness 10000) in paragraph at lines 5170--5179
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
[3224] [3225]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5280--5280
 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 

Underfull \hbox (badness 1038) in paragraph at lines 5322--5328
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival

Underfull \hbox (badness 3000) in paragraph at lines 5341--5343
[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3226]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5371--5371
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3227]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5457--5457
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5595
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (18.78088pt too wide) in paragraph at lines 5611--5611
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3230] [3231] [3232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5813--5813
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3233]
Underfull \hbox (badness 6332) in paragraph at lines 5917--5922
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3234] [3235]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6086--6086
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3236] [3237]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6246--6246
 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3238]
Underfull \hbox (badness 1354) in paragraph at lines 6287--6291
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3239] [3240]
Underfull \hbox (badness 2035) in paragraph at lines 6463--6470
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 6463--6470
\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1297) in paragraph at lines 6463--6470
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6524--6524
 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3242] [3243] [3244]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6682--6682
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3245] [3246]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813
 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 6816--6816
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3247] [3248] [3249] [3250]
Underfull \vbox (badness 10000) has occurred while \output is active [3251]
[3252]) (./fullrefman.ind [3253] [3254] [3255] [3256] [3257] [3258] [3259]
[3260] [3261] [3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270]
[3271] [3272]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2139--2141
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2141--2143
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2143--2145
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2145--2147
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (25.3567pt too wide) in paragraph at lines 2147--2149
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2149--2151
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2151--2153
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2153--2155
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (25.3567pt too wide) in paragraph at lines 2155--2157
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2157--2159
[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (43.3567pt too wide) in paragraph at lines 2159--2161
[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2161--2163
[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3273] [3274] [3275] [3276] [3277]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2671--2673
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2673--2675
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2675--2677
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2677--2679
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (25.3567pt too wide) in paragraph at lines 2679--2681
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2681--2683
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2683--2685
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2685--2687
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (25.3567pt too wide) in paragraph at lines 2687--2689
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
[3278]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2689--2691
[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (43.3567pt too wide) in paragraph at lines 2691--2693
[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2693--2695
[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3279]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2819--2821
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3280] [3281] [3282] [3283]
Underfull \vbox (badness 2285) has occurred while \output is active [3284]
[3285] [3286]
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3654--3656
[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3656--3658
[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3658--3660
[]\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3662--3664
[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 3664--3666
[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3666--3668
[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 3668--3670
[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3670--3672
[]\T1/pcr/m/n/10 [,Matrix,logical,missing,ANY-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 3672--3674
[]\T1/pcr/m/n/10 [,Matrix,logical,missing,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 3674--3676
[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,ANY-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 3676--3678
[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 3678--3680
[]\T1/pcr/m/n/10 [,Matrix,missing,index,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3680--3682
[]\T1/pcr/m/n/10 [,Matrix,missing,missing,ANY-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3682--3684
[]\T1/pcr/m/n/10 [,TsparseMatrix,index,index,logical-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3684--3686
[]\T1/pcr/m/n/10 [,TsparseMatrix,index,missing,logical-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3686--3688
[]\T1/pcr/m/n/10 [,TsparseMatrix,missing,index,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3690--3692
[]\T1/pcr/m/n/10 [,dMatrix,lMatrix,missing,ANY-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3692--3694
[]\T1/pcr/m/n/10 [,dMatrix,logical,missing,ANY-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 3694--3696
[]\T1/pcr/m/n/10 [,denseMatrix,index,index,logical-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3696--3698
[]\T1/pcr/m/n/10 [,denseMatrix,index,missing,logical-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 3698--3700
[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3700--3702
[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,missing-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3702--3704
[]\T1/pcr/m/n/10 [,denseMatrix,missing,index,logical-method 
[3287]
Overfull \hbox (68.8567pt too wide) in paragraph at lines 3704--3706
[]\T1/pcr/m/n/10 [,diagonalMatrix,index,index,logical-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 3706--3708
[]\T1/pcr/m/n/10 [,diagonalMatrix,index,missing,logical-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 3708--3710
[]\T1/pcr/m/n/10 [,diagonalMatrix,missing,index,logical-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 3710--3712
[]\T1/pcr/m/n/10 [,indMatrix,index,missing,logical-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 3712--3714
[]\T1/pcr/m/n/10 [,sparseMatrix,index,index,logical-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3714--3716
[]\T1/pcr/m/n/10 [,sparseMatrix,index,missing,logical-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3716--3718
[]\T1/pcr/m/n/10 [,sparseMatrix,missing,index,logical-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3718--3720
[]\T1/pcr/m/n/10 [,sparseVector,index,ANY,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3720--3722
[]\T1/pcr/m/n/10 [,sparseVector,lsparseVector,ANY,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3722--3724
[]\T1/pcr/m/n/10 [,sparseVector,nsparseVector,ANY,ANY-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3790--3792
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,Matrix,missing,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3792--3794
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3794--3796
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,sparseVector-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3796--3798
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3798--3800
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,sparseVector-method 

Overfull \hbox (140.8567pt too wide) in paragraph at lines 3800--3802
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ldenseMatrix,missing,replValue-method 

Overfull \hbox (146.8567pt too wide) in paragraph at lines 3802--3804
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,lsparseMatrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3804--3806
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,matrix,missing,replValue-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3806--3808
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3808--3810
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,sparseVector-method 

Overfull \hbox (140.8567pt too wide) in paragraph at lines 3810--3812
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ndenseMatrix,missing,replValue-method 

Overfull \hbox (146.8567pt too wide) in paragraph at lines 3812--3814
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,nsparseMatrix,missing,replValue-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 3816--3818
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,Matrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 3818--3820
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3820--3822
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,missing,Matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3822--3824
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,missing,matrix-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3824--3826
[]\T1/pcr/m/n/10 [<-,Matrix,ldenseMatrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3826--3828
[]\T1/pcr/m/n/10 [<-,Matrix,lsparseMatrix,missing,replValue-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3828--3830
[]\T1/pcr/m/n/10 [<-,Matrix,matrix,missing,replValue-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3830--3832
[]\T1/pcr/m/n/10 [<-,Matrix,missing,ANY,Matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3832--3834
[]\T1/pcr/m/n/10 [<-,Matrix,missing,ANY,matrix-method 

Underfull \vbox (badness 1824) has occurred while \output is active [3288]
Overfull \hbox (98.8567pt too wide) in paragraph at lines 3834--3836
[]\T1/pcr/m/n/10 [<-,Matrix,ndenseMatrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3836--3838
[]\T1/pcr/m/n/10 [<-,Matrix,nsparseMatrix,missing,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3838--3840
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,index,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3840--3842
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,index,sparseVector-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3842--3844
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,missing,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3844--3846
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,missing,sparseVector-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3846--3848
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,matrix,missing,replValue-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3848--3850
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,missing,index,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3850--3852
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,missing,index,sparseVector-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3852--3854
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,Matrix,missing,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3854--3856
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,index,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3856--3858
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,index,sparseVector-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3858--3860
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,missing,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3860--3862
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,missing,sparseVector-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3862--3864
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,lMatrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3864--3866
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,matrix,missing,replValue-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3866--3868
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,missing,index,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3868--3870
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,missing,index,sparseVector-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3870--3872
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,nMatrix,missing,replValue-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3872--3874
[]\T1/pcr/m/n/10 [<-,denseMatrix,index,index,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3874--3876
[]\T1/pcr/m/n/10 [<-,denseMatrix,index,missing,replValue-method 

Overfull \hbox (92.8567pt too wide) in paragraph at lines 3876--3878
[]\T1/pcr/m/n/10 [<-,denseMatrix,matrix,missing,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3878--3880
[]\T1/pcr/m/n/10 [<-,denseMatrix,missing,index,replValue-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3880--3882
[]\T1/pcr/m/n/10 [<-,denseMatrix,missing,missing,ANY-method 

Overfull \hbox (92.8567pt too wide) in paragraph at lines 3882--3884
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,replValue-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3884--3886
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,sparseMatrix-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3886--3888
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,sparseVector-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3888--3890
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,replValue-method 

Overfull \hbox (122.8567pt too wide) in paragraph at lines 3890--3892
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,sparseMatrix-method 

Overfull \hbox (122.8567pt too wide) in paragraph at lines 3892--3894
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,sparseVector-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3894--3896
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,matrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3896--3898
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,replValue-method 

Overfull \hbox (122.8567pt too wide) in paragraph at lines 3898--3900
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,sparseMatrix-method 

Overfull \hbox (122.8567pt too wide) in paragraph at lines 3900--3902
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,sparseVector-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 3902--3904
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,missing,ANY-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 3904--3906
[]\T1/pcr/m/n/10 [<-,indMatrix,index,ANY,ANY-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 3906--3908
[]\T1/pcr/m/n/10 [<-,indMatrix,missing,index,ANY-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 3908--3910
[]\T1/pcr/m/n/10 [<-,indMatrix,missing,missing,ANY-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3910--3912
[]\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,ANY,sparseMatrix-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3912--3914
[]\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,missing,sparseMatrix-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3914--3916
[]\T1/pcr/m/n/10 [<-,sparseMatrix,missing,ANY,sparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3916--3918
[]\T1/pcr/m/n/10 [<-,sparseMatrix,missing,missing,ANY-method 

Overfull \hbox (92.8567pt too wide) in paragraph at lines 3918--3920
[]\T1/pcr/m/n/10 [<-,sparseVector,index,missing,replValue-method 

Overfull \hbox (134.8567pt too wide) in paragraph at lines 3920--3922
[]\T1/pcr/m/n/10 [<-,sparseVector,sparseVector,missing,replValue-method 

Underfull \vbox (badness 1484) has occurred while \output is active [3289]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 3995--3997
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,CsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 3997--3999
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,ddenseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 3999--4001
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,diagonalMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4003--4005
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,numLike-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4023--4025
[]\T1/pcr/m/n/10 %*%,TsparseMatrix,TsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4031--4033
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,CsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 4033--4035
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4035--4037
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4037--4039
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4039--4041
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dtrMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4041--4043
[]\T1/pcr/m/n/10 %*%,denseMatrix,diagonalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4045--4047
[]\T1/pcr/m/n/10 %*%,dgeMatrix,diagonalMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4047--4049
[]\T1/pcr/m/n/10 %*%,dgeMatrix,dsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 4055--4057
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,CsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4057--4059
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,denseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4059--4061
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,dgeMatrix-method 
[3290]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4061--4063
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,diagonalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4063--4065
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,lgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4065--4067
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,matrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4067--4069
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4069--4071
[]\T1/pcr/m/n/10 %*%,dspMatrix,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4073--4075
[]\T1/pcr/m/n/10 %*%,dsparseMatrix,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4075--4077
[]\T1/pcr/m/n/10 %*%,dsparseMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4077--4079
[]\T1/pcr/m/n/10 %*%,dsyMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4083--4085
[]\T1/pcr/m/n/10 %*%,dtpMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4087--4089
[]\T1/pcr/m/n/10 %*%,dtrMatrix,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4107--4109
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,lsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4111--4113
[]\T1/pcr/m/n/10 %*%,lgeMatrix,diagonalMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4113--4115
[]\T1/pcr/m/n/10 %*%,lsparseMatrix,ldenseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4115--4117
[]\T1/pcr/m/n/10 %*%,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4123--4125
[]\T1/pcr/m/n/10 %*%,matrix,diagonalMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4141--4143
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,nsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4145--4147
[]\T1/pcr/m/n/10 %*%,nsparseMatrix,ndenseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4147--4149
[]\T1/pcr/m/n/10 %*%,nsparseMatrix,nsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4149--4151
[]\T1/pcr/m/n/10 %*%,numLike,CsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4161--4163
[]\T1/pcr/m/n/10 %*%,sparseMatrix,diagonalMatrix-method 
[3291]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4165--4167
[]\T1/pcr/m/n/10 %*%,sparseVector,sparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4173--4175
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4175--4177
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4177--4179
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ndenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4181--4183
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4183--4185
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4185--4187
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ndenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4191--4193
[]\T1/pcr/m/n/10 %%,ddiMatrix,ddenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4193--4195
[]\T1/pcr/m/n/10 %%,ddiMatrix,ldenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4195--4197
[]\T1/pcr/m/n/10 %%,ddiMatrix,ndenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4199--4201
[]\T1/pcr/m/n/10 %%,ldiMatrix,ddenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4201--4203
[]\T1/pcr/m/n/10 %%,ldiMatrix,ldenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4203--4205
[]\T1/pcr/m/n/10 %%,ldiMatrix,ndenseMatrix-method 

Underfull \vbox (badness 5022) has occurred while \output is active [3292]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 4341--4343
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ad.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3293]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4431--4433
[]\T1/pcr/m/n/10 all.equal,abIndex,abIndex-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4433--4435
[]\T1/pcr/m/n/10 all.equal,abIndex,numLike-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4437--4439
[]\T1/pcr/m/n/10 all.equal,ANY,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4439--4441
[]\T1/pcr/m/n/10 all.equal,ANY,sparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4445--4447
[]\T1/pcr/m/n/10 all.equal,numLike,abIndex-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4447--4449
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,ANY-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 4449--4451
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,sparseMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 4451--4453
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,sparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4453--4455
[]\T1/pcr/m/n/10 all.equal,sparseVector,ANY-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 4455--4457
[]\T1/pcr/m/n/10 all.equal,sparseVector,sparseMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 4457--4459
[]\T1/pcr/m/n/10 all.equal,sparseVector,sparseVector-method 
[3294]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4617--4619
[]\T1/pcr/m/n/10 Arith,CsparseMatrix,CsparseMatrix-method 
[3295]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4619--4621
[]\T1/pcr/m/n/10 Arith,CsparseMatrix,numeric-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4621--4623
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4623--4625
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,logical-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4625--4627
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,numeric-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4627--4629
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,sparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4633--4635
[]\T1/pcr/m/n/10 Arith,dgCMatrix,dgCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4639--4641
[]\T1/pcr/m/n/10 Arith,dgeMatrix,dgeMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4645--4647
[]\T1/pcr/m/n/10 Arith,dgeMatrix,sparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4657--4659
[]\T1/pcr/m/n/10 Arith,dsCMatrix,dsCMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4659--4661
[]\T1/pcr/m/n/10 Arith,dsparseMatrix,logical-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4661--4663
[]\T1/pcr/m/n/10 Arith,dsparseMatrix,numeric-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 4663--4665
[]\T1/pcr/m/n/10 Arith,dsparseVector,dsparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4665--4667
[]\T1/pcr/m/n/10 Arith,dtCMatrix,dtCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4671--4673
[]\T1/pcr/m/n/10 Arith,lgCMatrix,lgCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4673--4675
[]\T1/pcr/m/n/10 Arith,lgeMatrix,lgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4675--4677
[]\T1/pcr/m/n/10 Arith,lgTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4681--4683
[]\T1/pcr/m/n/10 Arith,logical,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4693--4695
[]\T1/pcr/m/n/10 Arith,logical,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4701--4703
[]\T1/pcr/m/n/10 Arith,lsparseMatrix,Matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4703--4705
[]\T1/pcr/m/n/10 Arith,Matrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4707--4709
[]\T1/pcr/m/n/10 Arith,Matrix,nsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4709--4711
[]\T1/pcr/m/n/10 Arith,ngeMatrix,ngeMatrix-method 

Underfull \vbox (badness 5022) has occurred while \output is active [3296]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4715--4717
[]\T1/pcr/m/n/10 Arith,nsparseMatrix,Matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4717--4719
[]\T1/pcr/m/n/10 Arith,numeric,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4719--4721
[]\T1/pcr/m/n/10 Arith,numeric,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4731--4733
[]\T1/pcr/m/n/10 Arith,numeric,dsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4741--4743
[]\T1/pcr/m/n/10 Arith,sparseVector,ddenseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4743--4745
[]\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4745--4747
[]\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 4747--4749
[]\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method 

Underfull \vbox (badness 3302) has occurred while \output is active [3297]
[3298]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5028--5030
[]\T1/pcr/m/n/10 as.vector,abIndex,character-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5030--5032
[]\T1/pcr/m/n/10 as.vector,dgCMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5032--5034
[]\T1/pcr/m/n/10 as.vector,dgeMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 5034--5036
[]\T1/pcr/m/n/10 as.vector,diagonalMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5036--5038
[]\T1/pcr/m/n/10 as.vector,dsCMatrix,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5038--5040
[]\T1/pcr/m/n/10 as.vector,ldenseMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5040--5042
[]\T1/pcr/m/n/10 as.vector,lgeMatrix,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5044--5046
[]\T1/pcr/m/n/10 as.vector,ndenseMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5046--5048
[]\T1/pcr/m/n/10 as.vector,ngeMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 5048--5050
[]\T1/pcr/m/n/10 as.vector,sparseVector,character-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5050--5052
[]\T1/pcr/m/n/10 as.vector,sparseVector,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5076--5078
[]\T1/pcr/m/n/10 aspell_write_personal_dictionary_file 
[3299] [3300] [3301] [3302]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 5576--5578
[]\T1/pcr/m/n/10 cbind2,atomicVector,ddiMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 5578--5580
[]\T1/pcr/m/n/10 cbind2,atomicVector,ldiMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5580--5582
[]\T1/pcr/m/n/10 cbind2,atomicVector,Matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 5582--5584
[]\T1/pcr/m/n/10 cbind2,ddiMatrix,atomicVector-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5586--5588
[]\T1/pcr/m/n/10 cbind2,denseMatrix,denseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 5588--5590
[]\T1/pcr/m/n/10 cbind2,denseMatrix,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5590--5592
[]\T1/pcr/m/n/10 cbind2,denseMatrix,numeric-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 5592--5594
[]\T1/pcr/m/n/10 cbind2,denseMatrix,sparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 5594--5596
[]\T1/pcr/m/n/10 cbind2,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 5596--5598
[]\T1/pcr/m/n/10 cbind2,ldiMatrix,atomicVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5602--5604
[]\T1/pcr/m/n/10 cbind2,Matrix,atomicVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 5606--5608
[]\T1/pcr/m/n/10 cbind2,matrix,denseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5616--5618
[]\T1/pcr/m/n/10 cbind2,matrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5620--5622
[]\T1/pcr/m/n/10 cbind2,numeric,denseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5622--5624
[]\T1/pcr/m/n/10 cbind2,numeric,sparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 5624--5626
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,denseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 5626--5628
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5628--5630
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5630--5632
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 5632--5634
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method 
[3303]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 5789--5791
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 

Underfull \vbox (badness 1484) has occurred while \output is active [3304]
[3305]
Underfull \vbox (badness 1019) has occurred while \output is active [3306]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 6155--6157
[]\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6157--6159
[]\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6159--6161
[]\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6165--6167
[]\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6167--6169
[]\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6171--6173
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,denseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6173--6175
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,lMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6175--6177
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,lsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6177--6179
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.coo-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6179--6181
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.csc-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6181--6183
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.csr-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6183--6185
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,nMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6185--6187
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,nsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6187--6189
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,sparseVector-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 6189--6191
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,symmetricMatrix-method 
[3307]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 6191--6193
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,TsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6193--6195
[]\T1/pcr/m/n/10 coerce,ddenseMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6195--6197
[]\T1/pcr/m/n/10 coerce,ddenseMatrix,matrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6197--6199
[]\T1/pcr/m/n/10 coerce,ddiMatrix,CsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6199--6201
[]\T1/pcr/m/n/10 coerce,ddiMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6201--6203
[]\T1/pcr/m/n/10 coerce,ddiMatrix,dgeMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6203--6205
[]\T1/pcr/m/n/10 coerce,ddiMatrix,dsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6205--6207
[]\T1/pcr/m/n/10 coerce,ddiMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6207--6209
[]\T1/pcr/m/n/10 coerce,ddiMatrix,triangularMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6209--6211
[]\T1/pcr/m/n/10 coerce,ddiMatrix,TsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6211--6213
[]\T1/pcr/m/n/10 coerce,denseMatrix,CsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6213--6215
[]\T1/pcr/m/n/10 coerce,denseMatrix,generalMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6215--6217
[]\T1/pcr/m/n/10 coerce,denseMatrix,RsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6217--6219
[]\T1/pcr/m/n/10 coerce,denseMatrix,sparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6219--6221
[]\T1/pcr/m/n/10 coerce,denseMatrix,symmetricMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6221--6223
[]\T1/pcr/m/n/10 coerce,denseMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6223--6225
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6225--6227
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6227--6229
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6229--6231
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dtCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6231--6233
[]\T1/pcr/m/n/10 coerce,dgCMatrix,lgCMatrix-method 

Underfull \vbox (badness 5022) has occurred while \output is active
Overfull \hbox (14.8567pt too wide) in paragraph at lines 6235--6237
[]\T1/pcr/m/n/10 coerce,dgCMatrix,matrix.csc-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6237--6239
[]\T1/pcr/m/n/10 coerce,dgCMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6241--6243
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6243--6245
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6245--6247
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6247--6249
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6249--6251
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6251--6253
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6253--6255
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6255--6257
[]\T1/pcr/m/n/10 coerce,dgeMatrix,lgeMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6259--6261
[]\T1/pcr/m/n/10 coerce,dgeMatrix,triangularMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6261--6263
[]\T1/pcr/m/n/10 coerce,dgRMatrix,matrix.csr-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6263--6265
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6265--6267
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6267--6269
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6269--6271
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dtCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6271--6273
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dtTMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 6273--6275
[]\T1/pcr/m/n/10 coerce,dgTMatrix,graphNEL-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6277--6279
[]\T1/pcr/m/n/10 coerce,dgTMatrix,matrix.coo-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6279--6281
[]\T1/pcr/m/n/10 coerce,dgTMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6281--6283
[]\T1/pcr/m/n/10 coerce,dgTMatrix,triangularMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6283--6285
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,denseMatrix-method 
[3308]
Overfull \hbox (62.8567pt too wide) in paragraph at lines 6285--6287
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,generalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6287--6289
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6289--6291
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,nMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 6291--6293
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,nsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6293--6295
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,sparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6299--6301
[]\T1/pcr/m/n/10 coerce,dpoMatrix,corMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6301--6303
[]\T1/pcr/m/n/10 coerce,dpoMatrix,dppMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6307--6309
[]\T1/pcr/m/n/10 coerce,dppMatrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6309--6311
[]\T1/pcr/m/n/10 coerce,dppMatrix,dpoMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6315--6317
[]\T1/pcr/m/n/10 coerce,dppMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6317--6319
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6319--6321
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6321--6323
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6323--6325
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsRMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6325--6327
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6327--6329
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsyMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6329--6331
[]\T1/pcr/m/n/10 coerce,dsCMatrix,generalMatrix-method 

Underfull \vbox (badness 3769) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6331--6333
[]\T1/pcr/m/n/10 coerce,dsCMatrix,lsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6335--6337
[]\T1/pcr/m/n/10 coerce,dsCMatrix,nsCMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6339--6341
[]\T1/pcr/m/n/10 coerce,dsparseMatrix,matrix.csr-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6341--6343
[]\T1/pcr/m/n/10 coerce,dspMatrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6343--6345
[]\T1/pcr/m/n/10 coerce,dspMatrix,dpoMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6345--6347
[]\T1/pcr/m/n/10 coerce,dspMatrix,dppMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6347--6349
[]\T1/pcr/m/n/10 coerce,dspMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6349--6351
[]\T1/pcr/m/n/10 coerce,dspMatrix,lspMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6353--6355
[]\T1/pcr/m/n/10 coerce,dspMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6355--6357
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6357--6359
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6359--6361
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6361--6363
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6363--6365
[]\T1/pcr/m/n/10 coerce,dsTMatrix,lsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6367--6369
[]\T1/pcr/m/n/10 coerce,dsyMatrix,corMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6369--6371
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dpoMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6371--6373
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6373--6375
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6375--6377
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6377--6379
[]\T1/pcr/m/n/10 coerce,dsyMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6381--6383
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgCMatrix-method 
[3309]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6383--6385
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6385--6387
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6387--6389
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6389--6391
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtRMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6391--6393
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6393--6395
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6395--6397
[]\T1/pcr/m/n/10 coerce,dtCMatrix,ltCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6399--6401
[]\T1/pcr/m/n/10 coerce,dtCMatrix,ntCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6401--6403
[]\T1/pcr/m/n/10 coerce,dtCMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6403--6405
[]\T1/pcr/m/n/10 coerce,dtpMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6405--6407
[]\T1/pcr/m/n/10 coerce,dtpMatrix,dtTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6407--6409
[]\T1/pcr/m/n/10 coerce,dtpMatrix,ltpMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6411--6413
[]\T1/pcr/m/n/10 coerce,dtrMatrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6413--6415
[]\T1/pcr/m/n/10 coerce,dtrMatrix,dtpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6415--6417
[]\T1/pcr/m/n/10 coerce,dtrMatrix,ltrMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6419--6421
[]\T1/pcr/m/n/10 coerce,dtrMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6421--6423
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6423--6425
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6425--6427
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dtCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6427--6429
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dtrMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6429--6431
[]\T1/pcr/m/n/10 coerce,dtTMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6435--6437
[]\T1/pcr/m/n/10 coerce,factor,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6437--6439
[]\T1/pcr/m/n/10 coerce,graph,CsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 6441--6443
[]\T1/pcr/m/n/10 coerce,graph,sparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6443--6445
[]\T1/pcr/m/n/10 coerce,graphAM,sparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6445--6447
[]\T1/pcr/m/n/10 coerce,graphNEL,CsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 6447--6449
[]\T1/pcr/m/n/10 coerce,graphNEL,dsCMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6449--6451
[]\T1/pcr/m/n/10 coerce,graphNEL,TsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6451--6453
[]\T1/pcr/m/n/10 coerce,indMatrix,CsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6455--6457
[]\T1/pcr/m/n/10 coerce,indMatrix,dsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6459--6461
[]\T1/pcr/m/n/10 coerce,indMatrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6463--6465
[]\T1/pcr/m/n/10 coerce,indMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6465--6467
[]\T1/pcr/m/n/10 coerce,indMatrix,ngTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6469--6471
[]\T1/pcr/m/n/10 coerce,indMatrix,nsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6471--6473
[]\T1/pcr/m/n/10 coerce,indMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6477--6479
[]\T1/pcr/m/n/10 coerce,ldenseMatrix,matrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6479--6481
[]\T1/pcr/m/n/10 coerce,ldiMatrix,CsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6481--6483
[]\T1/pcr/m/n/10 coerce,ldiMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6483--6485
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lgCMatrix-method 
[3310]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6485--6487
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lgTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6487--6489
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6489--6491
[]\T1/pcr/m/n/10 coerce,ldiMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6491--6493
[]\T1/pcr/m/n/10 coerce,ldiMatrix,triangularMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6493--6495
[]\T1/pcr/m/n/10 coerce,ldiMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6495--6497
[]\T1/pcr/m/n/10 coerce,lgCMatrix,dgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6497--6499
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6499--6501
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6501--6503
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6503--6505
[]\T1/pcr/m/n/10 coerce,lgCMatrix,ltCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6507--6509
[]\T1/pcr/m/n/10 coerce,lgeMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6509--6511
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6511--6513
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6513--6515
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6515--6517
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6517--6519
[]\T1/pcr/m/n/10 coerce,lgeMatrix,ltpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6519--6521
[]\T1/pcr/m/n/10 coerce,lgeMatrix,ltrMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6523--6525
[]\T1/pcr/m/n/10 coerce,lgeMatrix,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6525--6527
[]\T1/pcr/m/n/10 coerce,lgTMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6527--6529
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6529--6531
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6531--6533
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6533--6535
[]\T1/pcr/m/n/10 coerce,lgTMatrix,ltTMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6537--6539
[]\T1/pcr/m/n/10 coerce,lgTMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6539--6541
[]\T1/pcr/m/n/10 coerce,lgTMatrix,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6551--6553
[]\T1/pcr/m/n/10 coerce,lsCMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6553--6555
[]\T1/pcr/m/n/10 coerce,lsCMatrix,dsCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6555--6557
[]\T1/pcr/m/n/10 coerce,lsCMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6557--6559
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6559--6561
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6561--6563
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lsTMatrix-method 
[3311]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 6565--6567
[]\T1/pcr/m/n/10 coerce,lsparseMatrix,dsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6567--6569
[]\T1/pcr/m/n/10 coerce,lsparseMatrix,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6569--6571
[]\T1/pcr/m/n/10 coerce,lspMatrix,dspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6571--6573
[]\T1/pcr/m/n/10 coerce,lspMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6573--6575
[]\T1/pcr/m/n/10 coerce,lspMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6575--6577
[]\T1/pcr/m/n/10 coerce,lsTMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6577--6579
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6579--6581
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6581--6583
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6583--6585
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6587--6589
[]\T1/pcr/m/n/10 coerce,lsyMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6589--6591
[]\T1/pcr/m/n/10 coerce,lsyMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6591--6593
[]\T1/pcr/m/n/10 coerce,lsyMatrix,lspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6595--6597
[]\T1/pcr/m/n/10 coerce,ltCMatrix,dtCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6597--6599
[]\T1/pcr/m/n/10 coerce,ltCMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6599--6601
[]\T1/pcr/m/n/10 coerce,ltCMatrix,ltTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6603--6605
[]\T1/pcr/m/n/10 coerce,ltpMatrix,dtpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6605--6607
[]\T1/pcr/m/n/10 coerce,ltpMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6607--6609
[]\T1/pcr/m/n/10 coerce,ltpMatrix,ltrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6609--6611
[]\T1/pcr/m/n/10 coerce,ltrMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6611--6613
[]\T1/pcr/m/n/10 coerce,ltrMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6613--6615
[]\T1/pcr/m/n/10 coerce,ltrMatrix,ltpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6615--6617
[]\T1/pcr/m/n/10 coerce,ltTMatrix,dtTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6617--6619
[]\T1/pcr/m/n/10 coerce,ltTMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6619--6621
[]\T1/pcr/m/n/10 coerce,ltTMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6621--6623
[]\T1/pcr/m/n/10 coerce,ltTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6623--6625
[]\T1/pcr/m/n/10 coerce,ltTMatrix,ltCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6625--6627
[]\T1/pcr/m/n/10 coerce,ltTMatrix,ltrMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6635--6637
[]\T1/pcr/m/n/10 coerce,Matrix,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6637--6639
[]\T1/pcr/m/n/10 coerce,matrix,CsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 6639--6641
[]\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method 
[3312]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 6649--6651
[]\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6651--6653
[]\T1/pcr/m/n/10 coerce,matrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6681--6683
[]\T1/pcr/m/n/10 coerce,matrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6711--6713
[]\T1/pcr/m/n/10 coerce,matrix,ndenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6737--6739
[]\T1/pcr/m/n/10 coerce,matrix,RsparseMatrix-method 

Underfull \vbox (badness 4328) has occurred while \output is active [3313]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6739--6741
[]\T1/pcr/m/n/10 coerce,Matrix,sparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6741--6743
[]\T1/pcr/m/n/10 coerce,matrix,symmetricMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6743--6745
[]\T1/pcr/m/n/10 coerce,Matrix,TsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6745--6747
[]\T1/pcr/m/n/10 coerce,matrix,TsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6749--6751
[]\T1/pcr/m/n/10 coerce,matrix.coo,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6751--6753
[]\T1/pcr/m/n/10 coerce,matrix.coo,dgCMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6753--6755
[]\T1/pcr/m/n/10 coerce,matrix.coo,dgTMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6757--6759
[]\T1/pcr/m/n/10 coerce,matrix.coo,TsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6759--6761
[]\T1/pcr/m/n/10 coerce,matrix.csc,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6761--6763
[]\T1/pcr/m/n/10 coerce,matrix.csc,dgCMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6765--6767
[]\T1/pcr/m/n/10 coerce,matrix.csc,TsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6767--6769
[]\T1/pcr/m/n/10 coerce,matrix.csr,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6769--6771
[]\T1/pcr/m/n/10 coerce,matrix.csr,dgCMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6771--6773
[]\T1/pcr/m/n/10 coerce,matrix.csr,dgRMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6775--6777
[]\T1/pcr/m/n/10 coerce,matrix.csr,RsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6777--6779
[]\T1/pcr/m/n/10 coerce,matrix.csr,TsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6779--6781
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,CsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6781--6783
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6783--6785
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6785--6787
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,sparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6787--6789
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,TsparseMatrix-method 

Underfull \vbox (badness 2903) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6789--6791
[]\T1/pcr/m/n/10 coerce,ngCMatrix,dgCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6793--6795
[]\T1/pcr/m/n/10 coerce,ngCMatrix,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6795--6797
[]\T1/pcr/m/n/10 coerce,ngCMatrix,lgCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6799--6801
[]\T1/pcr/m/n/10 coerce,ngCMatrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6803--6805
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6805--6807
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ngTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6807--6809
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ntCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6809--6811
[]\T1/pcr/m/n/10 coerce,ngeMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6811--6813
[]\T1/pcr/m/n/10 coerce,ngeMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6815--6817
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6817--6819
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ngTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6819--6821
[]\T1/pcr/m/n/10 coerce,ngeMatrix,nspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6821--6823
[]\T1/pcr/m/n/10 coerce,ngeMatrix,nsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6823--6825
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ntpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6825--6827
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ntrMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6827--6829
[]\T1/pcr/m/n/10 coerce,ngeMatrix,triangularMatrix-method 
[3314]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6829--6831
[]\T1/pcr/m/n/10 coerce,ngTMatrix,dgTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6833--6835
[]\T1/pcr/m/n/10 coerce,ngTMatrix,dsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6835--6837
[]\T1/pcr/m/n/10 coerce,ngTMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6837--6839
[]\T1/pcr/m/n/10 coerce,ngTMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6839--6841
[]\T1/pcr/m/n/10 coerce,ngTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6845--6847
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6847--6849
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6849--6851
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ntTMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6851--6853
[]\T1/pcr/m/n/10 coerce,ngTMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6853--6855
[]\T1/pcr/m/n/10 coerce,ngTMatrix,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6867--6869
[]\T1/pcr/m/n/10 coerce,nsCMatrix,dsCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6869--6871
[]\T1/pcr/m/n/10 coerce,nsCMatrix,dsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6871--6873
[]\T1/pcr/m/n/10 coerce,nsCMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6875--6877
[]\T1/pcr/m/n/10 coerce,nsCMatrix,lsCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6877--6879
[]\T1/pcr/m/n/10 coerce,nsCMatrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6881--6883
[]\T1/pcr/m/n/10 coerce,nsCMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6883--6885
[]\T1/pcr/m/n/10 coerce,nsCMatrix,nsTMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6885--6887
[]\T1/pcr/m/n/10 coerce,nsparseMatrix,dsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6887--6889
[]\T1/pcr/m/n/10 coerce,nsparseVector,dsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6889--6891
[]\T1/pcr/m/n/10 coerce,nsparseVector,isparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6891--6893
[]\T1/pcr/m/n/10 coerce,nsparseVector,lsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6893--6895
[]\T1/pcr/m/n/10 coerce,nsparseVector,zsparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6895--6897
[]\T1/pcr/m/n/10 coerce,nspMatrix,dspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6897--6899
[]\T1/pcr/m/n/10 coerce,nspMatrix,lspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6899--6901
[]\T1/pcr/m/n/10 coerce,nspMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6901--6903
[]\T1/pcr/m/n/10 coerce,nspMatrix,nsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6903--6905
[]\T1/pcr/m/n/10 coerce,nsTMatrix,dsTMatrix-method 
[3315]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6907--6909
[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6909--6911
[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6911--6913
[]\T1/pcr/m/n/10 coerce,nsTMatrix,nsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6913--6915
[]\T1/pcr/m/n/10 coerce,nsTMatrix,nsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6915--6917
[]\T1/pcr/m/n/10 coerce,nsyMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6917--6919
[]\T1/pcr/m/n/10 coerce,nsyMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6919--6921
[]\T1/pcr/m/n/10 coerce,nsyMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6921--6923
[]\T1/pcr/m/n/10 coerce,nsyMatrix,nspMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6925--6927
[]\T1/pcr/m/n/10 coerce,ntCMatrix,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6927--6929
[]\T1/pcr/m/n/10 coerce,ntCMatrix,dtCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6931--6933
[]\T1/pcr/m/n/10 coerce,ntCMatrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6933--6935
[]\T1/pcr/m/n/10 coerce,ntCMatrix,ltCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6937--6939
[]\T1/pcr/m/n/10 coerce,ntCMatrix,ngCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6939--6941
[]\T1/pcr/m/n/10 coerce,ntCMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6941--6943
[]\T1/pcr/m/n/10 coerce,ntpMatrix,dtpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6943--6945
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ltpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6945--6947
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6947--6949
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ntrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6949--6951
[]\T1/pcr/m/n/10 coerce,ntrMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6951--6953
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ltrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6953--6955
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6955--6957
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ntpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6957--6959
[]\T1/pcr/m/n/10 coerce,ntTMatrix,dtTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6959--6961
[]\T1/pcr/m/n/10 coerce,ntTMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6963--6965
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6965--6967
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ngTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6967--6969
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ntCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6969--6971
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ntrMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6973--6975
[]\T1/pcr/m/n/10 coerce,numeric,CsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6981--6983
[]\T1/pcr/m/n/10 coerce,numeric,TsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6987--6989
[]\T1/pcr/m/n/10 coerce,pBunchKaufman,lMatrix-method 

Underfull \vbox (badness 4328) has occurred while \output is active [3316]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 6991--6993
[]\T1/pcr/m/n/10 coerce,pMatrix,CsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6995--6997
[]\T1/pcr/m/n/10 coerce,pMatrix,dsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7007--7009
[]\T1/pcr/m/n/10 coerce,pMatrix,nsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7009--7011
[]\T1/pcr/m/n/10 coerce,pMatrix,TsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7011--7013
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,CsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7013--7015
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,denseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7015--7017
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dgeMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7017--7019
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7019--7021
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7021--7023
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,generalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7023--7025
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,lMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7025--7027
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,lsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7027--7029
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,matrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7029--7031
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,nMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7031--7033
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,nsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7033--7035
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,TsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7039--7041
[]\T1/pcr/m/n/10 coerce,sparseMatrix,generalMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 7041--7043
[]\T1/pcr/m/n/10 coerce,sparseMatrix,graph-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7043--7045
[]\T1/pcr/m/n/10 coerce,sparseMatrix,graphNEL-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7045--7047
[]\T1/pcr/m/n/10 coerce,sparseMatrix,indMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7047--7049
[]\T1/pcr/m/n/10 coerce,sparseMatrix,pMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7049--7051
[]\T1/pcr/m/n/10 coerce,sparseMatrix,RsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7051--7053
[]\T1/pcr/m/n/10 coerce,sparseMatrix,sparseVector-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 7053--7055
[]\T1/pcr/m/n/10 coerce,sparseMatrix,symmetricMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7055--7057
[]\T1/pcr/m/n/10 coerce,sparseMatrix,triangularMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7057--7059
[]\T1/pcr/m/n/10 coerce,sparseVector,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7059--7061
[]\T1/pcr/m/n/10 coerce,sparseVector,integer-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7061--7063
[]\T1/pcr/m/n/10 coerce,sparseVector,logical-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7063--7065
[]\T1/pcr/m/n/10 coerce,sparseVector,Matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7065--7067
[]\T1/pcr/m/n/10 coerce,sparseVector,numeric-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7067--7069
[]\T1/pcr/m/n/10 coerce,sparseVector,sparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7069--7071
[]\T1/pcr/m/n/10 coerce,sparseVector,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7071--7073
[]\T1/pcr/m/n/10 coerce,sparseVector,vector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 7073--7075
[]\T1/pcr/m/n/10 coerce,table,sparseMatrix-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 7075--7077
[]\T1/pcr/m/n/10 coerce,triangularMatrix,symmetricMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7077--7079
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,CsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7079--7081
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,graphNEL-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7081--7083
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,lMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7083--7085
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,lsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7085--7087
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,matrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7087--7089
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,nMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7089--7091
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,nsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7091--7093
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,sparseVector-method 

Underfull \vbox (badness 2903) has occurred while \output is active [3317]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7093--7095
[]\T1/pcr/m/n/10 coerce,xsparseVector,dsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7095--7097
[]\T1/pcr/m/n/10 coerce,xsparseVector,isparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7097--7099
[]\T1/pcr/m/n/10 coerce,xsparseVector,lsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7099--7101
[]\T1/pcr/m/n/10 coerce,xsparseVector,nsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7101--7103
[]\T1/pcr/m/n/10 coerce,xsparseVector,zsparseVector-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 7210--7212
[]\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method 
[3318]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7216--7218
[]\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 7228--7230
[]\T1/pcr/m/n/10 Compare,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7230--7232
[]\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 7244--7246
[]\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method 
[3319] [3320]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7570--7572
[]\T1/pcr/m/n/10 crossprod,ANY,TsparseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7572--7574
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7574--7576
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,ddenseMatrix-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 7576--7578
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,diagonalMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7578--7580
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,matrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7580--7582
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,missing-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7582--7584
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,numLike-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7584--7586
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,CsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7586--7588
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,dgCMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7588--7590
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,dsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7590--7592
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7592--7594
[]\T1/pcr/m/n/10 crossprod,dgCMatrix,dgeMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7594--7596
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,dgeMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7596--7598
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7598--7600
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7600--7602
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7602--7604
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,numLike-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 7604--7606
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,CsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7606--7608
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,dgeMatrix-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 7608--7610
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,diagonalMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7610--7612
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,lgeMatrix-method 
[3321]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7612--7614
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7614--7616
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,missing-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7616--7618
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7618--7620
[]\T1/pcr/m/n/10 crossprod,dsparseMatrix,ddenseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7620--7622
[]\T1/pcr/m/n/10 crossprod,dsparseMatrix,dgeMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7622--7624
[]\T1/pcr/m/n/10 crossprod,dtpMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7624--7626
[]\T1/pcr/m/n/10 crossprod,dtpMatrix,matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7626--7628
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,ddenseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7628--7630
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7630--7632
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7632--7634
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7634--7636
[]\T1/pcr/m/n/10 crossprod,indMatrix,indMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7636--7638
[]\T1/pcr/m/n/10 crossprod,indMatrix,Matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7638--7640
[]\T1/pcr/m/n/10 crossprod,indMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7640--7642
[]\T1/pcr/m/n/10 crossprod,indMatrix,missing-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7642--7644
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,lsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7644--7646
[]\T1/pcr/m/n/10 crossprod,lgCMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7646--7648
[]\T1/pcr/m/n/10 crossprod,lgTMatrix,missing-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7648--7650
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,ldenseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7650--7652
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7652--7654
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7658--7660
[]\T1/pcr/m/n/10 crossprod,matrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7660--7662
[]\T1/pcr/m/n/10 crossprod,matrix,dgeMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7672--7674
[]\T1/pcr/m/n/10 crossprod,Matrix,sparseVector-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7674--7676
[]\T1/pcr/m/n/10 crossprod,Matrix,TsparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7676--7678
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,nsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7678--7680
[]\T1/pcr/m/n/10 crossprod,ngCMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7680--7682
[]\T1/pcr/m/n/10 crossprod,ngTMatrix,missing-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7682--7684
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,missing-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7684--7686
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,ndenseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7686--7688
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,nsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7690--7692
[]\T1/pcr/m/n/10 crossprod,numLike,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7692--7694
[]\T1/pcr/m/n/10 crossprod,numLike,dgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 7700--7702
[]\T1/pcr/m/n/10 crossprod,pMatrix,missing-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 7702--7704
[]\T1/pcr/m/n/10 crossprod,pMatrix,pMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7704--7706
[]\T1/pcr/m/n/10 crossprod,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7706--7708
[]\T1/pcr/m/n/10 crossprod,sparseVector,Matrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7708--7710
[]\T1/pcr/m/n/10 crossprod,sparseVector,missing-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 7710--7712
[]\T1/pcr/m/n/10 crossprod,sparseVector,sparseVector-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7712--7714
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,ANY-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7714--7716
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,Matrix-method 
[3322]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7716--7718
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7718--7720
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,ANY-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7720--7722
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,Matrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7722--7724
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,missing-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7724--7726
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,TsparseMatrix-method 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 7741--7743
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 7788--7790
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 7792--7794
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3323]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7967--7969
[]\T1/pcr/m/n/10 derivedDefaultMethodWithTrace-class 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7983--7985
[]\T1/pcr/m/n/10 determinant,CHMfactor,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7985--7987
[]\T1/pcr/m/n/10 determinant,CHMfactor,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7987--7989
[]\T1/pcr/m/n/10 determinant,ddenseMatrix,logical-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7989--7991
[]\T1/pcr/m/n/10 determinant,ddenseMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7991--7993
[]\T1/pcr/m/n/10 determinant,dgCMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7993--7995
[]\T1/pcr/m/n/10 determinant,dgeMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7995--7997
[]\T1/pcr/m/n/10 determinant,dgeMatrix,missing-method 
[3324]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7997--7999
[]\T1/pcr/m/n/10 determinant,diagonalMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7999--8001
[]\T1/pcr/m/n/10 determinant,dpoMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8001--8003
[]\T1/pcr/m/n/10 determinant,dpoMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8003--8005
[]\T1/pcr/m/n/10 determinant,dppMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8005--8007
[]\T1/pcr/m/n/10 determinant,dppMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8007--8009
[]\T1/pcr/m/n/10 determinant,dsCMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8009--8011
[]\T1/pcr/m/n/10 determinant,dsCMatrix,missing-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 8011--8013
[]\T1/pcr/m/n/10 determinant,dsparseMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8013--8015
[]\T1/pcr/m/n/10 determinant,dtCMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8015--8017
[]\T1/pcr/m/n/10 determinant,dtpMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8017--8019
[]\T1/pcr/m/n/10 determinant,dtpMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8019--8021
[]\T1/pcr/m/n/10 determinant,dtrMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8021--8023
[]\T1/pcr/m/n/10 determinant,dtrMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8023--8025
[]\T1/pcr/m/n/10 determinant,indMatrix,logical-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 8025--8027
[]\T1/pcr/m/n/10 determinant,Matrix,logical-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 8027--8029
[]\T1/pcr/m/n/10 determinant,Matrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 8029--8031
[]\T1/pcr/m/n/10 determinant,pMatrix,logical-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 8031--8033
[]\T1/pcr/m/n/10 determinant,sparseMatrix,logical-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 8033--8035
[]\T1/pcr/m/n/10 determinant,sparseMatrix,missing-method 
[3325] [3326]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 8249--8251
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
[3327]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 8492--8494
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3328] [3329]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8688--8690
[]\T1/pcr/m/n/10 expand,MatrixFactorization-method 

Overfull \hbox (10.01662pt too wide) in paragraph at lines 8688--8690
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 8802--8804
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3330] [3331]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 9003--9005
[]\T1/pcr/m/n/10 forceSymmetric,corMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9005--9007
[]\T1/pcr/m/n/10 forceSymmetric,corMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9007--9009
[]\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 9009--9011
[]\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9011--9013
[]\T1/pcr/m/n/10 forceSymmetric,denseMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9013--9015
[]\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9015--9017
[]\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9017--9019
[]\T1/pcr/m/n/10 forceSymmetric,dppMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9019--9021
[]\T1/pcr/m/n/10 forceSymmetric,dppMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9021--9023
[]\T1/pcr/m/n/10 forceSymmetric,dsCMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9023--9025
[]\T1/pcr/m/n/10 forceSymmetric,dsCMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9025--9027
[]\T1/pcr/m/n/10 forceSymmetric,dspMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9027--9029
[]\T1/pcr/m/n/10 forceSymmetric,dspMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9029--9031
[]\T1/pcr/m/n/10 forceSymmetric,dsRMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9031--9033
[]\T1/pcr/m/n/10 forceSymmetric,dsRMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9033--9035
[]\T1/pcr/m/n/10 forceSymmetric,dsTMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9035--9037
[]\T1/pcr/m/n/10 forceSymmetric,dsTMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9037--9039
[]\T1/pcr/m/n/10 forceSymmetric,dsyMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9039--9041
[]\T1/pcr/m/n/10 forceSymmetric,dsyMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9041--9043
[]\T1/pcr/m/n/10 forceSymmetric,lsCMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9043--9045
[]\T1/pcr/m/n/10 forceSymmetric,lsCMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9045--9047
[]\T1/pcr/m/n/10 forceSymmetric,lspMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9047--9049
[]\T1/pcr/m/n/10 forceSymmetric,lspMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9049--9051
[]\T1/pcr/m/n/10 forceSymmetric,lsRMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9051--9053
[]\T1/pcr/m/n/10 forceSymmetric,lsRMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9053--9055
[]\T1/pcr/m/n/10 forceSymmetric,lsTMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9055--9057
[]\T1/pcr/m/n/10 forceSymmetric,lsTMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9057--9059
[]\T1/pcr/m/n/10 forceSymmetric,lsyMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9059--9061
[]\T1/pcr/m/n/10 forceSymmetric,lsyMatrix,missing-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 9061--9063
[]\T1/pcr/m/n/10 forceSymmetric,matrix,ANY-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 9063--9065
[]\T1/pcr/m/n/10 forceSymmetric,Matrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9065--9067
[]\T1/pcr/m/n/10 forceSymmetric,nsCMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9067--9069
[]\T1/pcr/m/n/10 forceSymmetric,nsCMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9069--9071
[]\T1/pcr/m/n/10 forceSymmetric,nspMatrix,character-method 
[3332]
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9071--9073
[]\T1/pcr/m/n/10 forceSymmetric,nspMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9073--9075
[]\T1/pcr/m/n/10 forceSymmetric,nsRMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9075--9077
[]\T1/pcr/m/n/10 forceSymmetric,nsRMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9077--9079
[]\T1/pcr/m/n/10 forceSymmetric,nsTMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9079--9081
[]\T1/pcr/m/n/10 forceSymmetric,nsTMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9081--9083
[]\T1/pcr/m/n/10 forceSymmetric,nsyMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9083--9085
[]\T1/pcr/m/n/10 forceSymmetric,nsyMatrix,missing-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 9085--9087
[]\T1/pcr/m/n/10 forceSymmetric,sparseMatrix,ANY-method 
[3333] [3334] [3335] [3336]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 9792--9794
[]\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class 
[3337] [3338] [3339]
Underfull \vbox (badness 3769) has occurred while \output is active [3340]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 10270--10272
[]\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 10272--10274
[]\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 10280--10282
[]\T1/pcr/m/n/10 is.infinite,nsparseVector-method 
[3341]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 10412--10414
[]\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10418--10420
[]\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 10420--10422
[]\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10464--10466
[]\T1/pcr/m/n/10 isSymmetric,diagonalMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 10468--10470
[]\T1/pcr/m/n/10 isSymmetric,symmetricMatrix-method 
[3342]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 10470--10472
[]\T1/pcr/m/n/10 isSymmetric,triangularMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 10474--10476
[]\T1/pcr/m/n/10 isTriangular,BunchKaufman-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10478--10480
[]\T1/pcr/m/n/10 isTriangular,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 10482--10484
[]\T1/pcr/m/n/10 isTriangular,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10516--10518
[]\T1/pcr/m/n/10 isTriangular,pBunchKaufman-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10520--10522
[]\T1/pcr/m/n/10 isTriangular,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10522--10524
[]\T1/pcr/m/n/10 isTriangular,TsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 10586--10588
[]\T1/pcr/m/n/10 kronecker,ANY,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10590--10592
[]\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method 
[3343]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 10592--10594
[]\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10594--10596
[]\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 10596--10598
[]\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 10598--10600
[]\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 10600--10602
[]\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10602--10604
[]\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10604--10606
[]\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10606--10608
[]\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 10610--10612
[]\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10612--10614
[]\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 10614--10616
[]\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 10616--10618
[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 10618--10620
[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method 
[3344] [3345] [3346]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 11055--11057
[]\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11061--11063
[]\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 11063--11065
[]\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11065--11067
[]\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11067--11069
[]\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11069--11071
[]\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11075--11077
[]\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11085--11087
[]\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 11087--11089
[]\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 11089--11091
[]\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 11091--11093
[]\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11093--11095
[]\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11101--11103
[]\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11111--11113
[]\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 11113--11115
[]\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11121--11123
[]\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11123--11125
[]\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11125--11127
[]\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 11127--11129
[]\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method 

Underfull \vbox (badness 3302) has occurred while \output is active [3347]
Overfull \hbox (74.8567pt too wide) in paragraph at lines 11129--11131
[]\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method 
[3348] [3349]
Underfull \vbox (badness 1348) has occurred while \output is active [3350]
[3351]
Overfull \hbox (52.01662pt too wide) in paragraph at lines 11713--11715
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
[3352] [3353]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 12025--12027
[]\T1/pcr/m/n/10 nonstandardGenericWithTrace-class 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 12036--12038
[]\T1/pcr/m/n/10 norm,ddenseMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 12038--12040
[]\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12044--12046
[]\T1/pcr/m/n/10 norm,diagonalMatrix,character-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 12062--12064
[]\T1/pcr/m/n/10 norm,ldenseMatrix,character-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 12068--12070
[]\T1/pcr/m/n/10 norm,ndenseMatrix,character-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 12070--12072
[]\T1/pcr/m/n/10 norm,sparseMatrix,character-method 
[3354] [3355]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 12240--12242
[]\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 12246--12248
[]\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 12258--12260
[]\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 12260--12262
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 12262--12264
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12264--12266
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method 

Underfull \vbox (badness 6876) has occurred while \output is active
Overfull \hbox (62.8567pt too wide) in paragraph at lines 12266--12268
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12286--12288
[]\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12288--12290
[]\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 12304--12306
[]\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method 

Underfull \vbox (badness 5847) has occurred while \output is active [3356]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 12324--12326
[]\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12326--12328
[]\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12344--12346
[]\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method 

Underfull \vbox (badness 4328) has occurred while \output is active
Overfull \hbox (26.8567pt too wide) in paragraph at lines 12352--12354
[]\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12356--12358
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12358--12360
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 12360--12362
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 12378--12380
[]\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12380--12382
[]\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 12382--12384
[]\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 12384--12386
[]\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12388--12390
[]\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12392--12394
[]\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method 
[3357]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 12396--12398
[]\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 12497--12499
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3358] [3359] [3360] [3361] [3362] [3363]
Overfull \hbox (4.01662pt too wide) in paragraph at lines 13320--13322
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13322--13324
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 13324--13326
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 13326--13328
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (52.01662pt too wide) in paragraph at lines 13328--13330
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13330--13332
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 13332--13334
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Underfull \vbox (badness 1484) has occurred while \output is active
Overfull \hbox (4.01662pt too wide) in paragraph at lines 13334--13336
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (52.01662pt too wide) in paragraph at lines 13338--13340
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13340--13342
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13342--13344
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13344--13346
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13346--13348
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13348--13350
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Underfull \vbox (badness 1824) has occurred while \output is active [3364]
[3365]
Overfull \hbox (4.01662pt too wide) in paragraph at lines 13578--13580
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13641--13643
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3366] [3367] [3368]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 14015--14017
[]\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 14024--14026
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14026--14028
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14028--14030
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14030--14032
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14040--14042
[]\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 14049--14051
[]\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 14063--14065
[]\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14069--14071
[]\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method 

Underfull \vbox (badness 1642) has occurred while \output is active [3369]
[3370]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 14308--14310
[]\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 14310--14312
[]\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14312--14314
[]\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 14314--14316
[]\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 14318--14320
[]\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14320--14322
[]\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14322--14324
[]\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 14324--14326
[]\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 14326--14328
[]\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14328--14330
[]\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 14330--14332
[]\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14336--14338
[]\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14340--14342
[]\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method 

Underfull \vbox (badness 5022) has occurred while \output is active [3371]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14350--14352
[]\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14354--14356
[]\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 14356--14358
[]\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 14358--14360
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 14360--14362
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14362--14364
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 14364--14366
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 14366--14368
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14391--14393
[]\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14393--14395
[]\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 14395--14397
[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14397--14399
[]\T1/pcr/m/n/10 rcond,dgeMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14401--14403
[]\T1/pcr/m/n/10 rcond,dpoMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14405--14407
[]\T1/pcr/m/n/10 rcond,dppMatrix,character-method 

Underfull \vbox (badness 1484) has occurred while \output is active
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14409--14411
[]\T1/pcr/m/n/10 rcond,dspMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14413--14415
[]\T1/pcr/m/n/10 rcond,dsyMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14417--14419
[]\T1/pcr/m/n/10 rcond,dtpMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14421--14423
[]\T1/pcr/m/n/10 rcond,dtrMatrix,character-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14425--14427
[]\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14429--14431
[]\T1/pcr/m/n/10 rcond,ndenseMatrix,character-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14431--14433
[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method 
[3372] [3373] [3374] [3375] [3376]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 15066--15068
[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15068--15070
[]\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15072--15074
[]\T1/pcr/m/n/10 Schur,generalMatrix,logical-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15074--15076
[]\T1/pcr/m/n/10 Schur,generalMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15080--15082
[]\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15082--15084
[]\T1/pcr/m/n/10 Schur,symmetricMatrix,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 15084--15086
[]\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 15086--15088
[]\T1/pcr/m/n/10 Schur,triangularMatrix,missing-method 
[3377]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 15318--15320
[]\T1/pcr/m/n/10 show,genericFunctionWithTrace-method 
[3378]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 15322--15324
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 15326--15328
[]\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15330--15332
[]\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15340--15342
[]\T1/pcr/m/n/10 show,refClassRepresentation-method 
[3379]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 15514--15516
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15516--15518
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15519--15521
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (5.3567pt too wide) in paragraph at lines 15523--15524
[]\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15528--15530
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (5.3567pt too wide) in paragraph at lines 15532--15533
[]\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15533--15535
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (23.3567pt too wide) in paragraph at lines 15536--15538
[]\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15539--15541
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3380]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 15564--15566
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15584--15586
[]\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 15586--15588
[]\T1/pcr/m/n/10 solve,CHMfactor,diagonalMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15588--15590
[]\T1/pcr/m/n/10 solve,CHMfactor,dsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15598--15600
[]\T1/pcr/m/n/10 solve,ddenseMatrix,Matrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15600--15602
[]\T1/pcr/m/n/10 solve,ddenseMatrix,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 15602--15604
[]\T1/pcr/m/n/10 solve,ddenseMatrix,missing-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 15604--15606
[]\T1/pcr/m/n/10 solve,ddenseMatrix,numeric-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15608--15610
[]\T1/pcr/m/n/10 solve,dgCMatrix,ddenseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15610--15612
[]\T1/pcr/m/n/10 solve,dgCMatrix,dsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15616--15618
[]\T1/pcr/m/n/10 solve,dgeMatrix,ddenseMatrix-method 

Underfull \vbox (badness 2035) has occurred while \output is active
Overfull \hbox (20.8567pt too wide) in paragraph at lines 15622--15624
[]\T1/pcr/m/n/10 solve,dgeMatrix,sparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15624--15626
[]\T1/pcr/m/n/10 solve,diagonalMatrix,Matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15626--15628
[]\T1/pcr/m/n/10 solve,diagonalMatrix,matrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15628--15630
[]\T1/pcr/m/n/10 solve,diagonalMatrix,missing-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15630--15632
[]\T1/pcr/m/n/10 solve,dpoMatrix,dgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15636--15638
[]\T1/pcr/m/n/10 solve,dppMatrix,dgeMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15644--15646
[]\T1/pcr/m/n/10 solve,dsCMatrix,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15646--15648
[]\T1/pcr/m/n/10 solve,dsCMatrix,denseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15648--15650
[]\T1/pcr/m/n/10 solve,dsCMatrix,dsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15656--15658
[]\T1/pcr/m/n/10 solve,dspMatrix,ddenseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15662--15664
[]\T1/pcr/m/n/10 solve,dsyMatrix,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15664--15666
[]\T1/pcr/m/n/10 solve,dsyMatrix,denseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15670--15672
[]\T1/pcr/m/n/10 solve,dtCMatrix,CsparseMatrix-method 
[3381]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 15672--15674
[]\T1/pcr/m/n/10 solve,dtCMatrix,dgeMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15680--15682
[]\T1/pcr/m/n/10 solve,dtpMatrix,ddenseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15686--15688
[]\T1/pcr/m/n/10 solve,dtrMatrix,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15698--15700
[]\T1/pcr/m/n/10 solve,Matrix,diagonalMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15710--15712
[]\T1/pcr/m/n/10 solve,Matrix,sparseVector-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15712--15714
[]\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 15714--15716
[]\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 15716--15718
[]\T1/pcr/m/n/10 solve,MatrixFactorization,numeric-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15728--15730
[]\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method 
[3382]
Overfull \hbox (52.01662pt too wide) in paragraph at lines 15821--15823
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
[3383]
Overfull \hbox (44.8567pt too wide) in paragraph at lines 16080--16082
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16082--16084
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_results 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16084--16086
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings 
[3384]
Underfull \vbox (badness 2564) has occurred while \output is active [3385]
[3386] [3387] [3388]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 16702--16704
[]\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16704--16706
[]\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 16706--16708
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 16708--16710
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 16710--16712
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,diagonalMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16712--16714
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16714--16716
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16716--16718
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,numLike-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 16718--16720
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,CsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16720--16722
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dsCMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16722--16724
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dtrMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16724--16726
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,lsCMatrix-method 
[3389]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16726--16728
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,missing-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16728--16730
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,nsCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16730--16732
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,dgeMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 16732--16734
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,diagonalMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16734--16736
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,matrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16736--16738
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16738--16740
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,numLike-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 16740--16742
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,CsparseMatrix-method 

Overfull \hbox (92.8567pt too wide) in paragraph at lines 16742--16744
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,diagonalMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16744--16746
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,matrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16746--16748
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,missing-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 16748--16750
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16750--16752
[]\T1/pcr/m/n/10 tcrossprod,dtrMatrix,dtrMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16752--16754
[]\T1/pcr/m/n/10 tcrossprod,indMatrix,indMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16754--16756
[]\T1/pcr/m/n/10 tcrossprod,indMatrix,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16756--16758
[]\T1/pcr/m/n/10 tcrossprod,lgCMatrix,missing-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 16758--16760
[]\T1/pcr/m/n/10 tcrossprod,lgeMatrix,diagonalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16760--16762
[]\T1/pcr/m/n/10 tcrossprod,lgTMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16762--16764
[]\T1/pcr/m/n/10 tcrossprod,lsparseMatrix,missing-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16766--16768
[]\T1/pcr/m/n/10 tcrossprod,matrix,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16768--16770
[]\T1/pcr/m/n/10 tcrossprod,matrix,dgeMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16770--16772
[]\T1/pcr/m/n/10 tcrossprod,matrix,diagonalMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16772--16774
[]\T1/pcr/m/n/10 tcrossprod,matrix,dsCMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16774--16776
[]\T1/pcr/m/n/10 tcrossprod,matrix,dtrMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16776--16778
[]\T1/pcr/m/n/10 tcrossprod,Matrix,indMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16778--16780
[]\T1/pcr/m/n/10 tcrossprod,matrix,indMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16780--16782
[]\T1/pcr/m/n/10 tcrossprod,matrix,lsCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16788--16790
[]\T1/pcr/m/n/10 tcrossprod,Matrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16790--16792
[]\T1/pcr/m/n/10 tcrossprod,matrix,nsCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16792--16794
[]\T1/pcr/m/n/10 tcrossprod,Matrix,numLike-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16794--16796
[]\T1/pcr/m/n/10 tcrossprod,Matrix,pMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16796--16798
[]\T1/pcr/m/n/10 tcrossprod,matrix,pMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16798--16800
[]\T1/pcr/m/n/10 tcrossprod,Matrix,sparseVector-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16800--16802
[]\T1/pcr/m/n/10 tcrossprod,Matrix,symmetricMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16802--16804
[]\T1/pcr/m/n/10 tcrossprod,Matrix,TsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16804--16806
[]\T1/pcr/m/n/10 tcrossprod,ngCMatrix,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16806--16808
[]\T1/pcr/m/n/10 tcrossprod,ngTMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16808--16810
[]\T1/pcr/m/n/10 tcrossprod,nsparseMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16810--16812
[]\T1/pcr/m/n/10 tcrossprod,numLike,CsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16812--16814
[]\T1/pcr/m/n/10 tcrossprod,numLike,dgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16814--16816
[]\T1/pcr/m/n/10 tcrossprod,numLike,Matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 16816--16818
[]\T1/pcr/m/n/10 tcrossprod,pMatrix,missing-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 16818--16820
[]\T1/pcr/m/n/10 tcrossprod,pMatrix,pMatrix-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 16820--16822
[]\T1/pcr/m/n/10 tcrossprod,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 16822--16824
[]\T1/pcr/m/n/10 tcrossprod,sparseMatrix,sparseVector-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16824--16826
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,Matrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16826--16828
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,missing-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 16828--16830
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,sparseMatrix-method 
[3390]
Overfull \hbox (68.8567pt too wide) in paragraph at lines 16830--16832
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,sparseVector-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16832--16834
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,ANY-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16834--16836
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,Matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16836--16838
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,missing-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 16838--16840
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,TsparseMatrix-method 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 16860--16862
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 tensor.prod.model.matrix\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3391] [3392] [3393]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 17379--17381
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Underfull \vbox (badness 1348) has occurred while \output is active [3394]
[3395] [3396]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 17848--17850
[]\T1/pcr/m/n/10 updown,character,mMatrix,CHMfactor-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 17850--17852
[]\T1/pcr/m/n/10 updown,logical,mMatrix,CHMfactor-method 
[3397] [3398] [3399] [3400]) (./fullrefman.aux) )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.tree} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mem.limits} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced
 but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does 
not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.standardGeneric} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texlive
/fonts/type1/bluesky/ams/cmbsy7.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmbx10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmex10.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmmi5.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmib10.pfb>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmr5.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pfb></usr/share/texmf-texl
ive/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texmf-texlive/fonts/type1/ur
w/courier/ucrr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/courier/ucrro8a.
pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/t
exmf-texlive/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/t
ype1/urw/times/utmbi8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr
8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr8a.pfb></usr/share/t
exmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on fullrefman.pdf (3449 pages, 9032403 bytes).
Transcript written on fullrefman.log.
This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7)
 %&-line parsing enabled.
entering extended mode
(./fullrefman.tex
LaTeX2e <2005/12/01>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, farsi, arabic, bulgarian, ukrainian, russian, french, basque, germa
n, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18, polish, loaded.
(/usr/share/texmf-texlive/tex/latex/base/book.cls
Document Class: book 2005/09/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/bm.sty)
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def))
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty)
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))
(/etc/texmf/tex/latex/config/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty)))
(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hpdftex*
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def)

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 366.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 366.

) (/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
(/usr/share/texmf-texlive/tex/latex/base/utf8.def
(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu)))
(/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty
(/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty
(/usr/share/texmf-texlive/tex/latex/graphics/trig.sty)
(/etc/texmf/tex/latex/config/graphics.cfg)))
(/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
(./fullrefman.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./fullrefman.out)
(./fullrefman.out) (/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd)
(./version.tex) (/usr/share/texmf-texlive/tex/latex/psnfss/ts1ptm.fd) [1{/var/c
ache/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc
(/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5]
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]
[37] [38] [39] [40] [41] [42] [43] [44] [45] [46]) [47] [48] [1] [2]
(./base-pkg.tex
Chapter 1.

Underfull \hbox (badness 4595) in paragraph at lines 40--43
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[3]
Underfull \hbox (badness 4168) in paragraph at lines 94--99
[]\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one 
char-ac-ter vec-tors. The first en-try is al-ways
[4]
Underfull \hbox (badness 10000) in paragraph at lines 131--137
[]\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10
 x \T1/ptm/m/n/10 such that

Underfull \hbox (badness 10000) in paragraph at lines 131--137
\T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base 
^ ulp.digits \T1/ptm/m/n/10 if ei-

Underfull \hbox (badness 6236) in paragraph at lines 131--137
\T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m
/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise,

Underfull \hbox (badness 10000) in paragraph at lines 131--137
\T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt
m/m/n/10 . Nor-mally

Underfull \hbox (badness 10000) in paragraph at lines 137--145
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 137--145
\T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if

Underfull \hbox (badness 4328) in paragraph at lines 137--145
\T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is

Underfull \hbox (badness 10000) in paragraph at lines 137--145
\T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma
lly

Underfull \hbox (badness 10000) in paragraph at lines 148--155
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-

Underfull \hbox (badness 10000) in paragraph at lines 148--155
\T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) *
[5] [6]
Underfull \hbox (badness 4036) in paragraph at lines 291--295
\T1/ptm/m/n/10 ues \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.
binary"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 an
d
[7]
Underfull \hbox (badness 10000) in paragraph at lines 330--333
[][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys.
info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar,
[8]
Underfull \hbox (badness 2359) in paragraph at lines 375--378
[]\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[9] [10]
Underfull \hbox (badness 1072) in paragraph at lines 505--511
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [13] [14]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 807--807
 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[15] [16] [17] [18] [19]
Underfull \hbox (badness 1838) in paragraph at lines 1094--1097
[]\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[20] [21] [22]
Underfull \hbox (badness 5862) in paragraph at lines 1302--1308
[]\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[23] [24] [25] [26] [27]
Underfull \hbox (badness 2865) in paragraph at lines 1665--1669
[]\T1/ptm/m/n/10 A char-ac-ter string. If not spec-i-fied, it will try \T1/pcr/
m/n/10 "%Y-%m-%d" \T1/ptm/m/n/10 then

Underfull \hbox (badness 10000) in paragraph at lines 1669--1671
[]\T1/ptm/m/n/10 a Date ob-ject, or some-thing which can be co-erced by
[28] [29]
Overfull \hbox (112.38031pt too wide) in paragraph at lines 1808--1808
 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 

Overfull \hbox (19.13934pt too wide) in paragraph at lines 1843--1845
[]\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e
nv[][][](x,      parent = emptyenv())

Underfull \hbox (badness 10000) in paragraph at lines 1846--1848
[]\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru
e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an
[30] [31]
Underfull \hbox (badness 10000) in paragraph at lines 1993--1995
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[32] [33]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2100--2100
 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[34] [35]
Underfull \hbox (badness 1107) in paragraph at lines 2233--2235
[]\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1
0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see
[36] [37] [38] [39] [40]
Underfull \hbox (badness 5878) in paragraph at lines 2562--2567
[]\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to 
\T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at-

Underfull \hbox (badness 10000) in paragraph at lines 2562--2567
\T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p
cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53]
Underfull \hbox (badness 10000) in paragraph at lines 3446--3448
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[54] [55] [56] [57] [58] [59] [60]
Underfull \hbox (badness 4927) in paragraph at lines 3896--3900
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject

Underfull \hbox (badness 2012) in paragraph at lines 3896--3900
\T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or
[61]
Underfull \hbox (badness 5260) in paragraph at lines 4004--4009
[]\T1/ptm/m/n/10 Are the \T1/pcr/m/n/10 R.app \T1/ptm/m/n/10 GUI com-po-nents a
nd the [][]\T1/pcr/m/n/10 quartz[][][] \T1/ptm/m/n/10 func-tion op-er-a-

Underfull \hbox (badness 1354) in paragraph at lines 4004--4009
\T1/ptm/m/n/10 tional? Only on some OS X builds. Note that this is dis-tinct fr
om
[62] [63] [64]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4172--4172
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 
[65]
Underfull \hbox (badness 10000) in paragraph at lines 4273--4278
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j
ust a wrap-per for

Underfull \hbox (badness 10000) in paragraph at lines 4273--4278
[][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T
his means that it will split ma-

Underfull \hbox (badness 2181) in paragraph at lines 4273--4278
\T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter
 columns to fac-tors un-less
[66]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4352--4352
 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[67] [68] [69] [70]
Underfull \hbox (badness 2521) in paragraph at lines 4589--4591
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[71] [72] [73] [74] [75]
Underfull \hbox (badness 10000) in paragraph at lines 4922--4930
[]\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is 
ap-plied to an ob-ject with class at-tribute
[76] [77] [78] [79] [80] [81] [82] [83]
Underfull \hbox (badness 2443) in paragraph at lines 5465--5472
[]\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i
n-tro-duc-tion see [][]$\T1/pcr/m/n/10 http : / /
[84] [85] [86] [87]
Underfull \hbox (badness 1635) in paragraph at lines 5777--5780
[]\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1
0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class

Underfull \hbox (badness 3009) in paragraph at lines 5781--5784
[]\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. 
They can be es-tab-lished us-ing

Underfull \hbox (badness 1102) in paragraph at lines 5798--5811
[]\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in

Underfull \hbox (badness 1308) in paragraph at lines 5812--5820
[]\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i
s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should
[88] [89] [90] [91]
Underfull \hbox (badness 2158) in paragraph at lines 6032--6036
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 '). Prox-ies can be spe
c-i-fied for HTTP and FTP \T1/pcr/m/n/10 url \T1/ptm/m/n/10 con-nec-tions: see
[92]
Underfull \hbox (badness 10000) in paragraph at lines 6120--6123
[]\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is

Underfull \hbox (badness 2057) in paragraph at lines 6120--6123
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T
1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/
10 host
[93] [94]
Underfull \hbox (badness 3815) in paragraph at lines 6284--6290
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-


Underfull \hbox (badness 2343) in paragraph at lines 6284--6290
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1147) in paragraph at lines 6284--6290
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If it is re-quired (it is n
ot rec-om-mended) when writ-ing

Underfull \hbox (badness 10000) in paragraph at lines 6303--6305
[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[95]
Underfull \hbox (badness 1067) in paragraph at lines 6345--6352
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[96]
Underfull \vbox (badness 10000) has occurred while \output is active [97]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6518--6518
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[98] [99] [100] [101] [102]
Underfull \hbox (badness 10000) in paragraph at lines 6844--6846
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[103] [104]
Underfull \hbox (badness 4595) in paragraph at lines 6950--6953
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[105] [106] [107]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7143--7143
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[108]
Underfull \hbox (badness 8132) in paragraph at lines 7239--7243
[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The

Underfull \hbox (badness 4543) in paragraph at lines 7239--7243
\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting
[109]
Underfull \hbox (badness 10000) in paragraph at lines 7258--7269
[]\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing

Underfull \hbox (badness 1062) in paragraph at lines 7258--7269
[][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that
 is a generic func-tion, meth-ods can be

Overfull \hbox (4.63962pt too wide) in paragraph at lines 7291--7295
[]\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak
es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors")
[110] [111] [112] [113] [114] [115]
Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n
/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 7733--7745
\T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",  tz =
 "UTC") \T1/ptm/m/n/10 will give
[116] [117]
Underfull \hbox (badness 5802) in paragraph at lines 7938--7942
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 
reads the file byte-by-byte. This al-lows a
[118] [119]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8053--8057
\T1/pcr/m/n/10 trace("plot", browser, exit = browser, signature = c("track", "m
issing")) 
[120]
Underfull \hbox (badness 10000) in paragraph at lines 8106--8110
[]\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu
nc-tions should be listed in
[121]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8187--8187
 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO
! "); pi+2})[] 
[122] [123]
Underfull \hbox (badness 4254) in paragraph at lines 8340--8344
[]\T1/ptm/m/n/10 If the ob-ject has at-tributes (other than a \T1/pcr/m/n/10 so
urce \T1/ptm/m/n/10 at-tribute), use
[124]
Underfull \hbox (badness 1132) in paragraph at lines 8383--8390
\T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to
 make the re-sult parseable.
[125]
Underfull \hbox (badness 1603) in paragraph at lines 8492--8495
[]\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t
er-mi-nant if
[126] [127] [128] [129] [130] [131] [132] [133] [134]
Underfull \hbox (badness 1917) in paragraph at lines 9077--9080
[]\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim
names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has

Overfull \hbox (36.7804pt too wide) in paragraph at lines 9130--9130
 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 9131--9131
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[135] [136]
Underfull \hbox (badness 1168) in paragraph at lines 9231--9236
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p
cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[137] [138]
Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / IEEE _ 754-[]198
5$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / en . wikipedia .

Underfull \hbox (badness 10000) in paragraph at lines 9369--9373
\T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr
/m/n/10 http : / / en . wikipedia . org / wiki / Double _
[139] [140] [141]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9588--9588
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[142]
Underfull \hbox (badness 1629) in paragraph at lines 9661--9665
[]\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re
-sult of lazy-loading (when
[143] [144]
Underfull \hbox (badness 2150) in paragraph at lines 9760--9763
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 3690) in paragraph at lines 9774--9782
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for

Underfull \hbox (badness 10000) in paragraph at lines 9783--9785
[]\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent 
to but faster than
[145]
Underfull \hbox (badness 3735) in paragraph at lines 9815--9822
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[146] [147]
Underfull \hbox (badness 10000) in paragraph at lines 10010--10013
[]\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l
oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use
[148] [149] [150] [151] [152] [153] [154] [155] [156]
Underfull \hbox (badness 5288) in paragraph at lines 10669--10671
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of

Underfull \hbox (badness 3039) in paragraph at lines 10679--10684
[]\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 
dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10
 and
[157]
Underfull \hbox (badness 10000) in paragraph at lines 10737--10739
[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[158] [159]
Underfull \hbox (badness 4569) in paragraph at lines 10854--10858
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 10854--10858
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[160]
Underfull \hbox (badness 10000) in paragraph at lines 10965--10967
[]\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/
m/n/10 where \T1/ptm/m/n/10 as
[161] [162] [163]
Underfull \hbox (badness 4048) in paragraph at lines 11151--11161
[]\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me
nt into an ex-pres-sion ob-ject. It is

Underfull \hbox (badness 3657) in paragraph at lines 11151--11161
\T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d
e-fault method calls
[164] [165] [166]
Underfull \hbox (badness 5460) in paragraph at lines 11398--11407
[]\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-

Underfull \hbox (badness 2221) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes
e op-er-a-tions are those

Underfull \hbox (badness 2707) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x,    inherits = FALSE)\T1/ptm/m/
n/10 . If no match is found then \T1/pcr/m/n/10 NULL

Underfull \hbox (badness 2818) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T
1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again,

Underfull \hbox (badness 6978) in paragraph at lines 11398--11407
\T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th
is case are those of
[167] [168] [169] [170] [171]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 11761--11761
 []\T1/pcr/m/n/9 A <- data.frame(x = 1:3, y = I(matrix(4:6)), z = I(matrix(lett
ers[1:9], 3, 3)))[] 
[172] [173] [174] [175] [176]
Underfull \hbox (badness 2221) in paragraph at lines 12121--12127
\T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is
 true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas
s
[177] [178] [179] [180]
Underfull \hbox (badness 2253) in paragraph at lines 12350--12352
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[181]
Underfull \hbox (badness 10000) in paragraph at lines 12454--12456
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[182] [183]
Underfull \hbox (badness 10000) in paragraph at lines 12602--12604
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See

[184] [185]
Underfull \hbox (badness 10000) in paragraph at lines 12700--12704
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (30.78088pt too wide) in paragraph at lines 12750--12750
 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777") 
[186] [187]
Underfull \hbox (badness 10000) in paragraph at lines 12839--12842
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex
ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 12849--12849
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive  TRUE)[] 
[188]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12932--12932
 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE) 

Underfull \hbox (badness 7238) in paragraph at lines 12950--12957
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds
 the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr
/m/n/10 vec\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 12950--12957
\T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial
, equiv-a-lent to

Underfull \hbox (badness 2126) in paragraph at lines 12950--12957
\T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter
 of fact, the in-ter-nal al-go-

Underfull \hbox (badness 3965) in paragraph at lines 12958--12962
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
[189] [190]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13066--13066
 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 13067--13067
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[191]
Underfull \hbox (badness 10000) in paragraph at lines 13148--13152
[]\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined 
in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a

Underfull \hbox (badness 1389) in paragraph at lines 13148--13152
\T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m
ay not be equiv-a-lent to
[192]
Underfull \hbox (badness 1314) in paragraph at lines 13208--13210
[]\T1/ptm/m/n/10 In re-cent ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 most u
n-nec-es-sary copy-ing is avoided: on the other hand us-ing
[193] [194] [195]
Underfull \hbox (badness 1168) in paragraph at lines 13402--13406
[]\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real 
or com-plex vec-

Underfull \hbox (badness 2012) in paragraph at lines 13402--13406
\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[196]
Underfull \hbox (badness 6944) in paragraph at lines 13496--13499
[][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 toString[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 13521--13521
 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[197] [198] [199]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 13668--13668
 []          \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx 
= NA,[] 

Underfull \hbox (badness 2790) in paragraph at lines 13675--13678
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for

Underfull \hbox (badness 4254) in paragraph at lines 13691--13699
[]\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied,

Underfull \hbox (badness 1024) in paragraph at lines 13706--13710
[]\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 
xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 "E" \T1/ptm/m/n/10 give
[200]
Underfull \hbox (badness 10000) in paragraph at lines 13761--13763
[]\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
[]\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point,

Underfull \hbox (badness 10000) in paragraph at lines 13767--13771
\T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f
g") \T1/ptm/m/n/10 gives

Underfull \hbox (badness 10000) in paragraph at lines 13772--13780
[]\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti
-fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be
 com-plex (or
[201]
Underfull \hbox (badness 1009) in paragraph at lines 13806--13809
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 is
 not ap-pro-pri-ate for use within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/1
0 meth-ods: use
[202]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 13869--13869
 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big
.mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] 
[203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214]
[215]
Underfull \hbox (badness 2418) in paragraph at lines 14776--14780
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,

Underfull \hbox (badness 6510) in paragraph at lines 14783--14786
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b
ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/
m/n/10 , then the sin-gle

Underfull \hbox (badness 2326) in paragraph at lines 14811--14818
[][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte
rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 ,
[216] [217] [218] [219]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15057--15057
 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 

Underfull \hbox (badness 1867) in paragraph at lines 15082--15089
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[220] [221] [222] [223]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15316--15316
 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 15343--15343
 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 

Underfull \vbox (badness 10000) has occurred while \output is active [224]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15387--15387
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 

Underfull \hbox (badness 10000) in paragraph at lines 15393--15397
[]\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o
r fixed pat-tern for

Underfull \hbox (badness 1028) in paragraph at lines 15393--15397
\T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec-
tor. Co-erced by
[225] [226] [227] [228] [229] [230] [231]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 15921--15921
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[232] [233] [234] [235]
Underfull \hbox (badness 2435) in paragraph at lines 16174--16176
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /

Underfull \hbox (badness 2285) in paragraph at lines 16227--16229
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /

Overfull \hbox (9.78043pt too wide) in paragraph at lines 16235--16235
 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s
ettings, we can only reset to the default.[] 
[236]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16245--16245
 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 16265--16265
 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[237] [238] [239] [240] [241] [242] [243]
Underfull \hbox (badness 10000) in paragraph at lines 16701--16703
[]\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/
pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and
[244]
Underfull \hbox (badness 4217) in paragraph at lines 16785--16794
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2057) in paragraph at lines 16800--16816
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[245] [246] [247] [248] [249] [250]
Underfull \hbox (badness 4699) in paragraph at lines 17207--17210
[]\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the atomic types (\T1/pcr
/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "numeric"\T1/ptm/m/n/10 ,
[251] [252]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17329--17329
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[253] [254]
Underfull \hbox (badness 4739) in paragraph at lines 17460--17462
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[255] [256] [257] [258] [259] [260]
Underfull \hbox (badness 1430) in paragraph at lines 17858--17863
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i
f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 .


Underfull \hbox (badness 10000) in paragraph at lines 17858--17863
\T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10
 is the same as
[261]
Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
[]\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/
10 will pro-duce a (``higher

Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe
r = FALSE \T1/ptm/m/n/10 would

Underfull \hbox (badness 5008) in paragraph at lines 17919--17924
\T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon
d to

Underfull \hbox (badness 10000) in paragraph at lines 17919--17924
\T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s
implify = TRUE\T1/ptm/m/n/10 , re-
[262]
Underfull \hbox (badness 10000) in paragraph at lines 17979--17986
[]\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat
ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If

Underfull \hbox (badness 6364) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng
th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth-

Underfull \hbox (badness 5064) in paragraph at lines 17979--17986
\T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is
 not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix
 with

Underfull \hbox (badness 5908) in paragraph at lines 17979--17986
\T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length(
X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1
0 with

Underfull \hbox (badness 10000) in paragraph at lines 17995--17997
[]\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 
is equiv-a-lent to
[263]
Underfull \hbox (badness 1975) in paragraph at lines 18067--18070
[]\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p
hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to
[264] [265] [266] [267] [268]
Underfull \hbox (badness 10000) in paragraph at lines 18364--18368
[]\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory
[269]
Underfull \hbox (badness 10000) in paragraph at lines 18494--18498
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use

Underfull \hbox (badness 1454) in paragraph at lines 18494--18498
[][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi
ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self
[270] [271]
Underfull \hbox (badness 10000) in paragraph at lines 18589--18596
[][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/
m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 ,
[272] [273]
Underfull \hbox (badness 10000) in paragraph at lines 18710--18714
[]\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 
on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use

Underfull \hbox (badness 5161) in paragraph at lines 18765--18770
[]\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di
s-tributed un-der the

Underfull \hbox (badness 6592) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c
opy of

Underfull \hbox (badness 5133) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L
GPL-2.1\T1/ptm/m/n/10 ' and can be viewed

Underfull \hbox (badness 10000) in paragraph at lines 18765--18770
\T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 
3 of the li-cense can be dis-played by
[274] [275] [276]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 18927--18927
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 18931--18931
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[277]
Underfull \hbox (badness 3343) in paragraph at lines 18987--18991
[][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac
cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for
 many more file han-dling func-tions and
[278]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19073--19073
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 19084--19084
 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[279] [280]
Underfull \hbox (badness 6380) in paragraph at lines 19229--19234
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[281]
Underfull \hbox (badness 10000) in paragraph at lines 19258--19261
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC
_CTYPE"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1337) in paragraph at lines 19287--19294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t
ails of the string are system-specific: it might be

Underfull \hbox (badness 2229) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by 
\T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, OS X) or

Underfull \hbox (badness 1043) in paragraph at lines 19287--19294
\T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f
oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in

Underfull \hbox (badness 2564) in paragraph at lines 19306--19309
[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of
[282]
Underfull \hbox (badness 1205) in paragraph at lines 19359--19364
\T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put
es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form
[283] [284] [285] [286]
Underfull \hbox (badness 2469) in paragraph at lines 19668--19674
[]\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment 
to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s,

Underfull \hbox (badness 1939) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la
-bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri
butes in-clud-ing names.

Underfull \hbox (badness 10000) in paragraph at lines 19668--19674
\T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true"
) \T1/ptm/m/n/10 are re-garded as true,
[287] [288] [289] [290] [291]
Underfull \hbox (badness 10000) in paragraph at lines 19977--19979
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that
[292] [293] [294] [295] [296] [297]
Underfull \hbox (badness 1655) in paragraph at lines 20374--20378
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[298] [299] [300] [301] [302] [303] [304] [305] [306]
Underfull \hbox (badness 4366) in paragraph at lines 20965--20971
\T1/pcr/m/n/10 www . bzip . org/$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http 
: / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n
/10 http : / / tukaani .
[307] [308]
Underfull \hbox (badness 10000) in paragraph at lines 21094--21100
[]\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age
 space can-not ex-ceed

Underfull \hbox (badness 6316) in paragraph at lines 21094--21100
\T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er
-ror mes-sage be-gins
[309] [310]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 21203--21203
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[311]
Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by.
x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng
th zero vec-

Underfull \hbox (badness 10000) in paragraph at lines 21254--21258
\T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr
/m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/
n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i.
e.,
[312] [313] [314] [315] [316] [317] [318]
Underfull \hbox (badness 3849) in paragraph at lines 21797--21802
[]\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na
lly to a char-ac-ter vec-tor (so meth-ods for
[319]
Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 21877--21880
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
[320] [321] [322]
Underfull \hbox (badness 10000) in paragraph at lines 22025--22027
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[323] [324] [325] [326] [327] [328] [329] [330]
Underfull \hbox (badness 2197) in paragraph at lines 22624--22628
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by

Underfull \hbox (badness 4048) in paragraph at lines 22624--22628
\T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o
nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use
[331]
Underfull \hbox (badness 2846) in paragraph at lines 22638--22642
[]\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment 
\T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the 
pack-

Underfull \hbox (badness 1990) in paragraph at lines 22638--22642
\T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p
uted pack-age in-for-ma-tion ob-ject and pass this to
[332]
Underfull \hbox (badness 10000) in paragraph at lines 22722--22728
[]\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i
t loads to the search path.

Underfull \hbox (badness 1168) in paragraph at lines 22722--22728
\T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co
n-tain-ing the ex-ported val-ues of a
[333] [334] [335]
Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of

Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
[][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type
[][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\
T1/ptm/m/n/10 ) and not a fac-tor,

Underfull \hbox (badness 10000) in paragraph at lines 22925--22931
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T
1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or
[336]
Underfull \hbox (badness 4120) in paragraph at lines 22997--23004
[]\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/
n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from

[337]
Underfull \hbox (badness 1694) in paragraph at lines 23107--23110
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[338] [339] [340]
Underfull \hbox (badness 1603) in paragraph at lines 23346--23348
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[341] [342]
Overfull \hbox (73.28088pt too wide) in paragraph at lines 23464--23473
\T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats",        
"methods")\T1/ptm/m/n/10 .
[343]
Underfull \hbox (badness 5475) in paragraph at lines 23559--23569
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 3271) in paragraph at lines 23578--23581
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able

Underfull \hbox (badness 10000) in paragraph at lines 23593--23595
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[344] [345] [346]
Underfull \hbox (badness 3138) in paragraph at lines 23833--23839
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4132) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "http://www.bioconductor.org"\
T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror

Underfull \hbox (badness 4001) in paragraph at lines 23833--23839
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T
1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 1194) in paragraph at lines 23845--23848
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 1389) in paragraph at lines 23869--23871
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[347]
Underfull \hbox (badness 10000) in paragraph at lines 23886--23892
[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by

Underfull \hbox (badness 1009) in paragraph at lines 23897--23900
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 23907--23914
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see

Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 23916--23923
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Overfull \hbox (34.78088pt too wide) in paragraph at lines 23916--23923
\T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";

Underfull \hbox (badness 1881) in paragraph at lines 23930--23935
[]\T1/ptm/m/n/10 a char-ac-ter string, the path of the com-mand used for un-zip
-ping help files, or
[348] [349] [350] [351]
Underfull \vbox (badness 10000) has occurred while \output is active [352]
Underfull \hbox (badness 10000) in paragraph at lines 24227--24231
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 24227--24231
\T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[353] [354] [355] [356]
Underfull \hbox (badness 4341) in paragraph at lines 24550--24552
[]\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc
r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 ,
[357] [358] [359] [360] [361] [362] [363]
Underfull \hbox (badness 10000) in paragraph at lines 24977--24981
[]\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr
/m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully,
[364]
Underfull \hbox (badness 1796) in paragraph at lines 25040--25043
[]\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[365] [366] [367]
Underfull \hbox (badness 10000) in paragraph at lines 25235--25238
[]\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print
-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion
[368] [369] [370] [371] [372] [373] [374] [375] [376]
Underfull \hbox (badness 1226) in paragraph at lines 25855--25860
\T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T
1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/
n/10 ncol \T1/ptm/m/n/10 is greater than
[377]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25900--25900
 []           \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = 
rep(c(0,0,1),2))[] 
[378] [379] [380] [381]
Underfull \hbox (badness 7415) in paragraph at lines 26181--26185
[]\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver
sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use

Overfull \hbox (42.18039pt too wide) in paragraph at lines 26202--26202
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 
[382] [383]
Underfull \hbox (badness 2418) in paragraph at lines 26350--26361
[]\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra
mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n
ot
[384] [385] [386]
Underfull \hbox (badness 1533) in paragraph at lines 26583--26586
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[387]
Underfull \hbox (badness 1337) in paragraph at lines 26680--26683
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute
d, i.e.,
[388]
Underfull \hbox (badness 1038) in paragraph at lines 26745--26755
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[389]
Underfull \hbox (badness 10000) in paragraph at lines 26756--26759
[]\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: 
for \T1/pcr/m/n/10 na.last =     TRUE \T1/ptm/m/n/10 and
[390]
Underfull \hbox (badness 1117) in paragraph at lines 26840--26846
\T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \
T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing
[391] [392] [393] [394] [395] [396]
Underfull \hbox (badness 4048) in paragraph at lines 27210--27215
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to

Underfull \hbox (badness 4582) in paragraph at lines 27210--27215
\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:

Underfull \hbox (badness 1824) in paragraph at lines 27210--27215
\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 ,
[397] [398] [399] [400] [401] [402] [403] [404]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27743--27743
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[405] [406] [407] [408]
Overfull \hbox (13.9408pt too wide) in paragraph at lines 28025--28027
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( )
 * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T
1/ptm/m/n/10 '. 
[409] [410]
Underfull \hbox (badness 7558) in paragraph at lines 28234--28238
[]\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 5417) in paragraph at lines 28250--28253
[][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc
r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/
ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 ls[][][] \T1/ptm/m/n/10 and
[411]
Underfull \hbox (badness 10000) in paragraph at lines 28254--28256
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /

Underfull \hbox (badness 10000) in paragraph at lines 28257--28259
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[412] [413] [414] [415] [416] [417]
Underfull \hbox (badness 10000) in paragraph at lines 28664--28668
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[418] [419] [420] [421] [422] [423] [424] [425] [426] [427] [428] [429]
Underfull \hbox (badness 10000) in paragraph at lines 29470--29473
[]\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,

Underfull \hbox (badness 1430) in paragraph at lines 29470--29473
\T1/pcr/m/n/10 save(list = ls(all = TRUE), file =     ".RData")\T1/ptm/m/n/10 .
 It is also what hap-
[430] [431] [432]
Underfull \hbox (badness 2302) in paragraph at lines 29681--29688
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3815) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 29681--29688
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[433]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 29733--29733
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[434]
Underfull \hbox (badness 1158) in paragraph at lines 29834--29839
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 29861--29867
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1953) in paragraph at lines 29861--29867
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o
c-tal and hex-adec-i-mal rep-re-
[435]
Underfull \hbox (badness 10000) in paragraph at lines 29937--29942
[]\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by

Underfull \hbox (badness 6725) in paragraph at lines 29937--29942
\T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10
 will give an empty
[436]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30019--30019
 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[437] [438] [439] [440]
Underfull \hbox (badness 2809) in paragraph at lines 30282--30288
[]\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, 
..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment

Underfull \hbox (badness 7759) in paragraph at lines 30289--30292
[]\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/
n/10 1, 2, ...,  length.out \T1/ptm/m/n/10 un-less
[441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 1735) in paragraph at lines 31079--31085
\T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co
n-sole. Mes-sages sent

Underfull \hbox (badness 4303) in paragraph at lines 31095--31098
[]\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p
tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault
 out-put from
[453] [454] [455] [456] [457] [458] [459] [460]
Underfull \hbox (badness 2512) in paragraph at lines 31636--31638
[]\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s
kip if
[461] [462] [463] [464]
Underfull \vbox (badness 10000) has occurred while \output is active [465]
[466]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 32030--32030
 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m
/n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 32045--32045
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[467] [468] [469] [470] [471]
Underfull \hbox (badness 1087) in paragraph at lines 32416--32418
[]\T1/ptm/m/n/10 Markus Kuhn, ``ASCII and Uni-code quo-ta-tion marks''. [][]$\T
1/pcr/m/n/10 http : / / www . cl . cam . ac . uk /
[472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32480--32480
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 32481--32481
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[473] [474] [475]
Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
[]\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/
pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b
een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want

Underfull \hbox (badness 8113) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s
tart, in-sert a call

Underfull \hbox (badness 10000) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p
cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n
/10 ' file. For ex-am-ple,

Underfull \hbox (badness 6542) in paragraph at lines 32696--32706
\T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta
ch no ex-tra pack-ages on

Underfull \hbox (badness 5189) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (
or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-

Underfull \hbox (badness 4193) in paragraph at lines 32696--32706
\T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/
10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or

Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 32740--32746
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,

Underfull \hbox (badness 1496) in paragraph at lines 32740--32746
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be
[476]
Underfull \hbox (badness 1728) in paragraph at lines 32753--32760
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a
lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm
/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 32753--32760
\T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i
n site or user en-vi-ron-ment
[477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 33049--33055
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is
[481] [482]
Underfull \hbox (badness 1163) in paragraph at lines 33224--33231
[]\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 
%OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr
/m/n/10 0 <= n <= 6

Underfull \hbox (badness 8132) in paragraph at lines 33224--33231
\T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no
t fol-lowed by a digit, it uses the set-ting of
[483] [484] [485]
Underfull \hbox (badness 1142) in paragraph at lines 33440--33446
[]\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1
/ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or
[486]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 33455--33455
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[487] [488] [489]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 33707--33707
 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 33751--33751
 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[491] [492] [493] [494] [495] [496] [497]
Underfull \hbox (badness 10000) in paragraph at lines 34212--34215
[]\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10
 signif[][][]() \T1/ptm/m/n/10 (for
[498]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34259--34259
 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[499] [500] [501] [502]
Underfull \hbox (badness 2762) in paragraph at lines 34489--34498
\T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there
 is a match then that el-e-ment is eval-u-ated un-less

Underfull \hbox (badness 1466) in paragraph at lines 34489--34498
\T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is 
eval-u-ated, so for ex-am-ple

Overfull \hbox (31.3804pt too wide) in paragraph at lines 34548--34548
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[503] [504] [505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 34688--34688
 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS
1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. 
[506]
Underfull \hbox (badness 3219) in paragraph at lines 34770--34775
[]\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple

Underfull \hbox (badness 1107) in paragraph at lines 34770--34775
\T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr
/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match
[507]
Underfull \hbox (badness 2452) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/
ptm/m/n/10 sys-tem call. The lo-gin name comes

Underfull \hbox (badness 10000) in paragraph at lines 34864--34867
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam
es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and
[508] [509] [510]
Underfull \hbox (badness 10000) in paragraph at lines 35040--35044
[]\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents 
\T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n
/10 and

Underfull \hbox (badness 1584) in paragraph at lines 35055--35058
[]\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu
nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \
T1/ptm/m/n/10 and
[511] [512] [513]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 35248--35248
 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123))  # \TS1/pcr/
m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used 
[514] [515]
Underfull \hbox (badness 1082) in paragraph at lines 35377--35380
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[516] [517] [518]
Underfull \hbox (badness 1038) in paragraph at lines 35565--35568
[]\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i
ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or
[519] [520] [521] [522] [523]
Underfull \hbox (badness 1515) in paragraph at lines 35904--35907
[]\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc
r/m/n/10 stderr =     TRUE \T1/ptm/m/n/10 im-plies
[524]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 36020--36020
 []\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c
("no", 
[525]
Underfull \hbox (badness 1924) in paragraph at lines 36039--36042
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/pcr/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[526]
Underfull \hbox (badness 4096) in paragraph at lines 36123--36126
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i
ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[
][][]\T1/ptm/m/n/10 ,
[527] [528] [529]
Underfull \hbox (badness 10000) in paragraph at lines 36363--36365
[]\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha
t was reg-is-tered ear-lier via
[530]
Underfull \hbox (badness 10000) in paragraph at lines 36443--36446
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$http : / / developer .
[531] [532]
Underfull \hbox (badness 5475) in paragraph at lines 36564--36568
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http : / /
[533]
Underfull \hbox (badness 10000) in paragraph at lines 36626--36630
[][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http :
[534] [535] [536] [537] [538] [539]
Underfull \hbox (badness 5637) in paragraph at lines 37038--37047
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn
s the time-zone names known to the Ol-son/IANA

Underfull \hbox (badness 1629) in paragraph at lines 37038--37047
\T1/ptm/m/n/10 database on the cur-rent sys-tem. The system-specific lo-ca-tion
 in the file sys-tem varies,
[540]
Underfull \hbox (badness 3460) in paragraph at lines 37092--37094
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Time _ zone$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / www . twinsun . com /
[541] [542] [543]
Underfull \hbox (badness 10000) in paragraph at lines 37299--37301
[]\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f
rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal
l-ing
[544] [545] [546] [547] [548] [549]
Underfull \hbox (badness 6542) in paragraph at lines 37718--37720
[]\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10
 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x
)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and
[550] [551]
Underfull \hbox (badness 1708) in paragraph at lines 37841--37849
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 3713) in paragraph at lines 37841--37849
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less

Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
[]\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 
tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in-

Underfull \hbox (badness 10000) in paragraph at lines 37850--37854
\T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 ,
 some-thing like

Underfull \hbox (badness 3281) in paragraph at lines 37850--37854
\T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s
im-ple er-ror han-dler func-

Underfull \hbox (badness 4859) in paragraph at lines 37864--37869
[][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers
 and sup-press-ing the print-ing of er-ror mes-sages;
[552]
Underfull \hbox (badness 3895) in paragraph at lines 37926--37938
[]\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the
 struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in

Underfull \hbox (badness 1303) in paragraph at lines 37926--37938
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue
s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 "integer"\T1/ptm/m/n/10 ,
[553] [554] [555]
Underfull \hbox (badness 1515) in paragraph at lines 38113--38118
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[556] [557]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 38252--38252
 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[558] [559] [560] [561] [562] [563]
Underfull \hbox (badness 1803) in paragraph at lines 38707--38710
[]\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1
0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ),

Underfull \hbox (badness 2334) in paragraph at lines 38711--38718
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the
 atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and

Underfull \hbox (badness 4726) in paragraph at lines 38737--38741
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR
UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec
tor(x, mode = "numeric") \T1/ptm/m/n/10 can be

Underfull \hbox (badness 1122) in paragraph at lines 38737--38741
\T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/
10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x
, mode =
[564] [565] [566]
Underfull \hbox (badness 3668) in paragraph at lines 38915--38917
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[567] [568] [569] [570]
Underfull \hbox (badness 6220) in paragraph at lines 39189--39194
[]\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][]
(.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true,

Underfull \hbox (badness 3098) in paragraph at lines 39189--39194
\T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array
Ind() \T1/ptm/m/n/10 (and hence,

Underfull \hbox (badness 1533) in paragraph at lines 39189--39194
\T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na
mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty,

Underfull \hbox (badness 6592) in paragraph at lines 39205--39210
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[571]
Underfull \hbox (badness 1603) in paragraph at lines 39224--39228
[][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[]
[][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p
cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the
[572] [573] [574] [575] [576] [577]
Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/pcr/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to

Underfull \hbox (badness 10000) in paragraph at lines 39639--39644
\T1/pcr/m/n/10 rank(x, ties.method = "min",    na.last = "keep")\T1/ptm/m/n/10 
, so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are
[578]
Underfull \hbox (badness 2846) in paragraph at lines 39729--39733
[]\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[579]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 39769--39769
 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 

Underfull \hbox (badness 3209) in paragraph at lines 39790--39794
[]\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[580]) (./compiler-pkg.tex
Chapter 2.
[581] [582] [583]) (./datasets-pkg.tex [584]
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[585] [586] [587] [588] [589]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 294--294
 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[590]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 368--368
 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 
[591] [592] [593] [594] [595]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 691--694
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[596] [597]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 824--827
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[598] [599] [600] [601]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1131--1134
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[602] [603] [604] [605] [606]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1432--1432
 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[607] [608]
Underfull \hbox (badness 10000) in paragraph at lines 1517--1520
[]\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame 
with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r
evenue\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2903) in paragraph at lines 1517--1520
\T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m
/n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a
bove
[609]
Underfull \hbox (badness 1325) in paragraph at lines 1598--1603
[]\T1/ptm/m/n/10 Friendly, M. (1992a) Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[610] [611]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 1705--1708
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1799--1799
 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1807--1807
 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[613] [614]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1923--1923
 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1924--1924
 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[615] [616] [617] [618]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2127--2130
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[619] [620] [621] [622] [623] [624] [625] [626]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 2666--2669
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[627]
Overfull \vbox (13.87083pt too high) has occurred while \output is active
[628]
Underfull \vbox (badness 1789) has occurred while \output is active [629]
[630]
Overfull \vbox (12.25539pt too high) has occurred while \output is active
[631] [632]
Overfull \vbox (17.12102pt too high) has occurred while \output is active
[633]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3083--3083
 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[634] [635] [636] [637] [638] [639] [640]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3540--3540
 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[641]
Underfull \hbox (badness 5175) in paragraph at lines 3639--3642
[]\T1/ptm/m/n/10 Files for all 182 dis-tricts in 1888 and other years have been
 avail-able at [][]$\T1/pcr/m/n/10 http :

Underfull \hbox (badness 10000) in paragraph at lines 3639--3642
\T1/pcr/m/n/10 / / opr . princeton . edu / archive / eufert / switz . html$[][]
 \T1/ptm/m/n/10 or [][]$\T1/pcr/m/n/10 http : / / opr .
[642]
Overfull \hbox (66.81013pt too wide) in paragraph at lines 3689--3692
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou
pedData", "groupedData", "data.frame")
[643]
Overfull \vbox (10.49593pt too high) has occurred while \output is active
[644]
Overfull \vbox (27.49593pt too high) has occurred while \output is active
[645]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3891--3891
 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 

Underfull \hbox (badness 10000) in paragraph at lines 3920--3923
[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /
[646] [647] [648] [649] [650] [651] [652] [653] [654] [655]
Underfull \vbox (badness 10000) has occurred while \output is active [656]
[657] [658]) (./grDevices-pkg.tex
Chapter 4.
[659] [660] [661] [662] [663]
Underfull \hbox (badness 10000) in paragraph at lines 366--374
[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to

Underfull \hbox (badness 10000) in paragraph at lines 366--374
[][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal
 the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where
[664] [665]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462
 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[666] [667] [668] [669] [670] [671] [672] [673] [674]
Underfull \hbox (badness 5175) in paragraph at lines 1058--1060
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[675]
Underfull \hbox (badness 1325) in paragraph at lines 1120--1126
\T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co
lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 ,
[676]
Underfull \hbox (badness 10000) in paragraph at lines 1161--1163
[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /

Overfull \hbox (25.98041pt too wide) in paragraph at lines 1213--1213
 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[677]
Underfull \hbox (badness 1173) in paragraph at lines 1255--1258
[]\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[678] [679] [680]
Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
[]\T1/ptm/m/n/10 character: Which events can be gen-er-ated on

Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
\T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of

Underfull \hbox (badness 10000) in paragraph at lines 1470--1474
\T1/pcr/m/n/10 c("MouseDown",    "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10
 ,
[681]
Underfull \hbox (badness 2221) in paragraph at lines 1515--1518
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[682]
Underfull \hbox (badness 10000) in paragraph at lines 1584--1588
[]\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when

Underfull \hbox (badness 10000) in paragraph at lines 1584--1588
[][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc
r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is
[683] [684] [685]
Underfull \hbox (badness 1565) in paragraph at lines 1743--1748
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to
 pro-duce and print a postscript copy. This will not

Underfull \hbox (badness 1354) in paragraph at lines 1743--1748
\T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 
for how to set this up. Win-dows users may pre-fer to use
[686]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1826--1826
 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 

Underfull \hbox (badness 1184) in paragraph at lines 1867--1877
[]\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m
/n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in-

Underfull \hbox (badness 2057) in paragraph at lines 1867--1877
\T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p
tm/m/n/10 ,
[687] [688]
Underfull \hbox (badness 10000) in paragraph at lines 1972--1974
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[689] [690]
Underfull \hbox (badness 6758) in paragraph at lines 2133--2136
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[691] [692]
Underfull \hbox (badness 2326) in paragraph at lines 2240--2250
\T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra
phicsEventHandlers \T1/ptm/m/n/10 to re-place

Underfull \hbox (badness 2318) in paragraph at lines 2240--2250
\T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co
m-pat-i-bil-ity with pre-2.12.0

Underfull \hbox (badness 2460) in paragraph at lines 2240--2250
\T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e
vent han-dlers is to set them us-ing

Underfull \hbox (badness 1221) in paragraph at lines 2240--2250
\T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra
phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics
[693]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2324--2324
 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 
[694] [695] [696] [697] [698]
Underfull \hbox (badness 10000) in paragraph at lines 2650--2651

[699] [700] [701] [702] [703] [704]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3056--3056
 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 3057--3057
 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[705]
Underfull \hbox (badness 1210) in paragraph at lines 3088--3090
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[706] [707] [708]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3302--3302
 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al
pha = 1) 
[709] [710]
Underfull \hbox (badness 3525) in paragraph at lines 3409--3412
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

Underfull \hbox (badness 1968) in paragraph at lines 3423--3425
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[711] [712] [713] [714]
Underfull \hbox (badness 5939) in paragraph at lines 3717--3722
[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[715] [716] [717] [718] [719] [720] [721]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 4200--4200
 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[722]
Underfull \hbox (badness 1502) in paragraph at lines 4247--4252
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the 
type of anti-aliasing (if any) to be
[723] [724]
Underfull \hbox (badness 4765) in paragraph at lines 4407--4409
[][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices
 are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if

Overfull \hbox (9.78043pt too wide) in paragraph at lines 4421--4421
 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 
[725]
Underfull \hbox (badness 5077) in paragraph at lines 4461--4467
[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as

Underfull \hbox (badness 1342) in paragraph at lines 4477--4479
[]\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[726]
Underfull \hbox (badness 1874) in paragraph at lines 4554--4562
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as
[727]
Underfull \hbox (badness 1755) in paragraph at lines 4621--4623
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[728] [729]
Underfull \hbox (badness 7344) in paragraph at lines 4792--4794
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso

Underfull \hbox (badness 7397) in paragraph at lines 4803--4807
[][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D
evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm
/m/n/10 which is called from both
[730] [731]
Underfull \hbox (badness 1552) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG
othic"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4916--4925
\T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m
/n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW
Helvetica"\T1/ptm/m/n/10 ),
[732]
Underfull \hbox (badness 4686) in paragraph at lines 4959--4965
\T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap
an1Ryumin" \T1/ptm/m/n/10 for

Underfull \hbox (badness 10000) in paragraph at lines 4984--4992
[]\T1/pcr/m/n/10 Baekmuk-Batang \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m/n
/10 ftp : / / ftp . mizi . com / pub / baekmuk/$[][]\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 4984--4992
\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr/m
/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \vbox (badness 10000) has occurred while \output is active [733]
Underfull \hbox (badness 7344) in paragraph at lines 5003--5005
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[734] [735] [736]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5194--5194
 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 

Underfull \hbox (badness 1648) in paragraph at lines 5200--5204
[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[737]
Underfull \hbox (badness 10000) in paragraph at lines 5280--5282
[]\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc
r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10
 for on-screen de-vices and to
[738]
Underfull \hbox (badness 1072) in paragraph at lines 5316--5322
[]\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots 
due to cor-rupted or du-pli-
[739] [740] [741] [742]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5610--5610
 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 

Underfull \hbox (badness 10000) in paragraph at lines 5623--5626
[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[743] [744] [745] [746] [747] [748]
Underfull \hbox (badness 1189) in paragraph at lines 6019--6021
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[749] [750]
Underfull \hbox (badness 10000) in paragraph at lines 6117--6119
[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and

Underfull \hbox (badness 10000) in paragraph at lines 6156--6163
[]\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T
1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and

Underfull \hbox (badness 1584) in paragraph at lines 6156--6163
\T1/pcr/m/n/10 expression(10^degree))\T1/ptm/m/n/10 ) have been seen on Linux s
ys-tems which have the Wine
[751]
Underfull \hbox (badness 3088) in paragraph at lines 6240--6244
[]\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do-
Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and
[752]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6285--6285
 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 

Underfull \hbox (badness 10000) in paragraph at lines 6317--6320
[]\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][
] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 --
[753] [754]
Underfull \hbox (badness 5637) in paragraph at lines 6408--6414
\T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n
/10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1721) in paragraph at lines 6441--6444
[]\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt
p : / / www . schmidt-[]web-[]berlin . de /
[755] [756] [757]
Underfull \hbox (badness 6157) in paragraph at lines 6593--6596
\T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them
 via

Underfull \hbox (badness 1231) in paragraph at lines 6604--6606
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[758] [759] [760]) (./graphics-pkg.tex
Chapter 5.

Underfull \hbox (badness 10000) in paragraph at lines 16--18
[]\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag
es, use
[761] [762] [763] [764]
Underfull \hbox (badness 1412) in paragraph at lines 286--291
[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[765] [766] [767]
Underfull \hbox (badness 2726) in paragraph at lines 465--471
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark
 lo-ca-tions are com-puted in-ter-nally (the same way
[768] [769] [770]
Underfull \hbox (badness 10000) in paragraph at lines 655--659
[]\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m
/n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or

Underfull \hbox (badness 3250) in paragraph at lines 655--659
[][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/
m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1
0 if

Underfull \hbox (badness 2735) in paragraph at lines 683--690
[]\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[771]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 
[772] [773]
Underfull \hbox (badness 1062) in paragraph at lines 849--852
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic
h di-vide ad-ja-cent (non-stacked!) bars
[774] [775] [776] [777] [778] [779] [780]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1274--1274
 []    \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = 
NULL,[] 

Underfull \hbox (badness 1024) in paragraph at lines 1319--1327
\T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 cex.lab\T1/ptm/m/n/10 , and
[781]
Underfull \hbox (badness 1248) in paragraph at lines 1347--1353
\T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac
k-ground

Underfull \hbox (badness 6893) in paragraph at lines 1347--1353
\T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su
p-presses the point, and

Underfull \hbox (badness 3375) in paragraph at lines 1353--1355
[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),

Overfull \hbox (19.3703pt too wide) in paragraph at lines 1375--1379
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim =     range(at, *) + 
c(-0.5, 0.5)\T1/ptm/m/n/10 .
[782]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1423--1423
 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1424--1424
 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1430--1430
 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 1431--1431
 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[783] [784] [785] [786] [787]
Underfull \hbox (badness 10000) in paragraph at lines 1731--1737
[][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill
ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 
contourplot[][][] \T1/ptm/m/n/10 (and
[788]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1768--1768
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 1777--1777
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[789]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1860--1860
 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[790] [791]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1989--1989
 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1994--1994
 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[792] [793] [794] [795] [796]
Underfull \hbox (badness 1009) in paragraph at lines 2277--2284
\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
[797] [798] [799] [800] [801]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2605--2605
 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[802] [803]
Underfull \hbox (badness 5878) in paragraph at lines 2763--2767
\T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T
1/ptm/m/n/10 and in gen-eral sat-isfy

Underfull \hbox (badness 10000) in paragraph at lines 2791--2794
[]\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1
/ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n
/10 or
[804] [805]
Underfull \hbox (badness 10000) in paragraph at lines 2869--2872
[][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p
cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as
[806] [807] [808]
Underfull \hbox (badness 1755) in paragraph at lines 3121--3125
[]\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/
10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/
n/10 ,
[809]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied,
 raster im-ages are used when the

Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther

Underfull \hbox (badness 10000) in paragraph at lines 3196--3201
[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[810] [811] [812]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3379--3379
 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 3398--3398
 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 
[813]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3402--3402
 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[814] [815]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3578--3578
 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 3579--3579
 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[816]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3616--3616
 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [817]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3668--3668
 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 3688--3688
 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[818]
Underfull \hbox (badness 10000) in paragraph at lines 3751--3755
[][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method
; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for
[819] [820]
Underfull \hbox (badness 1867) in paragraph at lines 3903--3907
[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[821] [822] [823]
Underfull \hbox (badness 3930) in paragraph at lines 4066--4068
[]\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a 
mul-ti-ple of
[824] [825] [826] [827]
Underfull \hbox (badness 1924) in paragraph at lines 4354--4359
[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[828]
Underfull \hbox (badness 1286) in paragraph at lines 4376--4379
\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 
oma \T1/ptm/m/n/10 when chang-ing

Underfull \hbox (badness 2529) in paragraph at lines 4383--4386
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used: see
[829]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4468--4468
 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 4472--4472
 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[830]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4516--4516
 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[831]
Underfull \hbox (badness 1264) in paragraph at lines 4590--4603
\T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/
m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1
/ptm/m/n/10 ,
[832] [833]
Underfull \hbox (badness 7925) in paragraph at lines 4727--4733
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.
[834]
Underfull \hbox (badness 10000) in paragraph at lines 4857--4860


</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf, id=27864, 28
9.08pt x 289.08pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf> [835 </u
sr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/mai.pdf>]
Underfull \hbox (badness 10000) in paragraph at lines 4918--4920


</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf, id=27877, 25
9.97125pt x 332.24126pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>
Underfull \vbox (badness 10000) has occurred while \output is active [836]
[837 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/oma.pdf>]
[838]
Underfull \hbox (badness 10000) in paragraph at lines 5111--5113
[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[839]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5167--5167
 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5168--5168
 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[840]
Underfull \hbox (badness 3954) in paragraph at lines 5269--5272
[]\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm
/m/n/10 co-or-di-nates. Of-ten used with
[841]
Underfull \hbox (badness 10000) in paragraph at lines 5325--5329
\T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l
ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and
[842] [843] [844] [845]
Underfull \hbox (badness 10000) in paragraph at lines 5580--5584
[]\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing 
or an er-ror; us-ing, e.g.,

Underfull \hbox (badness 1024) in paragraph at lines 5580--5584
\T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/
n/10 type = "p" \T1/ptm/m/n/10 for S com-
[846] [847] [848] [849]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5850--5850
 []\T1/pcr/m/n/9 axis(2, at = at.y, labels = formatC(at.y, format = "fg"), col.
axis = "red")[] 
[850] [851]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6002--6002
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 
[852]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6008--6008
 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[853] [854] [855] [856] [857]
Underfull \hbox (badness 10000) in paragraph at lines 6378--6380
[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[858] [859]
Underfull \hbox (badness 1028) in paragraph at lines 6472--6474
[]\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th
is works as a mul-ti-ple of

</usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf, id=28276, 36
1.35pt x 50.1875pt>
<use /usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf>
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6515--6516
[][] 
[860 </usr/src/RPM/BUILD/R-3.1.2/library/graphics/help/figures/pch.pdf>]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6609--6609
 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[861]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6640--6640
 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [862]
[863]
Underfull \hbox (badness 10000) in paragraph at lines 6762--6764
[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr

Overfull \hbox (15.18042pt too wide) in paragraph at lines 6789--6789
 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 6795--6795
 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[864]
Underfull \hbox (badness 2600) in paragraph at lines 6855--6857
[]\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/
pcr/m/n/10 "winding" \T1/ptm/m/n/10 or
[865] [866] [867]
Underfull \hbox (badness 1881) in paragraph at lines 7044--7049
[]\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m
/n/10 par("fg")\T1/ptm/m/n/10 . Use
[868]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7087--7087
 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[869] [870] [871] [872] [873] [874]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7465--7465
 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 7476--7476
 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE))[] 
[875] [876] [877] [878] [879] [880]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7816--7816
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7819--7819
 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 7823--7823
 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[881] [882] [883]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 7994--7994
 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 7995--7995
 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[884] [885]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 8099--8099
 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 

Underfull \hbox (badness 2080) in paragraph at lines 8110--8115
[]\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1
/pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for
[886]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8214--8214
 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 
[887]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8229--8229
 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[888] [889]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8360--8360
 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[890]
Underfull \hbox (badness 7415) in paragraph at lines 8480--8487
[]\T1/ptm/m/n/10 The Euro sym-bol was in-tro-duced rel-a-tively re-cently and m
ay not be avail-able in

Underfull \hbox (badness 6808) in paragraph at lines 8480--8487
\T1/ptm/m/n/10 older fonts. In re-cent ver-sions of Adobe sym-bol fonts it is c
har-ac-ter 160, so
[891]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8532--8532
 []     \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: 
Règles, Liberté, Egalité, Fraternité...")[] 
[892]
Underfull \hbox (badness 6691) in paragraph at lines 8558--8561
[]\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex-
pan-sion)

Underfull \hbox (badness 1584) in paragraph at lines 8595--8601
[]\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m
/n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and 
\T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing
[893]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8643 \HeaderA{units}{Graphical Units}{units}
                                               [894]
Underfull \hbox (badness 1205) in paragraph at lines 8708--8710
[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[895] [896]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8827--8827
 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 
2, length = 0.1)[] 
[897]) (./grid-pkg.tex [898]
Chapter 6.
[899] [900] [901] [902] [903] [904]
Underfull \hbox (badness 10000) in paragraph at lines 383--389
\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,

Underfull \hbox (badness 1024) in paragraph at lines 383--389
\T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f
ault be-haviour for grobs is to
[905] [906] [907] [908] [909] [910] [911] [912] [913] [914]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029
 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 

Underfull \vbox (badness 10000) has occurred while \output is active [915]
Underfull \hbox (badness 1430) in paragraph at lines 1074--1079
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[916] [917] [918]
Underfull \hbox (badness 3219) in paragraph at lines 1288--1291
[]\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject 
de-scrib-ing a cir-cle), but only
[919] [920] [921] [922] [923] [924] [925]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675
 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[926] [927] [928]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891
 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[929]
Underfull \hbox (badness 2961) in paragraph at lines 1926--1931
[]\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio
ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 ,
[930]
Underfull \hbox (badness 1430) in paragraph at lines 1985--1990
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-

Underfull \hbox (badness 4479) in paragraph at lines 2014--2017
[]\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10
 to al-low a grob to per-form cus-tom ac-tions and
[931] [932] [933]
Underfull \hbox (badness 2894) in paragraph at lines 2221--2228
[]\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de
-scrib-ing a frame), but only
[934] [935] [936]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377
 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 

Underfull \hbox (badness 1430) in paragraph at lines 2389--2394
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[937] [938] [939]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2582--2582
 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 2614--2614
 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[940] [941] [942] [943]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2854--2854
 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[944] [945] [946] [947] [948]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3164--3164
 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[949]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3260--3260
 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[950]
Underfull \hbox (badness 2799) in paragraph at lines 3294--3300
[]\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage
" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see
[951]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3386--3386
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[952]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3393--3393
 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[953] [954] [955]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3587--3587
 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 3602--3602
 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 
[956] [957] [958] [959] [960] [961] [962] [963] [964]
Underfull \hbox (badness 1430) in paragraph at lines 4159--4164
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[965] [966] [967]
Underfull \hbox (badness 1067) in paragraph at lines 4342--4345
[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[968]
Underfull \hbox (badness 1430) in paragraph at lines 4388--4393
[]\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p
tm/m/n/10 should be treated as a reg-u-
[969] [970] [971]
Underfull \hbox (badness 7256) in paragraph at lines 4585--4587
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[972] [973] [974] [975] [976] [977] [978] [979] [980]
Underfull \hbox (badness 10000) in paragraph at lines 5174--5176
[]\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu
-ments above are passed to
[981] [982] [983] [984] [985] [986] [987] [988] [989] [990]
Underfull \hbox (badness 3449) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1,
 "npc") - unit(1, "inches")\T1/ptm/m/n/10 ),

Underfull \hbox (badness 10000) in paragraph at lines 5856--5862
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[991] [992] [993] [994] [995]
Underfull \hbox (badness 1867) in paragraph at lines 6157--6159
[]\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for 
use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or
[996]
Underfull \hbox (badness 10000) in paragraph at lines 6194--6200
[][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView
port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV
iewport[][][]\T1/ptm/m/n/10 ,
[997] [998]
Underfull \hbox (badness 7649) in paragraph at lines 6326--6329
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[999] [1000] [1001]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6530--6530
 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1002]) (./methods-pkg.tex
Chapter 7.
[1003] [1004] [1005]
Underfull \hbox (badness 10000) in paragraph at lines 278--285
[]\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method,
 \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her-

Underfull \hbox (badness 7704) in paragraph at lines 278--285
\T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \
T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the

Underfull \hbox (badness 10000) in paragraph at lines 278--285
\T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about 
it, you'll prob-a-bly agree that you wouldn't

Underfull \hbox (badness 5817) in paragraph at lines 278--285
\T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/
n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus,

Overfull \hbox (0.78088pt too wide) in paragraph at lines 278--285
\T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE
))
[1006] [1007] [1008] [1009] [1010] [1011]
Underfull \hbox (badness 1281) in paragraph at lines 658--667
[]\T1/ptm/m/n/10 Note that the pre-ced-ing def-i-ni-tion means that the next me
thod is de-fined uniquely when
[1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022]
[1023] [1024] [1025] [1026]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1841--1841
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1843--1843
 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 

Underfull \hbox (badness 10000) in paragraph at lines 1885--1887
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca
lls
[1027] [1028]
Underfull \hbox (badness 10000) in paragraph at lines 2028--2033
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class
[1029] [1030] [1031] [1032] [1033]
Underfull \hbox (badness 10000) in paragraph at lines 2382--2386
[]\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od
s dis-patch, call
[1034] [1035] [1036]
Underfull \hbox (badness 3792) in paragraph at lines 2628--2631
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1037]
Underfull \hbox (badness 1194) in paragraph at lines 2659--2663
[]\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10
 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and

Overfull \hbox (24.78088pt too wide) in paragraph at lines 2715--2715
 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1038] [1039] [1040]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 2951--2951
 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049]
Underfull \hbox (badness 10000) in paragraph at lines 3531--3535
[]\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge
tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class
[1050]
Underfull \hbox (badness 10000) in paragraph at lines 3637--3642
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

Overfull \hbox (28.78088pt too wide) in paragraph at lines 3645--3654
[]
[1051]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 3734--3734
 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1052]
Underfull \hbox (badness 1394) in paragraph at lines 3805--3810
\T1/ptm/m/n/10 If ar-gu-ment \T1/pcr/m/n/10 fullInfo \T1/ptm/m/n/10 is \T1/pcr/
m/n/10 TRUE\T1/ptm/m/n/10 , the call re-turns a named list of ob-jects of class

[1053] [1054] [1055]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4067--4067
 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1056] [1057] [1058]
Underfull \hbox (badness 10000) in paragraph at lines 4252--4254
[]\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method 
ex-ists for
[1059]
Underfull \hbox (badness 1629) in paragraph at lines 4354--4363
\T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is 
to mod-ify a field ex-plic-itly by
[1060]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4415--4415
 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 4416--4416
 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1061]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4473--4473
 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1062] [1063] [1064] [1065] [1066] [1067]
Underfull \hbox (badness 10000) in paragraph at lines 4945--4954
[]\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha
t eval-u-ates a call to
[1068]
Underfull \vbox (badness 10000) has occurred while \output is active [1069]
[1070]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5138--5138
 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5167--5167
 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier
 fails here)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 5181--5181
 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1071]
[1072]
Underfull \hbox (badness 1033) in paragraph at lines 5251--5258
\T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T
1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si
g-na-ture

Underfull \hbox (badness 10000) in paragraph at lines 5325--5327
[]\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t
er-nally by
[1073] [1074] [1075] [1076] [1077]
Underfull \hbox (badness 1087) in paragraph at lines 5619--5624
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing

Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 5632--5636
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1078]
Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 5723--5727
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1079] [1080]
Underfull \hbox (badness 10000) in paragraph at lines 5900--5916
[]\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m
/n/10 is equiv-a-lent to in-vok-ing the method
[1081] [1082] [1083]
Underfull \hbox (badness 1248) in paragraph at lines 6186--6190
[]\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt
m/m/n/10 method car-ries out its own com-pu-ta-tions,

Underfull \hbox (badness 1960) in paragraph at lines 6186--6190
\T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per
-form stan-dard ini-tial-iza-tion, as shown in the
[1084]
Underfull \hbox (badness 4647) in paragraph at lines 6274--6276
[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1085]
Underfull \hbox (badness 1072) in paragraph at lines 6348--6355
[]\T1/ptm/m/n/10 Establish a traced ver-sion of method
[1086] [1087] [1088] [1089] [1090]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6707 \aliasA{S4}{S3Part}{S4}
                               [1091] [1092] [1093]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6948--6948
 []\T1/pcr/m/n/9 ## note the these classes can insert an S3 subclass of "lm" as
 the S3 part:[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6953--6953
 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c
("mlm", "lm")[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex})
 has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6983 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.6985 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.6986 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored

<to be read again> 
                   \relax 
l.6988 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.6989 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1094]
Underfull \hbox (badness 2050) in paragraph at lines 7050--7054
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing

Underfull \hbox (badness 6708) in paragraph at lines 7063--7075
[]\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cummax"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2012) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/
pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr
/m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3209) in paragraph at lines 7063--7075
\T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T
1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m
/n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 ,
[1095] [1096]
Underfull \hbox (badness 1694) in paragraph at lines 7223--7225
[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see
[1097]
Underfull \hbox (badness 10000) in paragraph at lines 7247--7250
[]\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup
erClasses() \T1/ptm/m/n/10 which calls
[1098] [1099] [1100] [1101] [1102] [1103]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7702--7702
 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(),[] 
[1104] [1105]
Underfull \hbox (badness 2277) in paragraph at lines 7838--7846
[]\T1/ptm/m/n/10 Note that call-ing \T1/pcr/m/n/10 setGeneric() \T1/ptm/m/n/10 
in this form is not strictly nec-es-sary be-fore call-ing

Underfull \hbox (badness 3128) in paragraph at lines 7879--7884
[]\T1/ptm/m/n/10 If you \T1/ptm/m/it/10 don't \T1/ptm/m/n/10 want the ex-ist-in
g func-tion to be taken as de-fault, sup-ply the ar-gu-ment
[1106]
Underfull \hbox (badness 1052) in paragraph at lines 7916--7923
[]\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If
 \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it
[1107] [1108] [1109] [1110]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8236--8236
 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1111]
Underfull \hbox (badness 1755) in paragraph at lines 8270--8273
[]\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the 
method. For
[1112]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8413--8413
 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li
nk{setClass})[] 
[1113] [1114] [1115] [1116] [1117]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8819--8819
 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date 
= "POSIXt"))[] 
[1118]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8832--8832
 []\T1/pcr/m/n/9 # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m/n/9
 s class, then calls the S3 print method.[] 
[1119]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8930--8930
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 8941--8941
 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128]
Underfull \hbox (badness 10000) in paragraph at lines 9634--9636
[]\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function
" \T1/ptm/m/n/10 for class

Underfull \hbox (badness 1852) in paragraph at lines 9642--9646
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,

Underfull \hbox (badness 1681) in paragraph at lines 9642--9646
\T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func
tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends
[1129] [1130] [1131] [1132]) (./parallel-pkg.tex
Chapter 8.

Underfull \hbox (badness 2418) in paragraph at lines 15--17
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr
/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1133]
Underfull \hbox (badness 4242) in paragraph at lines 94--96
[]\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \
T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for
[1134] [1135]
Underfull \hbox (badness 1024) in paragraph at lines 194--197
[]\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has 
ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 
for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and
[1136]
Underfull \hbox (badness 5077) in paragraph at lines 281--284
[]\T1/ptm/m/n/10 It has meth-ods to do so for Linux, OS X, FreeBSD, So-laris, I
rix and Win-dows.
[1137] [1138]
Underfull \hbox (badness 10000) in paragraph at lines 413--415
[]\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/
10 Rscript \T1/ptm/m/n/10 such as
[1139] [1140] [1141] [1142]
Underfull \hbox (badness 1917) in paragraph at lines 702--711
[]\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr
/m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class

Underfull \hbox (badness 1178) in paragraph at lines 702--711
\T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in
-herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If
[1143] [1144]
Underfull \hbox (badness 10000) in paragraph at lines 839--842
[]\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T
1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1
\T1/ptm/m/n/10 : for
[1145] [1146] [1147]
Underfull \hbox (badness 5388) in paragraph at lines 1028--1033
[]\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1
/pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from
[1148]
Underfull \hbox (badness 10000) in paragraph at lines 1052--1060
[]\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/
m/n/10 is dif-fer-ent only if

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1088--1088
 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin
ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] 
[1149] [1150]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1203--1203
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 1217--1217
 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 

Underfull \hbox (badness 1577) in paragraph at lines 1246--1249
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1151]
Underfull \hbox (badness 3375) in paragraph at lines 1292--1294
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/
n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to
[1152] [1153]) (./splines-pkg.tex [1154]
Chapter 9.

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1155] [1156] [1157] [1158] [1159] [1160] [1161]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 467--467
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1162] [1163] [1164]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 678--678
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1165] [1166] [1167]) (./stats-pkg.tex [1168]
Chapter 10.
[1169]
Underfull \hbox (badness 2781) in paragraph at lines 65--68
[]\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of 
\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 ,
[1170] [1171] [1172] [1173] [1174]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 416--416
 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 437--437
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1175] [1176] [1177] [1178] [1179] [1180]
Underfull \hbox (badness 1024) in paragraph at lines 843--845
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189]
Underfull \hbox (badness 10000) in paragraph at lines 1387--1389
[]\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu-
ment
[1190]
Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class

Underfull \hbox (badness 10000) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e
r-ror strata of class

Underfull \hbox (badness 1490) in paragraph at lines 1503--1507
\T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\
T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \
T1/ptm/m/n/10 meth-ods avail-able for
[1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199]
Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
[]\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en-
sure

Underfull \hbox (badness 10000) in paragraph at lines 2076--2081
\T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo
r

Underfull \hbox (badness 1371) in paragraph at lines 2076--2081
\T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\
T1/ptm/m/n/10 , it has been ad-van-ta-geous

Underfull \hbox (badness 1221) in paragraph at lines 2082--2088
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-

Underfull \hbox (badness 4608) in paragraph at lines 2082--2088
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1200]
Underfull \hbox (badness 3965) in paragraph at lines 2163--2165
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1201] [1202] [1203] [1204]
Underfull \hbox (badness 1221) in paragraph at lines 2418--2423
[]\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num
-ber of pa-

Underfull \hbox (badness 4608) in paragraph at lines 2418--2423
\T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 
en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied.
[1205]
Underfull \hbox (badness 3965) in paragraph at lines 2495--2497
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1206] [1207]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2630--2630
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1208] [1209] [1210] [1211]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2866--2866
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1212] [1213] [1214]
Overfull \hbox (19.88992pt too wide) in paragraph at lines 3059--3061
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of variances"\T1/ptm/m/n/10 . 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 3106--3106
 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 3107--3107
 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1215] [1216] [1217] [1218] [1219] [1220]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3485--3485
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1221] [1222] [1223] [1224]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3755--3755
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1225] [1226] [1227] [1228] [1229]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4040--4040
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 4041--4041
 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1230] [1231] [1232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4276--4276
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1233] [1234] [1235]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4439--4439
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1236]
Underfull \hbox (badness 3989) in paragraph at lines 4528--4535
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1237] [1238] [1239] [1240] [1241]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4876--4876
 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1))
, ci = c(-1,-1))[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4878--4878
 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci
 = c(-0.9,0.1))[] 
[1242]
Underfull \hbox (badness 7397) in paragraph at lines 4965--4969
[]\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an 
ar-gu-ment to all these con-trast func-tions, how-ever

Underfull \hbox (badness 7326) in paragraph at lines 4965--4969
\T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p
tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for
[1243] [1244]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5099--5099
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 5117--5117
 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 
[1245]
Underfull \hbox (badness 2680) in paragraph at lines 5144--5146
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is 
given by

Underfull \hbox (badness 10000) in paragraph at lines 5149--5151
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m
/n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 ,
[1246] [1247] [1248]
Underfull \hbox (badness 1436) in paragraph at lines 5327--5332
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances

Underfull \hbox (badness 1377) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)

Underfull \hbox (badness 1448) in paragraph at lines 5327--5332
\T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \
T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/
n/10 ,
[1249] [1250]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5513--5513
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1251]
Underfull \hbox (badness 1168) in paragraph at lines 5585--5590
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1252] [1253]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5679--5679
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1254] [1255] [1256]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5864--5864
 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1257] [1258] [1259]
Underfull \hbox (badness 10000) in paragraph at lines 6027--6032
[]\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node
 of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When
[1260] [1261] [1262]
Underfull \hbox (badness 5954) in paragraph at lines 6215--6217
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1263]
Underfull \hbox (badness 2503) in paragraph at lines 6297--6300
[]\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 5563) in paragraph at lines 6301--6303
[]\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also

Underfull \hbox (badness 1655) in paragraph at lines 6304--6309
\T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm
/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2,

Underfull \hbox (badness 7238) in paragraph at lines 6339--6342
[][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion
 to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr
am[][][] \T1/ptm/m/n/10 and
[1264]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6374--6374
 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6389--6389
 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p
cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 6404--6404
 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1265]
[1266] [1267] [1268]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6645--6645
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1269] [1270] [1271] [1272] [1273] [1274]
Underfull \hbox (badness 10000) in paragraph at lines 7012--7016
\T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/
m/n/10 or
[1275]
Underfull \hbox (badness 6493) in paragraph at lines 7109--7112
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1276] [1277]
Underfull \hbox (badness 1430) in paragraph at lines 7246--7249
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht
tp : / / cran . r-[]project . org / web / views /
[1278] [1279] [1280] [1281] [1282] [1283]
Underfull \hbox (badness 10000) in paragraph at lines 7656--7661
[]\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T
1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ...,
[1284] [1285]
Overfull \hbox (33.6622pt too wide) in paragraph at lines 7794--7796
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log
 = TRUE)\T1/ptm/m/n/10 . 
[1286] [1287] [1288]
Underfull \hbox (badness 1210) in paragraph at lines 8011--8013
[]\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b
e sup-plied as named ar-gu-ments to
[1289] [1290] [1291] [1292] [1293] [1294] [1295]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8455--8455
 []    \T1/pcr/m/n/9 mu.eta <- function(eta) days * plogis(eta)^(days-1) * bino
mial()$mu_eta[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8477--8477
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 8480--8480
 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1296] [1297]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8618--8618
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 

Underfull \hbox (badness 1859) in paragraph at lines 8655--8660
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\
T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned,
 i.e., if
[1298] [1299] [1300] [1301] [1302]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8987--8987
 []                \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Moderate
S", "VeryS")))[] 
[1303] [1304] [1305]
Overfull \hbox (61.88992pt too wide) in paragraph at lines 9155--9157
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1306] [1307] [1308] [1309] [1310] [1311] [1312]
Underfull \hbox (badness 2443) in paragraph at lines 9607--9613
[][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te
r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment);
[1313] [1314] [1315]
Underfull \hbox (badness 10000) in paragraph at lines 9821--9824
[]\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org /
 wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or
[1316] [1317] [1318] [1319]
Underfull \hbox (badness 4518) in paragraph at lines 10081--10086
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1320]
Underfull \hbox (badness 4132) in paragraph at lines 10120--10124
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od
[1321]
Underfull \hbox (badness 10000) in paragraph at lines 10223--10226
[]\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie
nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 fitted.values \T1/ptm/m/n/10 and
[1322] [1323] [1324]
Underfull \hbox (badness 2142) in paragraph at lines 10423--10426
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@
[1325]
Underfull \hbox (badness 1708) in paragraph at lines 10504--10507
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1326]
Underfull \hbox (badness 10000) in paragraph at lines 10545--10551
[][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl
m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co
r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions,

Underfull \hbox (badness 1418) in paragraph at lines 10583--10588
\T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \
T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (=
[1327] [1328]
Underfull \hbox (badness 2635) in paragraph at lines 10716--10719
\T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1
/pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1
0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th
e
[1329] [1330]
Underfull \hbox (badness 1694) in paragraph at lines 10883--10886
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1331]
Underfull \hbox (badness 1337) in paragraph at lines 10902--10911
[]\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate
 den-dro-gram is re-ordered ac-cord-

Underfull \hbox (badness 3049) in paragraph at lines 10902--10911
\T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos
ed by the den-dro-gram, by
[1332]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 10984--10984
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 11017--11017
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 
[1333]
Underfull \hbox (badness 10000) in paragraph at lines 11030--11034
[]\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p
tm/m/n/10 (the de-fault) or
[1334] [1335] [1336] [1337] [1338]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11334--11334
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11349 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11401--11401
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1339]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11413--11413
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 

Underfull \hbox (badness 1062) in paragraph at lines 11460--11465
[]\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/
10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther
e to en-cour-age the use of these di-

Underfull \hbox (badness 1052) in paragraph at lines 11471--11473
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1340] [1341]
Underfull \hbox (badness 3623) in paragraph at lines 11600--11602
[]\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max
(50*.Machine$double.eps,    0.5e-28) \T1/ptm/m/n/10 if
[1342] [1343]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11688--11688
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1344]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 11781--11781
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1345]
Underfull \hbox (badness 10000) in paragraph at lines 11829--11832
[]\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i
t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1
/ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is
[1346] [1347] [1348]
Underfull \hbox (badness 4441) in paragraph at lines 12024--12026
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

Underfull \hbox (badness 10000) in paragraph at lines 12031--12033
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1349] [1350]
Underfull \hbox (badness 2753) in paragraph at lines 12121--12123
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1351] [1352]
Underfull \hbox (badness 1292) in paragraph at lines 12246--12250
\T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion
 \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for
[1353]
Underfull \hbox (badness 10000) in paragraph at lines 12359--12361
[]\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/
n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm
/m/n/10 of

Underfull \hbox (badness 2894) in paragraph at lines 12365--12369
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method

Underfull \hbox (badness 1038) in paragraph at lines 12365--12369
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive (
or true), trac-ing in-for-ma-tion on the
[1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364]
Underfull \hbox (badness 4518) in paragraph at lines 13059--13064
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1365] [1366] [1367]
Underfull \hbox (badness 10000) in paragraph at lines 13253--13257
[]\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a
ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/
10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10
 ,
[1368] [1369]
Underfull \hbox (badness 6995) in paragraph at lines 13438--13440
[][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a
nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had
[1370] [1371] [1372]
Underfull \hbox (badness 1163) in paragraph at lines 13586--13594
\T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t
hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual
s[][][]\T1/ptm/m/n/10 ,
[1373]
Underfull \hbox (badness 4518) in paragraph at lines 13706--13711
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1374] [1375] [1376]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13884--13884
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 13885--13885
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1377]
Underfull \hbox (badness 10000) in paragraph at lines 13940--13943
[]\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g
ent,

Underfull \hbox (badness 1715) in paragraph at lines 13940--13943
\T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i
s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts
[1378] [1379] [1380] [1381]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14226--14226
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 14227--14227
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1382]
Overfull \hbox (45.6622pt too wide) in paragraph at lines 14277--14279
[]\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1
 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1
/cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l
og = TRUE)\T1/ptm/m/n/10 . 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 14320--14320
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1383] [1384] [1385] [1386] [1387] [1388] [1389]
Underfull \hbox (badness 2726) in paragraph at lines 14722--14725
[]\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1
/pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 ,
[1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15436--15436
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1401] [1402] [1403]
Underfull \hbox (badness 1648) in paragraph at lines 15627--15629
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,

Underfull \hbox (badness 2591) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must
 sup-ply vari-ables with the same names as would

Underfull \hbox (badness 3930) in paragraph at lines 15641--15650
\T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/
ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing
[1404]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 15705--15705
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= "contr.poly"))[] 
[1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16258--16258
 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3))  # does not affect objects
 with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] 
[1413] [1414] [1415] [1416]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 16486--16486
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1417] [1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 2772) in paragraph at lines 16922--16925
[]\T1/ptm/m/n/10 a named list or named nu-meric vec-tor of start-ing es-ti-mate
s. When

Underfull \hbox (badness 10000) in paragraph at lines 16922--16925
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is miss-ing, a very cheap guess for \T1/pcr
/m/n/10 start \T1/ptm/m/n/10 is tried (if
[1423] [1424]
Underfull \hbox (badness 2359) in paragraph at lines 17041--17043
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1425]
Underfull \vbox (badness 10000) has occurred while \output is active [1426]
Underfull \vbox (badness 10000) has occurred while \output is active [1427]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17213--17213
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1428]
Underfull \hbox (badness 10000) in paragraph at lines 17293--17297
[]\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m
/n/10 b0 +
[1429] [1430]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17373--17373
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi
ty), DNase.2)[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 17420--17420
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1431]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 17467--17467
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439]
Underfull \hbox (badness 1248) in paragraph at lines 17957--17960
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on

Underfull \hbox (badness 1127) in paragraph at lines 17970--17974
\T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 1478) in paragraph at lines 17978--17982
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De
-faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and

[1440]
Underfull \hbox (badness 2042) in paragraph at lines 18031--18033
[]\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm
/m/n/10 method; see com-po-nent
[1441]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18127--18127
 []      \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no
t* at boundary[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1442]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18169--18169
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 
[1443]
Underfull \hbox (badness 2564) in paragraph at lines 18240--18251
[]\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u-
ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1
0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t
ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1082) in paragraph at lines 18240--18251
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately 
\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm
/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa
[1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18303--18303
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1445] [1446] [1447]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18518--18518
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1448]
Underfull \hbox (badness 1337) in paragraph at lines 18594--18597
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1449] [1450] [1451] [1452] [1453] [1454]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 18910--18910
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1455]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 18997--18997
 []       \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist
 vs Leverage  " * h[ii] / (1 - h[ii]))),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 19000--19000
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1456] [1457] [1458] [1459] [1460]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19313--19313
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 

Underfull \hbox (badness 4779) in paragraph at lines 19320--19322
[]\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

Underfull \hbox (badness 1194) in paragraph at lines 19323--19326
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1461]
Underfull \hbox (badness 1107) in paragraph at lines 19381--19383
[]\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to
[1462]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19436--19436
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1463]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 19443--19443
 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 
1, y.intersp = 1)[] 

Underfull \hbox (badness 10000) in paragraph at lines 19492--19495
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/
m/n/10 which gives

Underfull \hbox (badness 10000) in paragraph at lines 19492--19495
\T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for

[1464]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 19536--19536
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1465] [1466]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 19658--19658
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1467]
Underfull \hbox (badness 10000) in paragraph at lines 19716--19718
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478]
[1479] [1480] [1481]
Underfull \hbox (badness 6859) in paragraph at lines 20681--20688
[][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi
ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre
dict.poly[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 20692--20698
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492]
[1493] [1494] [1495] [1496] [1497] [1498]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 21684--21684
 []                          \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == 
"Pr(",[] 
[1499] [1500] [1501] [1502] [1503]
Underfull \hbox (badness 1337) in paragraph at lines 22007--22013
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 1028) in paragraph at lines 22690--22693
[]\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/
pcr/m/n/10 write() \T1/ptm/m/n/10 and
[1514] [1515]
Underfull \hbox (badness 10000) in paragraph at lines 22800--22803
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 5091) in paragraph at lines 22800--22803
\T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for
 ef-fi-ciency if
[1516] [1517] [1518]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23011--23011
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1519] [1520] [1521]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 23230--23230
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1522] [1523]
Underfull \hbox (badness 10000) in paragraph at lines 23375--23378
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1524]
Underfull \hbox (badness 2134) in paragraph at lines 23426--23430
[][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from

Overfull \hbox (9.78043pt too wide) in paragraph at lines 23439--23439
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1525] [1526] [1527] [1528]
Underfull \hbox (badness 7667) in paragraph at lines 23692--23694
[]\T1/ptm/m/n/10 a nu-meric vec-tor or an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-je
ct which is co-ercible to one by
[1529] [1530] [1531]
Underfull \hbox (badness 2591) in paragraph at lines 23895--23901
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getInitial[][
][]\T1/ptm/m/n/10 . Each of the fol-low-ing are \T1/pcr/m/n/10 "selfStart" \T1/
ptm/m/n/10 mod-els (with ex-am-
[1532] [1533] [1534] [1535] [1536] [1537]
Underfull \hbox (badness 1412) in paragraph at lines 24301--24303
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1538] [1539]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 24388--24388
 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS
S"), smooth(x)))[] 

Underfull \hbox (badness 10000) in paragraph at lines 24443--24448
[]\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when

Underfull \hbox (badness 2435) in paragraph at lines 24443--24448
\T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault
), the num-ber of
[1540] [1541]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 24600--24600
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 
[1542] [1543] [1544]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 24770--24770
 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"),
 sep = " = "),[] 
[1545]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 24837--24837
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1546] [1547] [1548] [1549] [1550] [1551]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 25213--25213
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 

Underfull \hbox (badness 6477) in paragraph at lines 25266--25269
[]\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p
tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of 
an
[1552] [1553]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 25392--25392
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 25393--25393
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1554]
Underfull \hbox (badness 2922) in paragraph at lines 25459--25464
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1555]
Underfull \hbox (badness 2922) in paragraph at lines 25521--25526
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion

Underfull \hbox (badness 3240) in paragraph at lines 25533--25537
[][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][]
[]\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap
h show-ing the \T1/pcr/m/n/10 SSasympOff
[1556]
Underfull \hbox (badness 2922) in paragraph at lines 25578--25583
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1557]
Underfull \hbox (badness 2922) in paragraph at lines 25639--25645
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1558]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25661--25661
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 25677--25677
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1559] [1560]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 25791--25791
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 25814--25814
 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response 
and gradient[] 
[1561]
Underfull \hbox (badness 2922) in paragraph at lines 25852--25857
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1562]
Underfull \hbox (badness 2922) in paragraph at lines 25908--25913
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion

Underfull \hbox (badness 2922) in paragraph at lines 25965--25970
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1563]
Underfull \hbox (badness 2922) in paragraph at lines 26020--26025
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1564]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26041--26041
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 

Underfull \hbox (badness 6493) in paragraph at lines 26089--26094
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1565]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26115--26115
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 26117--26117
 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1566] [1567] [1568] [1569] [1570] [1571] [1572]
Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

Underfull \hbox (badness 10000) in paragraph at lines 26611--26614
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1573] [1574] [1575] [1576] [1577] [1578] [1579]
Underfull \hbox (badness 3396) in paragraph at lines 27040--27042
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10
 , usu-ally, a re-sult of a call to
[1580] [1581] [1582]
Underfull \hbox (badness 2237) in paragraph at lines 27217--27219
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1583] [1584]
Underfull \hbox (badness 2591) in paragraph at lines 27381--27383
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10
 , usu-ally the re-sult of a call to
[1585]
Underfull \hbox (badness 2237) in paragraph at lines 27427--27430
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p
cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1586] [1587] [1588]
Underfull \hbox (badness 3407) in paragraph at lines 27606--27610
[]\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m
ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low)
[1589] [1590]
Underfull \hbox (badness 1337) in paragraph at lines 27739--27743
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1591] [1592]
Underfull \hbox (badness 10000) in paragraph at lines 27856--27859
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1593] [1594]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 27985--27985
 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 28013--28013
 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1595]
Underfull \hbox (badness 1616) in paragraph at lines 28039--28042
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1596]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 28118--28118
 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1597]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 28195--28195
 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1598]
Underfull \hbox (badness 5050) in paragraph at lines 28231--28236
[]\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject
 is re-turned. The ob-ject it-self is the re-ordered (un-less
[1599]
Underfull \hbox (badness 2205) in paragraph at lines 28281--28286
[]\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv
en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
[1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 28875--28875
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 
[1608]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 28876--28876
 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1609] [1610]
Underfull \hbox (badness 1178) in paragraph at lines 29008--29010
[]\T1/ptm/m/n/10 In \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.2 and ear-lier the re-
sults were \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 for fits with \T1/pcr/m/n/10 na.act
ion \T1/ptm/m/n/10 meth-ods such as
[1611] [1612]
Underfull \hbox (badness 10000) in paragraph at lines 29161--29165
[]\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p
cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect

Underfull \hbox (badness 1596) in paragraph at lines 29161--29165
\T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign(
f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at

Overfull \hbox (30.78088pt too wide) in paragraph at lines 29172--29172
 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 29173--29173
 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1613] [1614]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 29299--29299
 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 29308--29308
 []\T1/pcr/m/n/9 ## where as  \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1
/pcr/m/n/9 '  \T1/pcr/m/n/9 simply first enlarges the search interval:[] 
[1615] [1616] [1617] [1618]
Underfull \hbox (badness 1337) in paragraph at lines 29524--29528
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626]
Underfull \hbox (badness 1337) in paragraph at lines 30008--30012
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1627]
Underfull \hbox (badness 5161) in paragraph at lines 30101--30103
[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1628] [1629] [1630] [1631] [1632]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 30426--30426
 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 30427--30427
 []      \T1/pcr/m/n/10 na.action, exclude = c(NA, NaN), drop.unused.levels = F
ALSE)[] 

Underfull \hbox (badness 6775) in paragraph at lines 30465--30470
[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or
[1633] [1634]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 30531--30531
 [] \T1/pcr/m/n/9 print(xtabs(~ Type + Subj, data = d.ergo[sample(36, 10), ], s
parse = TRUE))[] 
[1635]) (./stats4-pkg.tex [1636]
Chapter 11.
[1637] [1638] [1639]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192
 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1640] [1641] [1642]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1643]
Underfull \hbox (badness 10000) in paragraph at lines 440--443
[]\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class
[1644] [1645]) (./tcltk-pkg.tex [1646]
Chapter 12.
[1647] [1648] [1649] [1650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 342--342
 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
[1651] [1652] [1653]
Underfull \vbox (badness 10000) has occurred while \output is active [1654]
Underfull \hbox (badness 1292) in paragraph at lines 649--656
[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665]
Underfull \hbox (badness 1490) in paragraph at lines 1390--1393
[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1666]) (./tools-pkg.tex
Chapter 13.
[1667]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69
 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1668]
Underfull \hbox (badness 10000) in paragraph at lines 138--140
[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
 which will be eval-u-ated via

Underfull \hbox (badness 1253) in paragraph at lines 164--167
[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1669]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215
 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1670]
Underfull \hbox (badness 5147) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12

Underfull \hbox (badness 4792) in paragraph at lines 285--298
\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-

Underfull \hbox (badness 2237) in paragraph at lines 285--298
\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 ,
[1671]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370
 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 

Underfull \hbox (badness 2460) in paragraph at lines 389--391
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1672] [1673] [1674]
Underfull \hbox (badness 10000) in paragraph at lines 538--539
[][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer / 
en / opentype / glyphlist .
[1675] [1676] [1677] [1678] [1679] [1680]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 900--900
 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 
[1681]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 948--948
 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1682]
Underfull \hbox (badness 1635) in paragraph at lines 1048--1050
[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1683]
Underfull \hbox (badness 5431) in paragraph at lines 1114--1117
[]\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa
ssed to

Underfull \hbox (badness 1112) in paragraph at lines 1117--1125
\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-fault:

Underfull \hbox (badness 3724) in paragraph at lines 1117--1125
\T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen
-den-cies (de-fault:
[1684]
Underfull \hbox (badness 1014) in paragraph at lines 1137--1139
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 10000) in paragraph at lines 1166--1169
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-

Underfull \hbox (badness 10000) in paragraph at lines 1166--1169
\T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p
tm/m/n/10 and
[1685] [1686]
Underfull \hbox (badness 10000) in paragraph at lines 1273--1276
[]\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p
tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1
0 and

Underfull \hbox (badness 10000) in paragraph at lines 1294--1296
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1687] [1688] [1689]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1454--1454
 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 

Underfull \hbox (badness 7981) in paragraph at lines 1464--1468
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 1464--1468
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1690] [1691] [1692]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1666 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1693] [1694]
Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList

Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
\T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i-
fied (for in-stance if

Underfull \hbox (badness 10000) in paragraph at lines 1792--1797
\T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1
/ptm/m/n/10 ', it would only re-turn
[1695] [1696] [1697] [1698]
Underfull \hbox (badness 1342) in paragraph at lines 2060--2066
\T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R
 \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in
[1699] [1700]
Underfull \hbox (badness 7981) in paragraph at lines 2183--2189
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 2183--2189
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 .
[1701]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2218--2218
 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 
[1702] [1703] [1704] [1705] [1706] [1707] [1708]
Underfull \hbox (badness 1072) in paragraph at lines 2679--2681
[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to
r of links, as re-turned by
[1709] [1710] [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3349--3349
 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 

Underfull \hbox (badness 10000) in paragraph at lines 3369--3371
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,

Underfull \hbox (badness 2932) in paragraph at lines 3386--3392
[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1719] [1720] [1721] [1722] [1723]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3671--3671
 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 

Underfull \hbox (badness 10000) in paragraph at lines 3682--3685
[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and

Underfull \hbox (badness 6859) in paragraph at lines 3698--3703
[]\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/
m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p
tm/m/n/10 ' are up-dated from

Underfull \hbox (badness 1184) in paragraph at lines 3706--3712
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
/\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T
he

Underfull \hbox (badness 2941) in paragraph at lines 3706--3712
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t
he pack-age are ex-am-ined to cre-ate a file
[1724]
Underfull \hbox (badness 3758) in paragraph at lines 3786--3791
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-

Underfull \hbox (badness 2865) in paragraph at lines 3786--3791
\T1/ptm/m/n/10 ject such that a min-i-mal set of de-pen-den-cies are spec-i-fie
d (for in-stance if there was
[1725] [1726]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3916--3916
 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 

Underfull \hbox (badness 1742) in paragraph at lines 3928--3940
\T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 ,
[1727]
Underfull \hbox (badness 1127) in paragraph at lines 3962--3966
[]\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for 
R pack-ages, ex-tracts in-for-ma-tion from

Underfull \hbox (badness 3623) in paragraph at lines 3989--3992
[]\T1/ptm/m/n/10 Invisibly re-turns the num-ber of pack-ages de-scribed in the 
re-sult-ing `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ' and
[1728] [1729] [1730]) (./utils-pkg.tex
Chapter 14.

Underfull \hbox (badness 1072) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ',
[1731] [1732] [1733]
Underfull \hbox (badness 1038) in paragraph at lines 197--200
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 by de-
[1734]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 253--253
 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1735] [1736] [1737]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 493--493
 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 
[1738]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 499--499
 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 500--500
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 501--501
 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 502--502
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

Underfull \hbox (badness 10000) in paragraph at lines 536--542
[]\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4416) in paragraph at lines 536--542
\T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_
package_C_files \T1/ptm/m/n/10 per-form spell check-
[1739] [1740]
Underfull \hbox (badness 4505) in paragraph at lines 647--653
\T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][]("
available_packages_filters") \T1/ptm/m/n/10 and to
[1741]
Underfull \hbox (badness 1603) in paragraph at lines 764--770
\T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/
pcr/m/n/10 infile \T1/ptm/m/n/10 starts

Underfull \hbox (badness 3029) in paragraph at lines 764--770
\T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 --
\T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are
[1742]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 817--817
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1743] [1744] [1745]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1746] [1747] [1748] [1749] [1750]
Underfull \hbox (badness 1859) in paragraph at lines 1379--1388
[]\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b
e quite large the com-
[1751] [1752]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 1506--1506
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1753] [1754]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1652--1652
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1672--1672
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL) 
[1755]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1714--1714
 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL) 
[1756] [1757]
Underfull \hbox (badness 10000) in paragraph at lines 1841--1843
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via
[1758]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1886--1886
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 

Underfull \hbox (badness 5189) in paragraph at lines 1931--1933
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1759]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2006--2006
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1760]
Underfull \hbox (badness 1082) in paragraph at lines 2080--2084
[][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou
t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files;

[1761]
Underfull \hbox (badness 1057) in paragraph at lines 2146--2153
\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the
 func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w
hen
[1762]
Underfull \hbox (badness 10000) in paragraph at lines 2158--2160
[]\T1/ptm/m/n/10 Factors \T1/pcr/m/n/10 x \T1/ptm/m/n/10 are ac-cepted from \T1
/phv/m/n/10 R \T1/ptm/m/n/10 3.1.0 (al-though co-in-ci-den-tally they worked fo
r
[1763] [1764] [1765]
Underfull \hbox (badness 10000) in paragraph at lines 2336--2338
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1766] [1767] [1768]
Underfull \hbox (badness 10000) in paragraph at lines 2568--2571
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m
/n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us-
ing

Overfull \hbox (55.10922pt too wide) in paragraph at lines 2572--2575
[]\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr
/m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][
](..., header = TRUE, sep = ";")\T1/ptm/m/n/10 ,
[1769]
Underfull \hbox (badness 10000) in paragraph at lines 2621--2624
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set
[1770]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 2693--2693
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1771]
Underfull \hbox (badness 2452) in paragraph at lines 2769--2772
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1772] [1773] [1774] [1775] [1776]
Underfull \hbox (badness 1077) in paragraph at lines 3116--3118
[]\T1/ptm/m/n/10 character vec-tor of ad-di-tional command-line ar-gu-ments for
 the \T1/pcr/m/n/10 "wget"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1072) in paragraph at lines 3155--3161
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the

Underfull \hbox (badness 1377) in paragraph at lines 3155--3161
\T1/pcr/m/n/10 internet.info \T1/ptm/m/n/10 op-tion. The de-tails de-pend on th
e plat-form and scheme, but set-ting
[1777]
Underfull \hbox (badness 1057) in paragraph at lines 3180--3194
[]\T1/ptm/m/n/10 Proxies can be spec-i-fied via en-vi-ron-ment vari-ables. Set-
ting \T1/pcr/m/n/10 "no_proxy" \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "*" \T1/ptm/m/n
/10 stops

Underfull \hbox (badness 1742) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 fail-ing that, the all upper-case ver-sion) is con-sulted and if
 non-empty used as a proxy

Underfull \hbox (badness 1360) in paragraph at lines 3180--3194
\T1/ptm/m/n/10 site. For FTP trans-fers, the user-name and pass-word on the pro
xy can be spec-i-fied by

Underfull \hbox (badness 1231) in paragraph at lines 3195--3201
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[1778]
Underfull \hbox (badness 4660) in paragraph at lines 3266--3269
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to
[1779] [1780] [1781]
Underfull \hbox (badness 1565) in paragraph at lines 3472--3476
[]\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c
har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of

Underfull \hbox (badness 10000) in paragraph at lines 3493--3499
[]\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i-
nal ob-ject if
[1782]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3555--3555
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 

Overfull \hbox (2.55087pt too wide) in paragraph at lines 3583--3590
\T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n
/10 . 
[1783] [1784] [1785] [1786] [1787]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3896--3896
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1788]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3967 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.3967 ...mat Unordered and Ordered Lists}{format}
                                                   [1789] [1790] [1791]
[1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802]
[1803]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4871--4871
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1804]
Underfull \hbox (badness 10000) in paragraph at lines 4955--4957
[]\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 http : / / www . r-[]p
roject . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also
[1805]
Underfull \hbox (badness 1502) in paragraph at lines 5004--5009
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-

Underfull \hbox (badness 2103) in paragraph at lines 5004--5009
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1806] [1807]
Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,

Underfull \hbox (badness 10000) in paragraph at lines 5166--5175
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 
', which can be re-made by
[1808] [1809]
Underfull \hbox (badness 3118) in paragraph at lines 5283--5285
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for

Underfull \hbox (badness 2409) in paragraph at lines 5316--5320
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1810] [1811]
Underfull \hbox (badness 1348) in paragraph at lines 5434--5439
[]\T1/ptm/m/n/10 logical in-di-cat-ing to also in-stall unin-stalled pack-ages 
which these pack-

Underfull \hbox (badness 3884) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 ages de-pend on/link to/import/suggest (and so on re-cur-sively)
. Not

Underfull \hbox (badness 1776) in paragraph at lines 5434--5439
\T1/ptm/m/n/10 used if \T1/pcr/m/n/10 repos = NULL\T1/ptm/m/n/10 . Can also be 
a char-ac-ter vec-tor, a sub-set of

Overfull \hbox (44.55087pt too wide) in paragraph at lines 5434--5439
\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/
ptm/m/n/10 . 

Overfull \hbox (48.30977pt too wide) in paragraph at lines 5447--5454
[]\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", "
Imports", "LinkingTo", "Suggests")

Underfull \hbox (badness 10000) in paragraph at lines 5460--5464
[]\T1/ptm/m/n/10 Possible val-ues are (cur-rently) \T1/pcr/m/n/10 "source"\T1/p
tm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2073) in paragraph at lines 5460--5464
\T1/pcr/m/n/10 "mac.binary.mavericks" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "win.bi
nary"\T1/ptm/m/n/10 : the bi-nary types
[1812]
Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed

Underfull \hbox (badness 10000) in paragraph at lines 5518--5521
\T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack
-age in-stall. E.g.,
[1813]
Underfull \hbox (badness 1314) in paragraph at lines 5628--5635
[]\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a
ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from
[1814]
Underfull \hbox (badness 10000) in paragraph at lines 5649--5654
[][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a
vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][
][]\T1/ptm/m/n/10 ,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 5670--5670
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 

Underfull \hbox (badness 5133) in paragraph at lines 5706--5710
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each
 pack-age's

Underfull \hbox (badness 1983) in paragraph at lines 5718--5721
[]\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE
SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along
[1815]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5765--5765
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1816]
Underfull \hbox (badness 4132) in paragraph at lines 5796--5798
[]\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion 
of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at
[1817] [1818]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5954--5954
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1819] [1820] [1821]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 6097--6097
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1822] [1823] [1824]
Underfull \hbox (badness 10000) in paragraph at lines 6270--6272
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if
[1825] [1826] [1827] [1828]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 6537--6537
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1829] [1830] [1831] [1832]
Underfull \hbox (badness 10000) in paragraph at lines 6810--6812
[]\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, 
al-low-ing things like

Underfull \hbox (badness 1259) in paragraph at lines 6815--6820
[]\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the 
given pack-age is found and can suc-cess-fully be read,
[1833] [1834]
Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[]\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p
tm/m/n/10 re-turned by

Underfull \hbox (badness 10000) in paragraph at lines 6972--6975
[][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 
"Status"\T1/ptm/m/n/10 , a fac-tor with lev-els
[1835] [1836]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7088--7088
 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 7089--7089
 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1837] [1838] [1839] [1840]
Underfull \hbox (badness 1789) in paragraph at lines 7353--7355
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1841]
Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7411--7415
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1842]
Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7524--7528
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1843] [1844]
Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA
\T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion

Underfull \hbox (badness 10000) in paragraph at lines 7587--7591
\T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am
ounts to
[1845] [1846] [1847] [1848]
Underfull \hbox (badness 5203) in paragraph at lines 7914--7917
[]\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10
 ex-trac-tor are de-ter-mined by the generic func-tion
[1849] [1850] [1851]
Underfull \hbox (badness 1776) in paragraph at lines 8136--8143
[]\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o
f pieces of code, you should set

Overfull \hbox (30.78088pt too wide) in paragraph at lines 8160--8160
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[1852] [1853]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8316--8316
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[1854] [1855] [1856]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8491--8491
 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 
456 98 76 54[] 
[1857]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8577--8577
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 8580--8580
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 8585--8585
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[1858]
Underfull \hbox (badness 1077) in paragraph at lines 8656--8659
[]\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro
w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL
[1859] [1860] [1861] [1862] [1863] [1864]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[1865] [1866]
Underfull \hbox (badness 10000) in paragraph at lines 9181--9183
[]\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/
m/n/10 in-stead of the de-fault one, use
[1867] [1868]
Underfull \hbox (badness 10000) in paragraph at lines 9313--9317
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s&oldid = 78252134$[][]\T1/ptm/m/n/10 .
[1869] [1870]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 9454--9454
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[1871] [1872] [1873] [1874]
Underfull \hbox (badness 6725) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \
T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first,

Underfull \hbox (badness 6428) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s
ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i-

Underfull \hbox (badness 10000) in paragraph at lines 9694--9703
\T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for
 re-verse al-pha-bet-i-cal or-der,

Underfull \hbox (badness 1997) in paragraph at lines 9694--9703
\T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/
n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or
[1875] [1876]
Underfull \hbox (badness 10000) in paragraph at lines 9820--9822
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Ctags$[][]\T1/pt
m/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / www . gnu . org / software /
[1877] [1878] [1879]
Underfull \hbox (badness 10000) in paragraph at lines 9998--10002
[]\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no
w taken from the en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 10029--10035
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[1880]
Underfull \hbox (badness 2012) in paragraph at lines 10124--10130
\T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments
 for fig-ures should be auto-generated. Use

Underfull \hbox (badness 2096) in paragraph at lines 10137--10139
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether EPS fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 2698) in paragraph at lines 10140--10142
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh
ether PDF fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1527) in paragraph at lines 10147--10150
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether PNG fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1067) in paragraph at lines 10151--10154
[]\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w
hether JPEG fig-ures should be gen-er-ated. Ig-nored if
[1881]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10205--10205
 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 

Underfull \hbox (badness 10000) in paragraph at lines 10212--10214
[]\T1/ptm/m/n/10 A re-place-ment for [][]\T1/pcr/m/n/10 dev.off[][][] \T1/ptm/m
/n/10 can be pro-vided as a func-tion with suf-fix \T1/pcr/m/n/10 .off\T1/ptm/m
/n/10 ,

Underfull \hbox (badness 1009) in paragraph at lines 10217--10228
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[1882] [1883]
Underfull \hbox (badness 2846) in paragraph at lines 10304--10314
\T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an
d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault
[1884] [1885]
Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. For re-cent v
er-

Underfull \hbox (badness 10000) in paragraph at lines 10443--10446
\T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form

Underfull \hbox (badness 10000) in paragraph at lines 10451--10454
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[1886]
Underfull \hbox (badness 10000) in paragraph at lines 10504--10508
\T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son
al copy in

Underfull \hbox (badness 2158) in paragraph at lines 10524--10527
[]\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe
-cially: the value is taken from the cur-rent set-ting of
[1887] [1888]
Underfull \hbox (badness 3333) in paragraph at lines 10704--10706
[]\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto
ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file-
[1889] [1890] [1891]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10865--10865
 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 

Underfull \hbox (badness 5970) in paragraph at lines 10893--10896
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive

Underfull \hbox (badness 2600) in paragraph at lines 10893--10896
[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less

Underfull \hbox (badness 2401) in paragraph at lines 10904--10913
[]\T1/ptm/m/n/10 string in-di-cat-ing if the \T1/pcr/m/n/10 width \T1/ptm/m/n/1
0 ar-gu-ment's spec-i-fi-ca-tion should be fol-

Underfull \hbox (badness 2735) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 to the \T1/pcr/m/n/10 strict.width \T1/ptm/m/n/10 com-po-nent of
 op-tion \T1/pcr/m/n/10 "str" \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][
][]\T1/ptm/m/n/10 )

Underfull \hbox (badness 1859) in paragraph at lines 10904--10913
\T1/ptm/m/n/10 which de-faults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back c
om-pat-i-bil-ity rea-sons; \T1/pcr/m/n/10 "wrap" \T1/ptm/m/n/10 uses

Underfull \hbox (badness 10000) in paragraph at lines 10904--10913
[][]\T1/pcr/m/n/10 strwrap[][][](*, width = width) \T1/ptm/m/n/10 whereas \T1/p
cr/m/n/10 "cut" \T1/ptm/m/n/10 cuts di-rectly to

Underfull \hbox (badness 1661) in paragraph at lines 10904--10913
\T1/pcr/m/n/10 width\T1/ptm/m/n/10 . Note that a small \T1/pcr/m/n/10 vec.lengt
h \T1/ptm/m/n/10 may be bet-ter than set-ting
[1892]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10948--10948
 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[1893] [1894]
Underfull \hbox (badness 10000) in paragraph at lines 11072--11074
[]\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/
10 ap-ply only to files pro-duced by
[1895] [1896]
Underfull \hbox (badness 4492) in paragraph at lines 11226--11233
[]\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) 
then the avail-able syn-tax ob-jects are con-sulted in

Underfull \hbox (badness 6252) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
n/10 com-po-nent matches (as a reg-exp) the file

Underfull \hbox (badness 2452) in paragraph at lines 11226--11233
\T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 (
with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and
[1897] [1898] [1899]
Underfull \hbox (badness 2020) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10
 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl
at-forms),

Underfull \hbox (badness 1194) in paragraph at lines 11386--11399
\T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud
e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s
im-i-lar) and on Win-dows
[1900]
Underfull \hbox (badness 10000) in paragraph at lines 11469--11472
[][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ fo
rmat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .

Underfull \hbox (badness 10000) in paragraph at lines 11469--11472
\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[1901] [1902] [1903] [1904] [1905] [1906] [1907]
Underfull \hbox (badness 4660) in paragraph at lines 11974--11977
\T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/
10 which makes an in-ter-nal call to

Overfull \hbox (36.87935pt too wide) in paragraph at lines 11987--11991
[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 .

Underfull \hbox (badness 3557) in paragraph at lines 11993--11995
[]\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T
1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be passed to

Underfull \hbox (badness 1052) in paragraph at lines 11996--11998
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[1908]
Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see

Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
[][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai
lable = NULL \T1/ptm/m/n/10 make a call to

Underfull \hbox (badness 10000) in paragraph at lines 12026--12031
\T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1
/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 12047--12052
[]\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/
10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with

Underfull \hbox (badness 10000) in paragraph at lines 12055--12058
[][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[]
[][]\T1/ptm/m/n/10 ,
[1909] [1910] [1911] [1912] [1913]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12331--12331
 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 

Underfull \hbox (badness 1454) in paragraph at lines 12358--12362
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[1914]
Underfull \hbox (badness 1715) in paragraph at lines 12383--12386
[]\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc
r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 12428--12430
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion

Underfull \hbox (badness 3271) in paragraph at lines 12440--12444
\T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1
/ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and
 \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if

[1915] [1916] [1917]) [1918] [1919] [1920] (./KernSmooth-pkg.tex
Chapter 15.
[1921]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124
 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[1922] [1923] [1924] [1925] [1926]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519
 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[1927] [1928] [1929] [1930]) (./MASS-pkg.tex
Chapter 16.
[1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772
 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952]
[1953]
Underfull \hbox (badness 7256) in paragraph at lines 1601--1603
[]\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo
r
[1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962] [1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2409--2409
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2413--2413
 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[1965] [1966] [1967] [1968]
Underfull \hbox (badness 6559) in paragraph at lines 2691--2694
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and
 graph-i-cal pa-ram-e-ters. Note that
[1969] [1970] [1971]
Underfull \hbox (badness 7362) in paragraph at lines 2861--2866
\T1/pcr/m/n/10 "f"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/p
cr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "lognormal"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3557) in paragraph at lines 2897--2905
[]\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start
-ing val-ues will be com-puted if

Underfull \hbox (badness 3118) in paragraph at lines 2897--2905
\T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied:
 \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 ,
 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,
[1972] [1973]
Underfull \hbox (badness 4686) in paragraph at lines 3029--3031
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds

Underfull \hbox (badness 1515) in paragraph at lines 3043--3047
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[1974] [1975] [1976]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3224--3224
 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 

Underfull \hbox (badness 5817) in paragraph at lines 3231--3233
[]\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1
0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with
[1977]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3354--3354
 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988]
[1989]
Underfull \hbox (badness 1845) in paragraph at lines 4160--4162
[]\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and
[1990] [1991] [1992] [1993] [1994] [1995] [1996]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4656--4656
 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[1997] [1998]
Underfull \hbox (badness 10000) in paragraph at lines 4808--4811
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[1999]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4878--4878
 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 

Underfull \hbox (badness 10000) in paragraph at lines 4886--4889
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2000] [2001] [2002] [2003] [2004]
Underfull \hbox (badness 5681) in paragraph at lines 5286--5288
[]\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/
n/10 . This is over-ridden if

Underfull \hbox (badness 5022) in paragraph at lines 5290--5293
[]\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_
\OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10  \OT1/cmr/m/n/10 ()$ \
T1/ptm/m/n/10 func-tions when
[2005]
Underfull \hbox (badness 1975) in paragraph at lines 5339--5341
[]\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in
 the case of
[2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 5925--5925
 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2014]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5987--5987
 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/
10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") 
[2015] [2016]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6129 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6129 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2017]
Underfull \hbox (badness 1783) in paragraph at lines 6247--6251
[]\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr
ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. 
That is
[2018] [2019] [2020] [2021]
Underfull \vbox (badness 10000) has occurred while \output is active [2022]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6545--6545
 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2023]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 6633--6633
 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2024] [2025] [2026] [2027] [2028] [2029]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7072--7072
 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 7089--7089
 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 

Underfull \hbox (badness 10000) in paragraph at lines 7096--7103
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[2030]
Underfull \hbox (badness 10000) in paragraph at lines 7112--7114
[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat

Underfull \hbox (badness 3138) in paragraph at lines 7167--7173
[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2031]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7237--7237
 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2032] [2033]
Underfull \hbox (badness 5091) in paragraph at lines 7346--7349
\T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na
nt com-po-nents are used (ex-cept for
[2034] [2035]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7476--7476
 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2036]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 7541--7541
 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2037] [2038] [2039] [2040] [2041] [2042]
Underfull \hbox (badness 4686) in paragraph at lines 7979--7981
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds

Underfull \hbox (badness 1515) in paragraph at lines 7995--7999
[]\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p
tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n
/10 cycles \T1/ptm/m/n/10 terms or when a
[2043] [2044]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 8098--8098
 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 

Underfull \hbox (badness 1590) in paragraph at lines 8122--8126
[]\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n
/10 NA\T1/ptm/m/n/10 s are found. The
[2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055]
[2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 9501--9501
 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2065]
Underfull \hbox (badness 1158) in paragraph at lines 9628--9631
[]\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10
 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly),
[2066]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 9710--9710
 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 9712--9712
 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 9715--9715
 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077]
[2078] [2079]) (./Matrix-pkg.tex [2080]
Chapter 17.

Underfull \hbox (badness 10000) in paragraph at lines 42--45
[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you

Underfull \hbox (badness 10000) in paragraph at lines 42--45
\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2081]
Underfull \hbox (badness 1769) in paragraph at lines 96--99
[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2082]
Underfull \hbox (badness 2229) in paragraph at lines 160--163
[]\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm
/m/n/10 ob-jects; here, when the first is

Underfull \hbox (badness 1147) in paragraph at lines 160--163
\T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th
ese ar-gu-ments will be con-cate-nated to a new
[2083]
Underfull \hbox (badness 10000) in paragraph at lines 258--261
[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing

Underfull \hbox (badness 10000) in paragraph at lines 264--266
[]\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][
]sparseVector[][][]"\T1/ptm/m/n/10 's, see
[2084] [2085]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 487--487
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 

Underfull \hbox (badness 5147) in paragraph at lines 494--496
[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2086]
Underfull \hbox (badness 5119) in paragraph at lines 506--510
[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class

Underfull \hbox (badness 4621) in paragraph at lines 510--514
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a

Overfull \hbox (4.38043pt too wide) in paragraph at lines 533--533
 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535
 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 544--544
 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2087] [2088]
Underfull \hbox (badness 3189) in paragraph at lines 681--685
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2089]
Underfull \hbox (badness 10000) in paragraph at lines 735--738
[]\T1/ptm/m/n/10 In some ver-sions of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 eigen[][][](CAex) \T1/ptm/m/n/10 fell into an in-fi-nite loop (where
as
[2090] [2091]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 873--873
 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2092]
Underfull \hbox (badness 10000) in paragraph at lines 948--950
[]\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-

Underfull \hbox (badness 10000) in paragraph at lines 971--976
[]\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of 
the lower tri-

Underfull \hbox (badness 10000) in paragraph at lines 971--976
\T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the
 de-com-po-si-tion. This method is equiv-a-lent to

Underfull \hbox (badness 1092) in paragraph at lines 971--976
\T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in 
the above de-scrip-tion of

Underfull \hbox (badness 10000) in paragraph at lines 994--1001
[]\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm =       "logical")
[2093]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho
l}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1060 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2094pdfTeX warning (ext4): 
destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha
s been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate i
gnored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        pdfTeX warning (ext4): destination with the same identi
fier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate i
gnored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1082 \end{Description}
                        ] [2095]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1192--1192
 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2096]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1286--1286
 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 
[2097]
Underfull \hbox (badness 2277) in paragraph at lines 1314--1317
[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use

Underfull \hbox (badness 1609) in paragraph at lines 1361--1365
[]\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt
m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion []
[]\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra
[2098]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1388--1388
 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1402--1402
 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p
cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/
pcr/m/n/9 , sep="") ## dQuote(<UTF-8>) gives bad plots[] 

Overfull \hbox (74.58035pt too wide) in paragraph at lines 1410--1410
 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1420--1420
 []\T1/pcr/m/n/9 ## each has a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' 
\T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n
/9 matrix %% FIXME !! --- "check" them  __unfinished__[] 
[2099]
Underfull \hbox (badness 6445) in paragraph at lines 1457--1464
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("Cholesky",    ...) \T1/ptm/m/n/10 or

Underfull \hbox (badness 3861) in paragraph at lines 1457--1464
\T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls
 of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or

Underfull \hbox (badness 1783) in paragraph at lines 1492--1496
[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend

Underfull \hbox (badness 1221) in paragraph at lines 1508--1514
\T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10
 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen
ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and
[2100]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1549 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1549 ... Row and Column Sums and Means}{colSums}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1550 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1571 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1582 \aliasA{rowSums}{colSums}{rowSums}
                                          [2101] [2102]
Underfull \hbox (badness 3547) in paragraph at lines 1757--1760
[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2103] [2104] [2105] [2106]
Underfull \hbox (badness 10000) in paragraph at lines 1994--1996
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix
", where =
[2107]
Underfull \hbox (badness 10000) in paragraph at lines 2116--2118
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
, where =

Underfull \hbox (badness 3068) in paragraph at lines 2177--2181
\T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10
 or sim-i-lar. Of-ten how-ever, more eas-ily via
[2108]
Underfull \hbox (badness 4713) in paragraph at lines 2212--2214
[]\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de
-com-po-si-tion of a square
[2109]
Underfull \hbox (badness 10000) in paragraph at lines 2327--2330
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 
or
[2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 2429--2433
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dgTMatrix",    ...)\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2429--2433
\T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or

Underfull \hbox (badness 2707) in paragraph at lines 2486--2490
[]\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T
1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d
gTMatrix" \T1/ptm/m/n/10 (and other
[2112]
Underfull \hbox (badness 2689) in paragraph at lines 2546--2548
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,
[2113]
Underfull \hbox (badness 1097) in paragraph at lines 2572--2575
[]\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1
/pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][
] \T1/ptm/m/n/10 (with ``su-per-class''
[2114]
Underfull \hbox (badness 3646) in paragraph at lines 2818--2821
[]\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T
1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][]
 \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally

Underfull \hbox (badness 10000) in paragraph at lines 2840--2841
[]\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1
/ptm/m/n/10 :

Underfull \hbox (badness 1810) in paragraph at lines 2847--2849
[]\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri
v-ially im-ple-mented, of

Underfull \hbox (badness 10000) in paragraph at lines 2850--2852
[]\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv
-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2115]
Underfull \hbox (badness 1371) in paragraph at lines 2857--2863
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : 
the re-sult is from class

Underfull \hbox (badness 10000) in paragraph at lines 2864--2868
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class

Underfull \hbox (badness 2318) in paragraph at lines 2874--2878
[][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 
ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr
/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and
[2116] [2117]
Underfull \hbox (badness 1859) in paragraph at lines 3054--3056
[]\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains

Underfull \hbox (badness 10000) in paragraph at lines 3099--3101
[][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2118]
Underfull \hbox (badness 1168) in paragraph at lines 3214--3217
[]\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T
1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10
 , via
[2119] [2120]
Underfull \hbox (badness 4967) in paragraph at lines 3376--3380
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne
w("dsCMatrix",    ...) \T1/ptm/m/n/10 or

Overfull \hbox (2.39853pt too wide) in paragraph at lines 3381--3383
[]\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][]
\T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . 
[2121]
Underfull \hbox (badness 6364) in paragraph at lines 3423--3426
[]\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2122] [2123]
Underfull \hbox (badness 10000) in paragraph at lines 3573--3578
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc
r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1
/ptm/m/n/10 , by

Underfull \hbox (badness 6961) in paragraph at lines 3573--3578
\T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m
/n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm
/m/n/10 by class

Underfull \hbox (badness 10000) in paragraph at lines 3583--3585
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a
 triv-ial

Underfull \hbox (badness 10000) in paragraph at lines 3585--3588
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 :
 if
[2124]
Underfull \hbox (badness 10000) in paragraph at lines 3693--3696
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or

Underfull \hbox (badness 1735) in paragraph at lines 3693--3696
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the

Underfull \hbox (badness 10000) in paragraph at lines 3696--3699
[]\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 ,
 or

Underfull \hbox (badness 2318) in paragraph at lines 3696--3699
\T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing
"\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion
[2125]
Underfull \hbox (badness 6364) in paragraph at lines 3700--3703
[]\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr
/m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves
[2126]
Underfull \hbox (badness 4060) in paragraph at lines 3817--3820
[]\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse 
tri-an-gu-lar solve (aka
[2127]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3857--3857
 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 

Underfull \hbox (badness 3635) in paragraph at lines 3923--3927
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class

Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-

Underfull \hbox (badness 10000) in paragraph at lines 3932--3935
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see
[2128]
Underfull \hbox (badness 10000) in paragraph at lines 3937--3941
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1
0 : the
[2129] [2130] [2131] [2132]
Underfull \hbox (badness 10000) in paragraph at lines 4225--4230
[]\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite 
Tay-lor se-ries
[2133] [2134]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4359--4359
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

Overfull \hbox (139.38028pt too wide) in paragraph at lines 4362--4362
 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
[2135] [2136] [2137] [2138]
Underfull \hbox (badness 10000) in paragraph at lines 4670--4675
[]\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an
d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1
/ptm/m/n/10 ,
[2139]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4751--4751
 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che
cking reasons" 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4753--4753
 []  \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4),   j=c(2:4,1),   x = 2,   
 dimnames=dns))[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 4757--4757
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 4764--4764
 []  \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give
C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] 
[2140] [2141]
Underfull \hbox (badness 4120) in paragraph at lines 4892--4895
[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4921--4921
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 
[2142]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4926--4926
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 4933--4933
 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a
nti-aliasing[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 4936--4936
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2143]
Underfull \hbox (badness 1817) in paragraph at lines 5024--5033
[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within 
the

Underfull \hbox (badness 5637) in paragraph at lines 5065--5067
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2144]
Underfull \hbox (badness 3138) in paragraph at lines 5091--5093
[]\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the
[2145]
Underfull \hbox (badness 1603) in paragraph at lines 5175--5177
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t
ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault,

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[]\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p
tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault,

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
\T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 )
, \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as

Underfull \hbox (badness 10000) in paragraph at lines 5183--5188
[][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis
t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to
[2146] [2147] [2148]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5411--5411
 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/
pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] 
[2149]
Underfull \hbox (badness 10000) in paragraph at lines 5487--5490
[][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c
lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and

Overfull \hbox (9.78043pt too wide) in paragraph at lines 5498--5498
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2150]
Underfull \hbox (badness 1622) in paragraph at lines 5535--5540
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say
 \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \
T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/
ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy
/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ),

Underfull \hbox (badness 1418) in paragraph at lines 5535--5540
\T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy
/m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m
/it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/
m/n/10 is the kro-necker prod-uct
[2151] [2152]
Underfull \hbox (badness 1062) in paragraph at lines 5720--5723
[]\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2153]
Underfull \hbox (badness 2809) in paragraph at lines 5749--5752
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2154]
Underfull \hbox (badness 2635) in paragraph at lines 5861--5866
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense
Matrix"\T1/ptm/m/n/10 .

Underfull \hbox (badness 4229) in paragraph at lines 5861--5866
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class

Underfull \hbox (badness 10000) in paragraph at lines 5869--5872
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2155]
Underfull \hbox (badness 1184) in paragraph at lines 6042--6045
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2156] [2157]
Underfull \hbox (badness 10000) in paragraph at lines 6140--6143
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2158]
Underfull \hbox (badness 10000) in paragraph at lines 6215--6218
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 6231--6231
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 

Underfull \hbox (badness 2443) in paragraph at lines 6269--6275
[]\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][
]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see

Underfull \hbox (badness 1776) in paragraph at lines 6269--6275
[][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr
/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is
 sin-gu-lar,
[2159]
Underfull \hbox (badness 1675) in paragraph at lines 6286--6289
[]\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth-
ods for dif-fer-ent types of ma-tri-ces. Use

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2160] [2161]
Underfull \hbox (badness 6268) in paragraph at lines 6480--6483
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2162]
Underfull \hbox (badness 5036) in paragraph at lines 6504--6508
[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10
 . How-ever,

Underfull \hbox (badness 10000) in paragraph at lines 6504--6508
\T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e
mpty'' [][]sparse-Ma-trix[][][], as does
[2163]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6596 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 1348) in paragraph at lines 6670--6673
[]\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 
diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing

Underfull \hbox (badness 10000) in paragraph at lines 6675--6678
[]\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \
T1/pcr/m/n/10 value \T1/ptm/m/n/10 is

Underfull \hbox (badness 10000) in paragraph at lines 6675--6678
\T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p
tm/m/n/10 Ma-trix ob-jects, but only when

Underfull \hbox (badness 10000) in paragraph at lines 6692--6695

[2164] [2165]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn..Rpcent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6761 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.6851 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.6933 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
Underfull \hbox (badness 1881) in paragraph at lines 7015--7021
\T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc
r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn

Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
[]\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma
-

Underfull \hbox (badness 10000) in paragraph at lines 7068--7071
\T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co
m-bi-na-tions, see

Underfull \hbox (badness 5637) in paragraph at lines 7071--7076
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2166pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros
sprod.Rdash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7076 \item[crossprod]
                        \code{signature(x = "dgeMatrix", y = "dgeMatrix")}:pdfT
eX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rd
ash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7076 \item[crossprod]
                        \code{signature(x = "dgeMatrix", y = "dgeMatrix")}:]
Underfull \hbox (badness 10000) in paragraph at lines 7080--7082
[]\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns

Underfull \hbox (badness 10000) in paragraph at lines 7082--7084
[]\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r
e-turns

Underfull \hbox (badness 10000) in paragraph at lines 7086--7087
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix", y =       "matrix") \T1/ptm/m/n/10 
and
[2167]
Underfull \hbox (badness 1062) in paragraph at lines 7203--7206
[]\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense
 \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both
[2168]
Underfull \hbox (badness 2809) in paragraph at lines 7237--7240
[]\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 
equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion

Underfull \hbox (badness 10000) in paragraph at lines 7289--7291
[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter
[2169]
Underfull \hbox (badness 1406) in paragraph at lines 7329--7333
[]\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b
y Jens Oehlschlaegel did not

Underfull \hbox (badness 1019) in paragraph at lines 7329--7333
\T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t
his sim-pli-fi-ca-tion, now only via
[2170] [2171]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7427--7427
 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 

Underfull \hbox (badness 2635) in paragraph at lines 7492--7497
[]\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly.
 Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense
Matrix"\T1/ptm/m/n/10 .

Underfull \hbox (badness 4229) in paragraph at lines 7492--7497
\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/
pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/
m/n/10 , by class

Underfull \hbox (badness 10000) in paragraph at lines 7500--7503
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us
e, e.g.,
[2172] [2173]
Underfull \hbox (badness 10000) in paragraph at lines 7686--7688
[]\T1/ptm/m/n/10 fast
[2174]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7724 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2175] [2176]
Underfull \hbox (badness 1184) in paragraph at lines 7971--7974
[]\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2177]
Underfull \hbox (badness 10000) in paragraph at lines 8061--8064
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,
[2178]
Underfull \hbox (badness 10000) in paragraph at lines 8137--8140
[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 
and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use
, e.g.,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 8153--8153
 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2179] [2180]
Underfull \hbox (badness 10000) in paragraph at lines 8263--8265
[]\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use

Underfull \hbox (badness 1596) in paragraph at lines 8279--8281
[]\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : 
co-er-cion to sparse

Underfull \hbox (badness 1721) in paragraph at lines 8285--8289
\T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide
n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S
ee
[2181]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 8369--8369
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 8374--8374
 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 
[2182]
Underfull \hbox (badness 3989) in paragraph at lines 8396--8406
[]\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T
1/pcr/m/n/10 x \T1/ptm/m/n/10 should

Underfull \hbox (badness 10000) in paragraph at lines 8396--8406
\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2183]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}
) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8488 \aliasA{qr}{qr-methods}{qr}
                                   [2184]
Underfull \hbox (badness 5119) in paragraph at lines 8530--8533
[]\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma-
trix with

Overfull \hbox (36.7804pt too wide) in paragraph at lines 8550--8550
 []                  \T1/pcr/m/n/9 c1=rep(c(1,0,0), 2), c2=rep(c(0,1,0), 2), c3
=rep(c(0,0,1),2)),[] 
[2185]
Underfull \hbox (badness 10000) in paragraph at lines 8599--8605
[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of

Underfull \hbox (badness 10000) in paragraph at lines 8616--8619
[]\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 , it cor-re-sponds to
[2186]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 8687--8687
 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/
n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale
 free"[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8708--8708
 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                #  wa
rning +  ~1.5 sec[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 8709--8709
 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h
as been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8723 ... the Reciprocal Condition Number}{rcond}
                                                   [2187] [2188]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 8836--8836
 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2189] [2190] [2191]
Underfull \hbox (badness 2126) in paragraph at lines 9014--9019
[]\T1/ptm/m/n/10 the ran-dom num-ber gen-er-a-tor for the \T1/pcr/m/n/10 x \T1/
ptm/m/n/10 slot, a [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 such that

Underfull \hbox (badness 10000) in paragraph at lines 9019--9021
[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably
[2192] [2193]
Underfull \hbox (badness 1558) in paragraph at lines 9164--9167
[]\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1
0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional
[2194]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 9226--9226
 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 9230--9230
 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2195]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9292 \aliasA{solve}{solve-methods}{solve}
                                           
Overfull \hbox (54.78088pt too wide) in paragraph at lines 9389--9389
 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 

Overfull \hbox (60.78088pt too wide) in paragraph at lines 9394--9394
 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2196]
Underfull \hbox (badness 6047) in paragraph at lines 9429--9441
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods

Underfull \hbox (badness 10000) in paragraph at lines 9446--9449
[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via

Underfull \hbox (badness 7203) in paragraph at lines 9451--9452
[]\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar

Underfull \hbox (badness 7851) in paragraph at lines 9455--9462
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list

Underfull \hbox (badness 10000) in paragraph at lines 9455--9462
\T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U
ses the sparse

Underfull \hbox (badness 10000) in paragraph at lines 9468--9478
[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list

Underfull \hbox (badness 2165) in paragraph at lines 9468--9478
\T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che
cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-

Underfull \hbox (badness 1194) in paragraph at lines 9502--9504
[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines
[2197]
Underfull \hbox (badness 10000) in paragraph at lines 9516--9519
[]\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing

Underfull \hbox (badness 10000) in paragraph at lines 9525--9526
[]\T1/ptm/m/n/10 works via

Underfull \hbox (badness 10000) in paragraph at lines 9531--9533
[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use

Underfull \hbox (badness 10000) in paragraph at lines 9535--9536
[]\T1/ptm/m/n/10 all work via

Underfull \hbox (badness 10000) in paragraph at lines 9543--9546
[][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1
/ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9561--9561
 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 9565--9565
 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2198]
Underfull \hbox (badness 10000) in paragraph at lines 9586--9589
[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame

Underfull \hbox (badness 1648) in paragraph at lines 9614--9616
[]\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][
]\T1/ptm/m/n/10 . If an-other sort of ob-ject,

Underfull \hbox (badness 10000) in paragraph at lines 9622--9625
[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
er-ca-ble to)

Underfull \hbox (badness 2591) in paragraph at lines 9622--9625
\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t
rasts to be ap-plied to the

Underfull \hbox (badness 10000) in paragraph at lines 9633--9637
[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for


Underfull \hbox (badness 2828) in paragraph at lines 9633--9637
\T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m
/n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for
[2199]
Underfull \hbox (badness 6592) in paragraph at lines 9644--9646
[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a
[2200]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 9721--9721
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9722--9722
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9723--9723
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2201]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9804--9804
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2202]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 9900--9900
 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2203]
Underfull \hbox (badness 4621) in paragraph at lines 9937--9941
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2204]
Underfull \hbox (badness 10000) in paragraph at lines 10008--10011
[]\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][](
*, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10025--10025
 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 10028--10028
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 10051--10051
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 10052--10052
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2205]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10096--10096
 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10101--10101
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2206]
Underfull \hbox (badness 10000) in paragraph at lines 10193--10201
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class

Underfull \hbox (badness 1325) in paragraph at lines 10214--10218
[]\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a
l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a

Underfull \hbox (badness 10000) in paragraph at lines 10244--10248
[][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s
uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or
[2207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10284 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2208]
Underfull \hbox (badness 1430) in paragraph at lines 10394--10396
[]\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p
cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses
[2209]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 10420--10420
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 
[2210]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.toe
plitz}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.10559 ...toeplitz}{sparseVector-class}{toeplitz}
                                                  
Underfull \hbox (badness 2970) in paragraph at lines 10571--10577
[]\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/
10 "sparseVector" \T1/ptm/m/n/10 has the five ac-

Underfull \hbox (badness 3679) in paragraph at lines 10571--10577
\T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec
tor"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 10622--10625
[]\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/
10 co-erces
[2211]
Underfull \hbox (badness 10000) in paragraph at lines 10644--10647
[]\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m
/n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list

Underfull \hbox (badness 10000) in paragraph at lines 10660--10665
[]\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/
10 logical[][][] \T1/ptm/m/n/10 or

Underfull \hbox (badness 10000) in paragraph at lines 10671--10673
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2212] [2213]
Underfull \hbox (badness 3525) in paragraph at lines 10767--10771
[]\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/
pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c
mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/
ptm/m/n/10 , where
[2214]
Underfull \hbox (badness 2591) in paragraph at lines 10868--10873
\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 
, and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1
/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or
[2215]
Underfull \hbox (badness 2057) in paragraph at lines 10930--10932
[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2216]
Underfull \hbox (badness 6641) in paragraph at lines 10999--11002
[]\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm
/m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit
h

Underfull \hbox (badness 5133) in paragraph at lines 11036--11040
[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the
 vir-tual class of all sparse ma-tri-ces coded in

Underfull \hbox (badness 2818) in paragraph at lines 11036--11040
\T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c
re-ated from it. See
[2217] [2218] [2219]
Underfull \hbox (badness 7362) in paragraph at lines 11245--11247
[]\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a
 sparse ma-trix (i.e., of sub-class of
[2220]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 11283--11283
 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 11284--11284
 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 
1:6, dimnames = dn)[] 
[2221] [2222]
Underfull \hbox (badness 6910) in paragraph at lines 11533--11535
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2223] [2224]) (./boot-pkg.tex
Chapter 18.
[2225] [2226] [2227] [2228] [2229] [2230] [2231]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2232]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r
e-quired. Pos-si-ble

Underfull \hbox (badness 1275) in paragraph at lines 583--588
[]\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m
ulti-sample prob-

Underfull \hbox (badness 1264) in paragraph at lines 583--588
\T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n
ored when
[2233]
Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649
[]\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1
0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0
[2234]
Underfull \hbox (badness 6268) in paragraph at lines 797--807
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de
-fault clus-ter, a sec-ond ap-proach is used if
[2235]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.

Underfull \hbox (badness 6493) in paragraph at lines 851--855
[][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c
i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 ,
[2236]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2237]
[2238]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-

Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues
[2239]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari-
ance of the

Underfull \hbox (badness 2005) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i
n-ter-vals. If it

Underfull \hbox (badness 2343) in paragraph at lines 1082--1091
\T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10
 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to

Underfull \hbox (badness 2150) in paragraph at lines 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2240] [2241] [2242] [2243] [2244]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2245] [2246] [2247] [2248]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2249] [2250] [2251] [2252]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2253]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2254] [2255] [2256] [2257]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set

Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis
tic \T1/ptm/m/n/10 is called.
[2258]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.

Underfull \hbox (badness 2057) in paragraph at lines 2437--2438
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][]
[]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 ,
[2259]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n
/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the
 sam-ple

Underfull \hbox (badness 1112) in paragraph at lines 2533--2537
\T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1
0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10
 is used. This is mul-ti-plied by
[2260] [2261] [2262] [2263] [2264]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2265] [2266] [2267]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][
]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 ,
[2268]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2269] [2270] [2271]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2272] [2273] [2274] [2275] [2276] [2277] [2278]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2279] [2280]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2281] [2282] [2283]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2284]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2285] [2286]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f

Underfull \hbox (badness 1430) in paragraph at lines 4368--4372
\T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T
1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied
 then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to

Underfull \hbox (badness 2269) in paragraph at lines 4386--4389
[]\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with 
fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by
[2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] [2295]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2296] [2297] [2298] [2299]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap

Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2300]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2309]
Underfull \hbox (badness 1127) in paragraph at lines 5983--6001
\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t
han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then
[2310]
Underfull \hbox (badness 2837) in paragraph at lines 6016--6019
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad
dle.distn"\T1/ptm/m/n/10 . See the help file for
[2311] [2312] [2313] [2314]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6301--6301
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2315] [2316]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6490--6490
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 6492--6492
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2317] [2318] [2319]
Underfull \hbox (badness 1596) in paragraph at lines 6737--6741
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2320] [2321]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6897--6897
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2322] [2323] [2324] [2325] [2326] [2327] [2328] [2329]) (./class-pkg.tex
[2330]
Chapter 19.
[2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338]
Underfull \hbox (badness 10000) in paragraph at lines 608--610
[]\T1/ptm/m/n/10 the size of the code-book. De-faults to
[2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346]) (./cluster-pkg.tex
Chapter 20.
[2347]
Underfull \hbox (badness 10000) in paragraph at lines 133--140
[]\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when 
us-ing \T1/pcr/m/n/10 method = "flexible"

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 par-tic-u-larly for the case when \T1/pcr/m/n/10 par.method \T1/
ptm/m/n/10 is spec-i-fied of longer length

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 than one. The \T1/ptm/m/it/10 weighted av-er-age \T1/ptm/m/n/10 
(\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n/10 . Fur-ther, \T
1/pcr/m/n/10 method= "single" \T1/ptm/m/n/10 is

Underfull \hbox (badness 10000) in paragraph at lines 133--140
\T1/ptm/m/n/10 equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c
(.5,.5,0,-.5)\T1/ptm/m/n/10 , and

Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--140
\T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/
10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . 
[2348]
Underfull \hbox (badness 10000) in paragraph at lines 165--167
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \
T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method =
[2349]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 250--250
 []  \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met
hod = 0.5)[iC])   ,[] 

Overfull \hbox (63.78036pt too wide) in paragraph at lines 251--251
 []  \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, -.5))[iC]),[] 

Overfull \hbox (63.78036pt too wide) in paragraph at lines 252--252
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2350] [2351]
Underfull \vbox (badness 7685) has occurred while \output is active [2352]
[2353]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 516--516
 []           \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot
 = axes,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 520--520
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2354]
Underfull \hbox (badness 5374) in paragraph at lines 537--539
[]\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use
d when
[2355] [2356]
Underfull \hbox (badness 3078) in paragraph at lines 680--683
[]\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem-
ory (and hence time), but dis-ables
[2357]
Underfull \hbox (badness 2941) in paragraph at lines 761--764
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 
,
[2358]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 799--799
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2359]
Underfull \hbox (badness 10000) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see

Overfull \hbox (12.78088pt too wide) in paragraph at lines 893--893
 []\T1/pcr/m/n/10 clusGap(x, FUNcluster, K.max, B = 100, verbose = interactive(
), ...) 
[2360]
Underfull \hbox (badness 4872) in paragraph at lines 934--936
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is
[2361]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1036--1036
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2362] [2363]
Underfull \hbox (badness 4144) in paragraph at lines 1112--1116
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent,
 e.g., for
[2364]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1188--1188
 []          \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1,
 cex.txt = cex,[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 1194--1194
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2365] [2366]
Underfull \hbox (badness 10000) in paragraph at lines 1394--1398
[][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 ,
[2367]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1412--1412
 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a
nd label ellipses[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 1421--1421
 []         \T1/pcr/m/n/9 axes=FALSE,ann=FALSE, sub="", col.p=NA, col.txt="dark
 green", labels=3)[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 1429--1429
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2368]
Underfull \hbox (badness 5741) in paragraph at lines 1469--1472
[]\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der
-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only
[2369] [2370]
Underfull \hbox (badness 5008) in paragraph at lines 1645--1653
\T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh
ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1
0 w[]^^N[]$\T1/ptm/m/n/10 , where
[2371]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1736--1736
 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord
ratio = 7)))[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 1755--1755
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2372] [2373] [2374] [2375] [2376]
Underfull \hbox (badness 10000) in paragraph at lines 2057--2059
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as

Underfull \hbox (badness 3179) in paragraph at lines 2081--2087
[][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [
][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips
oid \T1/ptm/m/n/10 ob-jects.
[2377] [2378]
Underfull \hbox (badness 10000) in paragraph at lines 2239--2242
[][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence
s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par
tition.object[][][]\T1/ptm/m/n/10 ,
[2379]
Underfull \hbox (badness 1292) in paragraph at lines 2307--2310
[]\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t
he num-ber of it-er-a-tions needed and
[2380]
Underfull \hbox (badness 6675) in paragraph at lines 2316--2318
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see

Underfull \hbox (badness 10000) in paragraph at lines 2339--2342
[][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny
[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 ,

Overfull \vbox (12.60576pt too high) has occurred while \output is active
[2381] [2382] [2383]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2546--2546
 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to
 \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/
9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] 
[2384] [2385] [2386]
Underfull \hbox (badness 1067) in paragraph at lines 2734--2739
[]\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger
 \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g
o-rithm, whereas
[2387] [2388]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 2889--2889
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2389] [2390] [2391]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3085--3085
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3086--3086
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2392]
Underfull \hbox (badness 10000) in paragraph at lines 3153--3156
[]\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n
/10 pltree() \T1/ptm/m/n/10 is pro-vided by
[2393]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3203--3203
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3204--3204
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2394] [2395] [2396]
Underfull \hbox (badness 10000) in paragraph at lines 3389--3392
[]\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m
/n/10 diss \T1/ptm/m/n/10 com-po-nent as for

Underfull \hbox (badness 3471) in paragraph at lines 3389--3392
[][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10
 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a
[2397]
Underfull \hbox (badness 10000) in paragraph at lines 3452--3457
[][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 ,
[2398]
Underfull \hbox (badness 1735) in paragraph at lines 3521--3523
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "twins"\T1/ptm/m/n/10 , typ
-i-cally cre-ated by ei-ther [][]\T1/pcr/m/n/10 agnes[][][]() \T1/ptm/m/n/10 or


Underfull \hbox (badness 4621) in paragraph at lines 3538--3543
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc
r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1990) in paragraph at lines 3538--3543
\T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1
/ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider

Underfull \hbox (badness 6268) in paragraph at lines 3550--3553
[][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec
t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
plot.agnes[][][]\T1/ptm/m/n/10 ,
[2399]
Underfull \hbox (badness 10000) in paragraph at lines 3614--3615
[]\T1/ptm/m/n/10 currently [][]$\T1/pcr/m/n/10 http : / / www . agoras . ua . a
c . be / datasets / clusplot-[]examples . tar .
[2400] [2401]
Underfull \hbox (badness 10000) in paragraph at lines 3733--3736
[][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2402]
Underfull \hbox (badness 10000) in paragraph at lines 3764--3767
[][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu
t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje
ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 ,
[2403]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3817--3817
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 

Underfull \hbox (badness 2035) in paragraph at lines 3828--3830
[]\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1
/pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2404] [2405] [2406]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4021--4021
 []     \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w
idth "* s[i]),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 4023--4023
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2407]
Underfull \hbox (badness 1946) in paragraph at lines 4052--4057
[]\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n
/10 ; note that the de-fault used to be \T1/pcr/m/n/10 col

Underfull \hbox (badness 1062) in paragraph at lines 4107--4109
[]\T1/ptm/m/n/10 numeric (rank 1) ar-ray of clus-ter-wise \T1/ptm/m/it/10 means
 \T1/ptm/m/n/10 of sil-hou-ette widths where
[2408]
Underfull \hbox (badness 10000) in paragraph at lines 4118--4126
\T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing
 if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by

Overfull \hbox (31.3804pt too wide) in paragraph at lines 4160--4160
 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus
ter-wise coloring[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4169--4169
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE)[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4171--4171
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 4174--4174
 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol
denrod4", "gray20")[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4176--4176
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 
[2409]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4190--4190
 []   \T1/pcr/m/n/9 stopifnot(all.equal(sf, s.full, check.attributes = FALSE, t
olerance = 0))[] 
[2410] [2411] [2412] [2413] [2414] [2415] [2416]) (./codetools-pkg.tex
Chapter 21.

Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16
 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17
 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18
 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2417]
Underfull \hbox (badness 10000) in paragraph at lines 65--70
[]\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack
age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply
[2418]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119
 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2419] [2420] [2421]) (./foreign-pkg.tex [2422]
Chapter 22.
[2423]
Underfull \hbox (badness 1231) in paragraph at lines 67--70
[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a

Underfull \hbox (badness 6708) in paragraph at lines 78--81
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2424] [2425]
Underfull \hbox (badness 3601) in paragraph at lines 234--242
[]\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n
/10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 ,
[2426]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 293--293
 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2427] [2428] [2429]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame)[] 
[2430]
Underfull \hbox (badness 10000) in paragraph at lines 515--523
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]
[2431]
Underfull \hbox (badness 7613) in paragraph at lines 533--539
[]\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/
m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute
[2432] [2433] [2434]
Underfull \hbox (badness 10000) in paragraph at lines 730--731


Overfull \hbox (4.38043pt too wide) in paragraph at lines 740--740
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2435]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 816--816
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2436]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 879--879
 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 

Underfull \hbox (badness 6708) in paragraph at lines 905--908
[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2437] [2438]
Underfull \hbox (badness 10000) in paragraph at lines 989--990
[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .

Overfull \hbox (24.78088pt too wide) in paragraph at lines 1025--1025
 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2439]
Underfull \hbox (badness 1286) in paragraph at lines 1110--1114
[]\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = 
FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec
ts
[2440]
Underfull \hbox (badness 10000) in paragraph at lines 1183--1189
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign:
::writeForeignStata\T1/ptm/m/n/10 ,
[2441] [2442]) (./lattice-pkg.tex
Chapter 23.
[2443] [2444] [2445]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 287--287
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 291--291
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2446]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 299--299
 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 

Overfull \hbox (54.78088pt too wide) in paragraph at lines 306--306
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 

Overfull \hbox (66.78088pt too wide) in paragraph at lines 314--314
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 335--335
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 339--339
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2447]
Underfull \hbox (badness 4060) in paragraph at lines 358--370
[]\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a
lly of the

Underfull \hbox (badness 10000) in paragraph at lines 358--370
\T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ
iv-a-lently, \T1/pcr/m/n/10 y ~ x |

Underfull \hbox (badness 1028) in paragraph at lines 398--413
\T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot
 both

Underfull \hbox (badness 10000) in paragraph at lines 414--416
[]\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum,
 one can ei-ther set
[2448]
Underfull \hbox (badness 7631) in paragraph at lines 480--485
[]\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \
T1/ptm/m/n/10 in this case may be
[2449] [2450]
Underfull \hbox (badness 1221) in paragraph at lines 651--659
[]\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as
 ar-gu-ments to
[2451] [2452] [2453] [2454]
Underfull \hbox (badness 2005) in paragraph at lines 986--998
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of 
fac-tors will be

Underfull \hbox (badness 1199) in paragraph at lines 986--998
\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2455]
Underfull \hbox (badness 1661) in paragraph at lines 1099--1105
[]\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be
 num-bers be-tween 0 and 1, giv-ing co-or-di-nates
[2456] [2457]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a

Underfull \hbox (badness 1917) in paragraph at lines 1239--1240
[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2458] [2459] [2460]
Underfull \hbox (badness 1540) in paragraph at lines 1479--1485
[]\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/
10 plot.trellis[][][]\T1/ptm/m/n/10 ,
[2461]
Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel
.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt
m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 ,
[2462]
Underfull \vbox (badness 10000) has occurred while \output is active [2463]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671
 []                  \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar
dSprays$rowpos))),[] 

Underfull \hbox (badness 2012) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][]
[]\T1/ptm/m/n/10 , which may pass them on to
[2464]
Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to

Underfull \hbox (badness 10000) in paragraph at lines 1772--1775
[]\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt
m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 
, etc; see
[2465]
Underfull \hbox (badness 10000) in paragraph at lines 1825--1827
[]\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix
 An-drews
[2466] [2467] [2468]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 

Underfull \hbox (badness 10000) in paragraph at lines 2086--2093
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/
m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form

Underfull \hbox (badness 1997) in paragraph at lines 2086--2093
\T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra
ms or ker-nel den-sity
[2469]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t
he value of

Underfull \hbox (badness 1320) in paragraph at lines 2141--2144
\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch
ecked. If
[2470] [2471] [2472]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2347--2347
 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 2351--2351
 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 

Underfull \hbox (badness 4441) in paragraph at lines 2364--2368
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2473] [2474] [2475]
Underfull \hbox (badness 4441) in paragraph at lines 2549--2556
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form
[2476] [2477]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 2691--2691
 []          \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev
elplot.raster")[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2478]
Underfull \hbox (badness 10000) in paragraph at lines 2763--2768
[]\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu
la of the form \T1/pcr/m/n/10 z ~ x * y
[2479]
Underfull \hbox (badness 2913) in paragraph at lines 2793--2798
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.

Underfull \hbox (badness 3058) in paragraph at lines 2793--2798
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as

Underfull \hbox (badness 6758) in paragraph at lines 2879--2883
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be


Underfull \hbox (badness 7576) in paragraph at lines 2879--2883
\T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast
er[][][]\T1/ptm/m/n/10 . See also

Underfull \hbox (badness 10000) in paragraph at lines 2885--2887
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2480]
Underfull \hbox (badness 1609) in paragraph at lines 2937--2943
[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti
ons should be used,

Underfull \hbox (badness 2772) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-

Underfull \hbox (badness 1400) in paragraph at lines 2937--2943
\T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 
changes the de-fault panel func-tion from

Underfull \hbox (badness 2486) in paragraph at lines 2961--2965
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2481] [2482]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 3063--3063
 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 3064--3064
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 3075--3075
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 

Overfull \hbox (66.78088pt too wide) in paragraph at lines 3087--3087
 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2483]
Underfull \hbox (badness 10000) in paragraph at lines 3112--3120
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo
r-mula of the form \T1/pcr/m/n/10 z ~ x

Underfull \hbox (badness 2913) in paragraph at lines 3145--3152
[]\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc
r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix.

Underfull \hbox (badness 3058) in paragraph at lines 3145--3152
\T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p
tm/m/n/10 must have the same lengths as
[2484] [2485] [2486] [2487]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3433 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3475--3475
 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2488]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3498--3498
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2489] [2490] [2491] [2492] [2493]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3834--3834
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2494]
Underfull \hbox (badness 10000) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white
bg")\T1/ptm/m/n/10 .

Underfull \hbox (badness 2435) in paragraph at lines 3924--3928
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2495] [2496]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4054--4054
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 

Underfull \hbox (badness 1173) in paragraph at lines 4063--4067
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in

Underfull \hbox (badness 3219) in paragraph at lines 4090--4092
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when

Underfull \hbox (badness 1728) in paragraph at lines 4107--4111
\T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se
t-tings (ob-tained by
[2497]
Underfull \hbox (badness 5161) in paragraph at lines 4172--4176
[]\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis
.settings \T1/ptm/m/n/10 has not been fi-nal-ized,

Underfull \hbox (badness 4913) in paragraph at lines 4172--4176
\T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca
n be ob-tained by
[2498] [2499]
Underfull \hbox (badness 1067) in paragraph at lines 4286--4296
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i
s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm
/m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1735) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p
olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points

Underfull \hbox (badness 10000) in paragraph at lines 4286--4296
\T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f
or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and

Underfull \hbox (badness 5231) in paragraph at lines 4286--4296
\T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c
ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for

Underfull \hbox (badness 1701) in paragraph at lines 4311--4314
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot
.symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4314--4316
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl
ot.polygon \T1/ptm/m/n/10 and
[2500] [2501] [2502] [2503] [2504] [2505]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4718--4718
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2506] [2507]
Underfull \hbox (badness 10000) in paragraph at lines 4905--4908
[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by 
de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 .
[2508] [2509]
Underfull \hbox (badness 1442) in paragraph at lines 5037--5040
[]\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles 
via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and
[2510] [2511] [2512] [2513] [2514] [2515]
Underfull \hbox (badness 3646) in paragraph at lines 5369--5372
[][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , 
and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f
or

Overfull \hbox (36.78088pt too wide) in paragraph at lines 5399--5399
 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 5400--5400
 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2516]
Underfull \hbox (badness 10000) in paragraph at lines 5488--5491
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

Underfull \hbox (badness 2103) in paragraph at lines 5488--5491
\T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef
t of pan-els us-ing

Underfull \hbox (badness 6412) in paragraph at lines 5505--5511
[]\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl
y be-cause of the \T1/pcr/m/n/10 style

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive
, es-pe-cially when

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm
/m/n/10 are small. Tra-di-tional use is as

Underfull \hbox (badness 10000) in paragraph at lines 5505--5511
\T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 ,
 though this can be
[2517]
Underfull \hbox (badness 1635) in paragraph at lines 5514--5519
[]\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh
ich is to draw a strip ap-pro-pri-ate for
[2518]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5663--5663
 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2519]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 5677--5677
 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 5678--5678
 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 5681--5681
 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 5684--5684
 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 5686--5686
 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692
 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 5694--5694
 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 5695--5695
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 5696--5696
 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 

Underfull \hbox (badness 10000) in paragraph at lines 5712--5714
[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of

[2520]
Underfull \hbox (badness 2376) in paragraph at lines 5723--5725
[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2521]
Underfull \hbox (badness 2538) in paragraph at lines 5848--5852
\T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is
 \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and

Underfull \hbox (badness 4205) in paragraph at lines 5859--5866
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr
a pa-ram-e-ters are passed on to

Underfull \hbox (badness 4792) in paragraph at lines 5859--5866
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are
 used (in com-bi-na-tion with
[2522] [2523]
Underfull \hbox (badness 10000) in paragraph at lines 6012--6016
[][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , []
[]\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 ,
[2524] [2525]
Underfull \hbox (badness 4242) in paragraph at lines 6159--6164
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2526] [2527]
Underfull \hbox (badness 3601) in paragraph at lines 6275--6280
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1
0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round

Underfull \hbox (badness 2486) in paragraph at lines 6275--6280
\T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault,
 the ac-tual box-plot statis-tics are cal-cu-lated us-ing
[2528] [2529]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 6362--6362
 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2530]
Underfull \hbox (badness 1888) in paragraph at lines 6494--6501
\T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col.
regions \T1/ptm/m/n/10 a vec-tor of col-ors, and
[2531]
Underfull \hbox (badness 10000) in paragraph at lines 6551--6554
[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The

Underfull \hbox (badness 1558) in paragraph at lines 6551--6554
\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2532]
Underfull \hbox (badness 1005) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T
1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 z \T1/ptm/m/n/10 are all passed to

Underfull \hbox (badness 1571) in paragraph at lines 6601--6609
\T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For 
wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/
10 y \T1/ptm/m/n/10 are in-
[2533] [2534] [2535] [2536] [2537]
Underfull \hbox (badness 1320) in paragraph at lines 6957--6964
[]\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan
el func-tion that uses the raster draw-

Underfull \hbox (badness 1715) in paragraph at lines 6957--6964
\T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more
 ef-fi-cient. When us-ing
[2538]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7027--7027
 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2539]
Underfull \hbox (badness 10000) in paragraph at lines 7057--7060
[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to

Underfull \hbox (badness 1584) in paragraph at lines 7057--7060
\T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu
nc-tion is passed
[2540]
Underfull \hbox (badness 10000) in paragraph at lines 7161--7164
\T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10
 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by
[2541] [2542]
Underfull \hbox (badness 2012) in paragraph at lines 7327--7330
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2543]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7373--7373
 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2544] [2545]
Underfull \hbox (badness 2644) in paragraph at lines 7514--7518
\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to

Underfull \hbox (badness 2772) in paragraph at lines 7527--7530
[]\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a 
list of ar-gu-ments to be sup-plied to

Underfull \hbox (badness 4242) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos
-si-bly

Underfull \hbox (badness 1147) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is
 co-erced to a list. This al-lows ar-

Underfull \hbox (badness 2351) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline =     c(0, 1)\T1/ptm/
m/n/10 , which adds the di-

Underfull \hbox (badness 1675) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v     = 0)\T1
/ptm/m/n/10 , which adds the

Underfull \hbox (badness 1769) in paragraph at lines 7541--7549
\T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol;
 e.g.,
[2546]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597
 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7607--7607
 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2547]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 7668--7668
 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 7673--7673
 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2548] [2549] [2550]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 7854--7854
 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2551]
Underfull \hbox (badness 1436) in paragraph at lines 7909--7915
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for

Underfull \hbox (badness 1231) in paragraph at lines 7909--7915
\T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti
ngs. The
[2552] [2553] [2554] [2555] [2556] [2557] [2558] [2559]
Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se

Underfull \hbox (badness 10000) in paragraph at lines 8467--8470
\T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1
/pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from
[2560] [2561]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8642--8642
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 8643--8643
 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 

Overfull \hbox (30.78088pt too wide) in paragraph at lines 8655--8655
 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2562]
Underfull \hbox (badness 3118) in paragraph at lines 8674--8677
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1
/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2563]
Underfull \hbox (badness 1515) in paragraph at lines 8750--8754
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2564]
Underfull \hbox (badness 6316) in paragraph at lines 8856--8861
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2565] [2566]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8963--8963
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2567] [2568]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9102--9102
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2569]
Overfull \hbox (84.94879pt too wide) in paragraph at lines 9161--9165
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr
/m/n/10 left,    right, left.name, right.name, condition

Overfull \hbox (104.63074pt too wide) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,    right.x, right.y, left.name
, right.x.name, right.y.name, condition
[2570] [2571] [2572] [2573] [2574] [2575] [2576]
Underfull \hbox (badness 4205) in paragraph at lines 9619--9623
[]\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , 
\T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/
10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 4518) in paragraph at lines 9619--9623
\T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10
 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n
/10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 6300) in paragraph at lines 9624--9627
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/
n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm"
\T1/ptm/m/n/10 ,
[2577] [2578] [2579]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9850 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2580] [2581] [2582] [2583])
(./mgcv-pkg.tex [2584]
Chapter 24.

Underfull \hbox (badness 1052) in paragraph at lines 40--42
[]\T1/ptm/m/n/10 selects ex-act test statis-tic to use for sin-gle smooth term 
p-values. See
[2585] [2586]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147
 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 150--150
 []    \T1/pcr/m/n/10 chunk.size=10000,rho=0,AR.start=NULL,sparse=FALSE,cluster
=NULL,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 151--151
 []    \T1/pcr/m/n/10 gc.level=1,use.chol=FALSE,samfrac=1,drop.unused.levels=TR
UE,...)[] 
[2587]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

Underfull \hbox (badness 1043) in paragraph at lines 193--198
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2588]
Underfull \hbox (badness 2626) in paragraph at lines 248--251
[]\T1/ptm/m/n/10 If all smooths are P-splines and all ten-sor prod-ucts are of 
the form
[2589] [2590]
Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 340--346
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2591] [2592] [2593]
Underfull \hbox (badness 2922) in paragraph at lines 521--522
[]\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/
n/10 and

Underfull \hbox (badness 1158) in paragraph at lines 563--565
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2594] [2595]
Underfull \vbox (badness 10000) has occurred while \output is active [2596]
[2597] [2598] [2599] [2600]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 956--956
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 957--957
 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 982--982
 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights=
d,data=surv)[] 
[2601] [2602] [2603] [2604] [2605] [2606] [2607]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 1382--1382
 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2608] [2609] [2610] [2611] [2612] [2613]
Underfull \hbox (badness 1221) in paragraph at lines 1743--1749
\T1/ptm/m/n/10 de-grees of free-dom (mix-tures of the two are per-mit-ted). Mul
ti-dimensional smooths are

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1758--1758
 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 1762--1762
 []    \T1/pcr/m/n/10 fit=TRUE,paraPen=NULL,G=NULL,in.out,drop.unused.levels=TR
UE,...)[] 

Underfull \hbox (badness 1142) in paragraph at lines 1783--1787
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2614]
Underfull \hbox (badness 1043) in paragraph at lines 1806--1811
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2615] [2616]
Underfull \hbox (badness 1043) in paragraph at lines 1966--1972
\T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v
en-tion mech-a-nism de-scribed in
[2617] [2618]
Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO
bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/
n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 2093--2099
[][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid
e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , 
[][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 ,
[2619]
Underfull \vbox (badness 10000) has occurred while \output is active [2620]
Underfull \vbox (badness 10000) has occurred while \output is active [2621]
Underfull \vbox (badness 10000) has occurred while \output is active [2622]
[2623] [2624] [2625] [2626] [2627] [2628]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2720--2720
 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 2723--2723
 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2629] [2630] [2631] [2632] [2633]
Underfull \hbox (badness 5189) in paragraph at lines 3038--3042
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n
/10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2634] [2635]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2636]
[2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3709--3709
 []  \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i
d=1)+s(x1,id=1)+[] 
[2645] [2646]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3824--3824
 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 

Underfull \hbox (badness 1142) in paragraph at lines 3855--3859
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2647] [2648] [2649]
Underfull \hbox (badness 5970) in paragraph at lines 4035--4041
[][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r
e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[
][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 ,
[2650]
Underfull \vbox (badness 10000) has occurred while \output is active [2651]
[2652] [2653]
Underfull \hbox (badness 1577) in paragraph at lines 4280--4283
[]\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see []
[]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment

Underfull \hbox (badness 2181) in paragraph at lines 4287--4288
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2654] [2655] [2656] [2657] [2658] [2659] [2660] [2661] [2662] [2663] [2664]
[2665]
Underfull \vbox (badness 10000) has occurred while \output is active [2666]
[2667] [2668]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 5234--5234
 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 5261--5261
 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2669] [2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] [2679]
[2680] [2681] [2682] [2683] [2684] [2685] [2686] [2687] [2688] [2689] [2690]
[2691] [2692] [2693]
Underfull \vbox (badness 10000) has occurred while \output is active [2694]
[2695]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p
dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\
T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3118) in paragraph at lines 6923--6926
\T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su
mmary.pdIdnot\T1/ptm/m/n/10 .
[2696]
Underfull \hbox (badness 10000) in paragraph at lines 6979--6982
[]\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc
r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p
tm/m/n/10 ,

Underfull \hbox (badness 3108) in paragraph at lines 6979--6982
\T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p
tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally
 be
[2697] [2698] [2699]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 7199--7199
 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 7200--7200
 []         \T1/pcr/m/n/10 n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xla
b=NULL,[] 

Overfull \hbox (72.78088pt too wide) in paragraph at lines 7203--7203
 []         \T1/pcr/m/n/10 shift=0,trans=I,seWithMean=FALSE,unconditional=FALSE
,by.resids=FALSE,[] 
[2700] [2701] [2702]
Underfull \hbox (badness 1629) in paragraph at lines 7355--7360
\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is
 some-times to clone the
[2703] [2704] [2705]
Overfull \hbox (114.78088pt too wide) in paragraph at lines 7554--7554
 []        \T1/pcr/m/n/10 block.size=50000,newdata.guaranteed=FALSE,na.action=n
a.pass,cluster=NULL,...)[] 
[2706] [2707]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 7704--7704
 []        \T1/pcr/m/n/10 block.size=NULL,newdata.guaranteed=FALSE,na.action=na
.pass,[] 
[2708] [2709] [2710]
Underfull \vbox (badness 10000) has occurred while \output is active [2711]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7945--7945
 []  \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s
mooth deriv i[] 
[2712]
Underfull \hbox (badness 1205) in paragraph at lines 7983--7985
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 7983--7985
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

Underfull \hbox (badness 1975) in paragraph at lines 7989--7994
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2713]
Underfull \hbox (badness 1205) in paragraph at lines 8073--8075
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 8073--8075
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2714]
Underfull \hbox (badness 10000) in paragraph at lines 8142--8145
[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from

Underfull \hbox (badness 2057) in paragraph at lines 8142--8145
[][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho
ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n
/10 are not needed,
[2715] [2716]
Underfull \hbox (badness 1253) in paragraph at lines 8272--8274
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2717] [2718] [2719] [2720]
Underfull \hbox (badness 1946) in paragraph at lines 8450--8457
[]\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef-
fects in a GAM in the same

Underfull \hbox (badness 2221) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method

Underfull \hbox (badness 2042) in paragraph at lines 8450--8457
\T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by 
mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s
ee

Underfull \hbox (badness 2846) in paragraph at lines 8458--8461
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1
0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n
/10 can be used:

Underfull \hbox (badness 5862) in paragraph at lines 8458--8461
\T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot
h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2721]
Underfull \hbox (badness 10000) in paragraph at lines 8537--8540
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10
 "deviance"\T1/ptm/m/n/10 ,
[2722] [2723] [2724] [2725] [2726] [2727] [2728] [2729]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 9044--9044
 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 

Underfull \hbox (badness 1975) in paragraph at lines 9055--9060
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2730] [2731]
Underfull \hbox (badness 1803) in paragraph at lines 9132--9136
\T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var
i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T
1/ptm/m/n/10 .

Underfull \hbox (badness 1502) in paragraph at lines 9144--9156
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec

Underfull \hbox (badness 2401) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. 
Plot meth-ods can be

Underfull \hbox (badness 2970) in paragraph at lines 9161--9165
\T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/
m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 ,
[2732] [2733] [2734]
Underfull \hbox (badness 6876) in paragraph at lines 9354--9360
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like
[2735]
Underfull \hbox (badness 10000) in paragraph at lines 9395--9396
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2736] [2737]
Underfull \hbox (badness 10000) in paragraph at lines 9524--9526
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term

Underfull \hbox (badness 10000) in paragraph at lines 9524--9526
\T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs",
...) \T1/ptm/m/n/10 or
[2738] [2739]
Underfull \hbox (badness 10000) in paragraph at lines 9652--9653
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2740] [2741]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9733--9733
 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9734--9734
 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi
ed 2nd deriv[] 

Underfull \hbox (badness 7613) in paragraph at lines 9772--9775
\T1/ptm/m/n/10 method an ob-ject of class \T1/pcr/m/n/10 "fs.interaction" \T1/p
tm/m/n/10 pro-duced by the
[2742] [2743] [2744] [2745]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9985--9985
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2746]
Underfull \hbox (badness 10000) in paragraph at lines 10030--10032
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2747] [2748]
Underfull \hbox (badness 10000) in paragraph at lines 10138--10141
[]\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method 
a smooth spec-i-fi-ca-tion ob-

Underfull \hbox (badness 3312) in paragraph at lines 10138--10141
\T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs="
re",)\T1/ptm/m/n/10 . For the

Underfull \hbox (badness 7099) in paragraph at lines 10138--10141
\T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr
/m/n/10 "random.effect"
[2749]
Underfull \hbox (badness 10000) in paragraph at lines 10237--10243
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a

Underfull \hbox (badness 2698) in paragraph at lines 10237--10243
\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1
/pcr/m/n/10 gam \T1/ptm/m/n/10 for-
[2750] [2751] [2752]
Underfull \vbox (badness 10000) has occurred while \output is active [2753]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 10451--10451
 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1
/pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] 


Overfull \hbox (58.38037pt too wide) in paragraph at lines 10453--10453
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sf","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))+[] 

Overfull \hbox (52.98038pt too wide) in paragraph at lines 10454--10454
 [] \T1/pcr/m/n/9 te(v,w,t,bs=c("sw","cr"),k=c(25,4),d=c(2,1),xt=list(list(bnd=
fsb,nmax=nmax),NULL))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [2754]
Overfull \hbox (90.78033pt too wide) in paragraph at lines 10535--10535
 []\T1/pcr/m/n/9 b <- gam(z~s(x,y,k=c(30,15),bs="so",xt=list(bnd=bnd,nmax=nmax)
),knots=knots,method="REML")[] 

Overfull \hbox (85.38034pt too wide) in paragraph at lines 10541--10541
 []          \T1/pcr/m/n/9 s(x,y,k=c(30,15),bs="sw",xt=list(bnd=bnd,nmax=nmax))
,knots=knots,method="REML")[] 
[2755]
Underfull \hbox (badness 10000) in paragraph at lines 10555--10563
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like

Underfull \hbox (badness 10000) in paragraph at lines 10581--10582
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2756] [2757]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 10683--10683
 []\T1/pcr/m/n/9 bk <- gam(y~s(la,lo,bs="sos",k=60),knots=list(la=dat$la[ind],l
o=dat$lo[ind]),data=dat)[] 
[2758] [2759]
Underfull \hbox (badness 3396) in paragraph at lines 10841--10846
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any 
num-ber of vari-ables, spec-i-fied via terms like
[2760]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10888
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2761] [2762] [2763] [2764]
Underfull \hbox (badness 10000) in paragraph at lines 11074--11077
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-

Underfull \hbox (badness 3068) in paragraph at lines 11074--11077
\T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see []
[]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas
s (see

Underfull \hbox (badness 10000) in paragraph at lines 11107--11111
[][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr
/m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression
.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 5652) in paragraph at lines 11107--11111
[][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , code[][]soap[][][], code[][]Spheri
cal.Spline[][][], [][]\T1/pcr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 ,
[2765] [2766]
Underfull \hbox (badness 2158) in paragraph at lines 11259--11259
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2767] [2768]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 11334--11334
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[2769] [2770]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11468--11468
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[2771] [2772]
Underfull \hbox (badness 4846) in paragraph at lines 11604--11607
[]\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or 
es-ti-ma-tors if
[2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783]
[2784] [2785] [2786] [2787]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 12501--12501
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[2788] [2789] [2790] [2791] [2792] [2793] [2794]) (./nlme-pkg.tex
Chapter 25.
[2795]
Underfull \hbox (badness 1009) in paragraph at lines 84--93
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2796]
Underfull \hbox (badness 1009) in paragraph at lines 174--183
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[2797] [2798] [2799] [2800] [2801]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454
 []  \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2802] [2803] [2804] [2805] [2806] [2807] [2808] [2809] [2810] [2811]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1094--1094
 []                  \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil
lary fissure"),[] 
[2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819]
Underfull \hbox (badness 10000) in paragraph at lines 1633--1636
[][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe
cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m
/n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 ,
[2820]
Underfull \hbox (badness 3780) in paragraph at lines 1650--1652
[]\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a
ted with each com-po-nent of the
[2821] [2822] [2823] [2824] [2825]
Underfull \hbox (badness 2042) in paragraph at lines 1997--2003
\T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou
p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[2826]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2059--2059
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[2827]
Underfull \hbox (badness 1132) in paragraph at lines 2147--2149
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[2828] [2829]
Underfull \hbox (badness 4168) in paragraph at lines 2258--2264
[][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T
1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize
.corStruct[][][]\T1/ptm/m/n/10 ,
[2830]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[2831] [2832] [2833] [2834] [2835] [2836] [2837] [2838]
Underfull \hbox (badness 10000) in paragraph at lines 2846--2850
[][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr
ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1
/ptm/m/n/10 ,
[2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849]
[2850]
Underfull \hbox (badness 6493) in paragraph at lines 3582--3590
[][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 ,
[2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 4348--4348
 []\T1/pcr/m/n/10 fdHess(pars, fun, ..., .relStep=(.Machine$double.eps)^(1/3), 
minAbsPar=0) 
[2862] [2863] [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] [2872]
[2873] [2874]
Underfull \hbox (badness 10000) in paragraph at lines 5158--5162
[][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m
/n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879]
Underfull \hbox (badness 10000) in paragraph at lines 5475--5479
[]\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit-
ted in the fit if

Underfull \hbox (badness 2671) in paragraph at lines 5475--5479
\T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if 
\T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 .
[2880] [2881]
Underfull \hbox (badness 10000) in paragraph at lines 5590--5593
[][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][]
[]\T1/ptm/m/n/10 ,
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
Underfull \hbox (badness 2799) in paragraph at lines 6096--6102
\T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/
ptm/m/n/10 for the random-effects
[2891]
Underfull \hbox (badness 7133) in paragraph at lines 6157--6161
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2892]
Underfull \hbox (badness 2057) in paragraph at lines 6241--6252
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon
trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [
][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 ,
[2893]
Underfull \hbox (badness 10000) in paragraph at lines 6305--6307
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

Overfull \hbox (9.78043pt too wide) in paragraph at lines 6334--6334
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2894] [2895] [2896] [2897]
Underfull \hbox (badness 7133) in paragraph at lines 6553--6557
[]\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \
T1/pcr/m/n/10 model\T1/ptm/m/n/10 ,
[2898]
Underfull \hbox (badness 10000) in paragraph at lines 6652--6658
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo
ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict
.gnls[][][]\T1/ptm/m/n/10 ,
[2899]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6718
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2900]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6743--6743
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2901] [2902] [2903]
Underfull \hbox (badness 10000) in paragraph at lines 6986--6993
[][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][
]\T1/ptm/m/n/10 ,

Overfull \hbox (15.18042pt too wide) in paragraph at lines 7003--7003
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 7011--7011
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 
[2904]
Underfull \hbox (badness 2875) in paragraph at lines 7033--7035
[]\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou
pedData \T1/ptm/m/n/10 ob-ject or a
[2905] [2906] [2907]
Underfull \hbox (badness 10000) in paragraph at lines 7248--7253
[][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl
sStruct[][][]\T1/ptm/m/n/10 ,
[2908] [2909]
Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-

Underfull \hbox (badness 10000) in paragraph at lines 7400--7408
\T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme
\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 1817) in paragraph at lines 7400--7408
\T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 
20 EM it-er-a-

Underfull \hbox (badness 3118) in paragraph at lines 7423--7426
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re
Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 ,
[2910] [2911] [2912] [2913]
Underfull \hbox (badness 3354) in paragraph at lines 7638--7640
[]\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10
 which \T1/ptm/m/n/10 is not equal to
[2914] [2915] [2916] [2917] [2918] [2919]
Underfull \hbox (badness 1642) in paragraph at lines 8030--8052
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2920] [2921]
Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm
List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/
10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme
Object[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 8150--8167
[][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][
][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (12.78088pt too wide) in paragraph at lines 8193--8193
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 

Underfull \hbox (badness 1642) in paragraph at lines 8202--8224
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[2922] [2923] [2924] [2925] [2926]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 8466--8466
 []\T1/pcr/m/n/10 lmeControl(maxIter, msMaxIter, tolerance, niterEM, msMaxEval,
 msTol, 

Underfull \hbox (badness 10000) in paragraph at lines 8509--8511
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[2927]
Underfull \hbox (badness 1320) in paragraph at lines 8522--8526
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][] \T1/ptm/m/n/10 (those from

Overfull \hbox (9.78043pt too wide) in paragraph at lines 8544--8544
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2928] [2929] [2930]
Underfull \hbox (badness 10000) in paragraph at lines 8707--8719
[]\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo
r-mula ob-ject of the form
[2931] [2932] [2933] [2934] [2935] [2936] [2937] [2938] [2939]
Underfull \hbox (badness 10000) in paragraph at lines 9297--9304
[][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p
cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS
truct[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (4.38043pt too wide) in paragraph at lines 9308--9308
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[2940]
Underfull \hbox (badness 6300) in paragraph at lines 9390--9393
[]\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr
/m/n/10 lm \T1/ptm/m/n/10 com-po-nents of
[2941] [2942] [2943] [2944]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9659 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [2945]
Underfull \hbox (badness 10000) in paragraph at lines 9679--9682
[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s
[2946]
Underfull \hbox (badness 3108) in paragraph at lines 9727--9730
[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite

Underfull \hbox (badness 2521) in paragraph at lines 9727--9730
\T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M
ust have the same di-men-sions as
[2947] [2948]
Underfull \hbox (badness 2435) in paragraph at lines 9900--9905
[]\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form
ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/
10 ,
[2949] [2950] [2951] [2952] [2953]
Underfull \hbox (badness 7291) in paragraph at lines 10190--10192
[]\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D
imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to
[2954] [2955] [2956]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10406--10406
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[2957]
Underfull \hbox (badness 1596) in paragraph at lines 10435--10461
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[2958] [2959] [2960]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10611--10611
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[2961] [2962] [2963]
Underfull \hbox (badness 10000) in paragraph at lines 10808--10810
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

Underfull \hbox (badness 1092) in paragraph at lines 10818--10821
[]\T1/ptm/m/n/10 Further named con-trol ar-gu-ments to be passed to [][]\T1/pcr
/m/n/10 nlminb[][][]\T1/ptm/m/n/10 , where used

Overfull \hbox (9.78043pt too wide) in paragraph at lines 10840--10840
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[2964] [2965] [2966]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 10996--10996
 []\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool) 
[2967]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 11091--11091
 []\T1/pcr/m/n/10 nlsList(model, data, start, control, level, subset, na.action
, pool)[] 
[2968] [2969] [2970] [2971] [2972] [2973] [2974] [2975] [2976] [2977] [2978]
Underfull \hbox (badness 6268) in paragraph at lines 11852--11862
[][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T
1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1
0 pdMatrix[][][]\T1/ptm/m/n/10 ,
[2979] [2980] [2981] [2982]
Underfull \hbox (badness 10000) in paragraph at lines 12113--12119
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c
oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1
0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon
struct[][][]\T1/ptm/m/n/10 ,
[2983] [2984] [2985] [2986] [2987] [2988] [2989]
Underfull \hbox (badness 2452) in paragraph at lines 12576--12583
[][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS
ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\
T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\
T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n
/10 reStruct[][][]\T1/ptm/m/n/10 ,
[2990]
Underfull \hbox (badness 10000) in paragraph at lines 12641--12647
[][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p
dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 
, [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re
Struct[][][]\T1/ptm/m/n/10 ,
[2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001]
[3002] [3003] [3004]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13593--13593
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3005]
Underfull \hbox (badness 10000) in paragraph at lines 13620--13623
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 6016) in paragraph at lines 13648--13651
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i-
zon-tal axis.

Underfull \hbox (badness 2653) in paragraph at lines 13648--13651
\T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T
1/pcr/m/n/10 attr(object,     "labels") \T1/ptm/m/n/10 and

Underfull \hbox (badness 1975) in paragraph at lines 13655--13658
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot

Underfull \hbox (badness 1838) in paragraph at lines 13663--13670
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/
10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner

Underfull \hbox (badness 3713) in paragraph at lines 13663--13670
\T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n
/10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner
[3006]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 13720--13720
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 

Underfull \hbox (badness 10000) in paragraph at lines 13727--13730
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD
ata\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 2469) in paragraph at lines 13727--13730
\T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v
ari-ate and a sin-gle
[3007]
Underfull \hbox (badness 4582) in paragraph at lines 13755--13758
[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is

Underfull \hbox (badness 2418) in paragraph at lines 13755--13758
\T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,  
   "labels") \T1/ptm/m/n/10 and

Underfull \hbox (badness 2990) in paragraph at lines 13759--13762
[]\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/
ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot
[3008]
Underfull \hbox (badness 10000) in paragraph at lines 13835--13838
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa
ta\T1/ptm/m/n/10 , rep-re-sent-ing a

Underfull \hbox (badness 1472) in paragraph at lines 13860--13867
\T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to
 \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ,
[3009]
Underfull \hbox (badness 10000) in paragraph at lines 13929--13931
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla
pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][
][]\T1/ptm/m/n/10 ,
[3010] [3011] [3012] [3013]
Underfull \hbox (badness 1540) in paragraph at lines 14144--14149
\T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p
lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1
/ptm/m/n/10 in-cludes an

Underfull \hbox (badness 1215) in paragraph at lines 14191--14193
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3014] [3015] [3016] [3017] [3018]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14434--14434
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15072 ...Extract Random Effects}{random.effects}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15072 ...Extract Random Effects}{random.effects}
                                                   [3028] [3029] [3030]
[3031] [3032] [3033] [3034] [3035] [3036] [3037]
Underfull \hbox (badness 1009) in paragraph at lines 15729--15738
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3038] [3039] [3040]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15876--15876
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3041] [3042] [3043] [3044]
Underfull \hbox (badness 10000) in paragraph at lines 16154--16172
[]\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form

Underfull \hbox (badness 1708) in paragraph at lines 16154--16172
\T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+..
.+xn \T1/ptm/m/n/10 spec-i-fy-ing the model
[3045]
Underfull \hbox (badness 10000) in paragraph at lines 16211--16217
[][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr
/m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc
t[][][]\T1/ptm/m/n/10 ,
[3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053]
Underfull \hbox (badness 1728) in paragraph at lines 16731--16734
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3054] [3055] [3056] [3057] [3058]
Underfull \hbox (badness 1867) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked"
 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal"

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip
le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17064--17073
\T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization"
[3059]
Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu
nc-tion:

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varComb\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/
n/10 varConstPower\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m
/n/10 varExp\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for

Underfull \hbox (badness 10000) in paragraph at lines 17128--17136
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 ,
[3060] [3061] [3062] [3063]
Underfull \hbox (badness 10000) in paragraph at lines 17375--17382
[][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP
ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][]
\T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][]
\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3064] [3065] [3066] [3067] [3068] [3069] [3070]
Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][]
[]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 17904--17914
[][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 
Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe
r[][][]\T1/ptm/m/n/10 ,
[3071]
Underfull \hbox (badness 3579) in paragraph at lines 17942--17947
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3072]
Underfull \hbox (badness 3579) in paragraph at lines 18006--18011
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3073]
Underfull \hbox (badness 3579) in paragraph at lines 18069--18074
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3074]
Underfull \hbox (badness 1577) in paragraph at lines 18130--18132
[]\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat
io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal

Underfull \hbox (badness 3579) in paragraph at lines 18132--18137
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3075]
Underfull \hbox (badness 3579) in paragraph at lines 18195--18200
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3076]
Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog
ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n
/10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 18228--18237
[][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V
ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][]
[]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3579) in paragraph at lines 18267--18272
\T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m
/n/10 , in which case a se-quence
[3077] [3078]
Underfull \hbox (badness 1009) in paragraph at lines 18416--18425
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3079] [3080] [3081]
Underfull \hbox (badness 1009) in paragraph at lines 18550--18559
\T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi
t-ted) are used; else, if
[3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089]) (./nnet-pkg.tex
[3090]
Chapter 26.
[3091]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 

Underfull \hbox (badness 10000) in paragraph at lines 78--87
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm
[3092] [3093] [3094] [3095]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 383--383
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 440--440
 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c(
0,0,1),50)),[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 443--443
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3096]
Underfull \hbox (badness 4013) in paragraph at lines 488--491
\T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if 
the net was gen-er-ated by
[3097]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 523--523
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3098]) (./rpart-pkg.tex
Chapter 27.
[3099] [3100] [3101] [3102]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324
 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3103]
Underfull \hbox (badness 10000) in paragraph at lines 373--377
[]\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm
/m/n/10 ) or ma-trix of left and right splits
[3104] [3105] [3106]
Underfull \hbox (badness 1442) in paragraph at lines 591--597
[]\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be
 at the hor-i-zon-tal plot co-or-di-nates of
[3107] [3108]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3109]
Underfull \hbox (badness 2941) in paragraph at lines 785--787
[]\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i
ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice
 if
[3110]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902
 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3111]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921
 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3112] [3113] [3114]
Underfull \hbox (badness 2310) in paragraph at lines 1113--1116
[]\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees 
all three resid-ual def-i-ni-tions re-duce to

Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163
 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164
 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 

Underfull \hbox (badness 2837) in paragraph at lines 1187--1196
[]\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "
poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1
0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method

Underfull \hbox (badness 2088) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu
ess. If \T1/pcr/m/n/10 y

Underfull \hbox (badness 1817) in paragraph at lines 1187--1196
\T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p
tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2
[3115]
Underfull \hbox (badness 2846) in paragraph at lines 1226--1228
[]\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1
0 rpart \T1/ptm/m/n/10 al-go-rithm. See
[3116]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270
 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286
 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 

Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287
 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3117] [3118] [3119] [3120] [3121] [3122]
Underfull \hbox (badness 1565) in paragraph at lines 1739--1742
[]\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val-
ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ',
[3123] [3124]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833
 []     \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n =
 FALSE,[] 
[3125] [3126] [3127]) (./spatial-pkg.tex [3128]
Chapter 28.
[3129] [3130] [3131] [3132] [3133] [3134]
Underfull \hbox (badness 10000) in paragraph at lines 423--427

[3135] [3136] [3137] [3138] [3139] [3140] [3141] [3142] [3143] [3144] [3145]
[3146] [3147]) (./survival-pkg.tex [3148]
Chapter 29.
[3149] [3150]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171
 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190
 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2)  # Nearly the same, until t
he last point[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193
 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease.  See section 8.5 of Therneau a
nd Grambsch.[] 
[3151]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 226--226
 []\T1/pcr/m/n/10 agreg.fit(x, y, strata, offset, init, control, weights, metho
d, rownames) 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 227--227
 []\T1/pcr/m/n/10 coxph.fit(x, y, strata, offset, init, control, weights, metho
d, rownames)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.267 ... Myelogenous Leukemia survival data}{aml}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.267 ... Myelogenous Leukemia survival data}{aml}
                                                   [3152] [3153]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 364--364
 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 366--366
 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3154]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 403--403
 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3155] [3156]
Underfull \vbox (badness 10000) has occurred while \output is active [3157]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 597--597
 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 598--598
 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3158] [3159]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 741--741
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3160] [3161]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 891--891
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3162]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.957 ...herapy for Stage B/C colon cancer}{colon}
                                                   [3163] [3164] [3165]
[3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1747--1747
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 
[3174] [3175]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1877--1877
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3176] [3177] [3178] [3179]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2159--2159
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 

Underfull \hbox (badness 1389) in paragraph at lines 2172--2174
[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
[3180] [3181]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2274--2274
 []\T1/pcr/m/n/9 lines(fit[1], lwd=2, xscale=365.24)    #darken the first curve
 and add marks[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 2280--2280
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2916--2916
 [] \T1/pcr/m/n/10 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysc
ale=1,[] 
[3192] [3193]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3072--3072
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3194] [3195]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3163--3163
 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] 
[3196]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3253--3253
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3197] [3198]
Underfull \hbox (badness 1852) in paragraph at lines 3401--3403
[]\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/
n/10 , which is the re-sult of the
[3199] [3200]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 3534--3534
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 
[3201] [3202]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 3694--3694
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3203]
Underfull \hbox (badness 1540) in paragraph at lines 3749--3752
[]\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per
-son years if
[3204]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3792--3792
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 3813--3813
 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 3815--3815
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3205] [3206]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3960--3960
 []\T1/pcr/m/n/9 efit <- survexp(~ ratetable(sex=sex,age=age*365.35,year=as.Dat
e(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/1/1\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )) +[] 
[3207] [3208] [3209] [3210] [3211]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 4287--4287
 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/pcr/m/n/10 "response"
\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
\T1/pcr/m/n/10 "dfbeta"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 
, \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4299--4304
\T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "matrix"\T1/ptm/m/n
/10 . See the La-TeX doc-u-men-ta-tion
[3212] [3213]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4407--4407
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 4408--4408
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
[3214] [3215] [3216] [3217] [3218] [3219] [3220]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4910--4910
 []    \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/
10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p
cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/
n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 
, \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T
S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] 
[3221] [3222] [3223]
Underfull \hbox (badness 10000) in paragraph at lines 5170--5179
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
[3224] [3225]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5280--5280
 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 

Underfull \hbox (badness 1038) in paragraph at lines 5322--5328
\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival

Underfull \hbox (badness 3000) in paragraph at lines 5341--5343
[]\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab
le \T1/ptm/m/n/10 is in units/day,
[3226]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 5371--5371
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3227]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5457--5457
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3228] [3229]
Underfull \hbox (badness 10000) in paragraph at lines 5591--5595
[][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s
urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p
tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (18.78088pt too wide) in paragraph at lines 5611--5611
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none"), censor=T
RUE, id,[] 
[3230] [3231] [3232]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5813--5813
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3233]
Underfull \hbox (badness 6332) in paragraph at lines 5917--5922
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val-
ues are
[3234] [3235]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6086--6086
 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3236] [3237]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6246--6246
 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3238]
Underfull \hbox (badness 1354) in paragraph at lines 6287--6291
[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3239] [3240]
Underfull \hbox (badness 2035) in paragraph at lines 6463--6470
\T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv
reg.distributions[][][]\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 6463--6470
\T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/
m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 1297) in paragraph at lines 6463--6470
\T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n
/10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is
[3241]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6524--6524
 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3242] [3243] [3244]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 6682--6682
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3245] [3246]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813
 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 6816--6816
 []                 \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 '
\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3247] [3248] [3249] [3250]
Underfull \vbox (badness 10000) has occurred while \output is active [3251]
[3252]) (./fullrefman.ind [3253] [3254] [3255] [3256] [3257] [3258] [3259]
[3260] [3261] [3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270]
[3271] [3272]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2139--2141
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2141--2143
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2143--2145
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2145--2147
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (25.3567pt too wide) in paragraph at lines 2147--2149
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2149--2151
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2151--2153
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2153--2155
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (25.3567pt too wide) in paragraph at lines 2155--2157
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2157--2159
[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (43.3567pt too wide) in paragraph at lines 2159--2161
[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2161--2163
[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3273] [3274] [3275] [3276] [3277]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2671--2673
[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2673--2675
[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2675--2677
[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2677--2679
[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (25.3567pt too wide) in paragraph at lines 2679--2681
[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2681--2683
[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2683--2685
[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2685--2687
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (25.3567pt too wide) in paragraph at lines 2687--2689
[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
[3278]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2689--2691
[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (43.3567pt too wide) in paragraph at lines 2691--2693
[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (19.3567pt too wide) in paragraph at lines 2693--2695
[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3279]
Overfull \hbox (19.3567pt too wide) in paragraph at lines 2819--2821
[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3280] [3281] [3282] [3283]
Underfull \vbox (badness 2285) has occurred while \output is active [3284]
[3285] [3286]
Overfull \hbox (62.8567pt too wide) in paragraph at lines 3654--3656
[]\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3656--3658
[]\T1/pcr/m/n/10 [,CsparseMatrix,index,missing,logical-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3658--3660
[]\T1/pcr/m/n/10 [,CsparseMatrix,missing,index,logical-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3662--3664
[]\T1/pcr/m/n/10 [,Matrix,index,index,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 3664--3666
[]\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3666--3668
[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,ANY-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 3668--3670
[]\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3670--3672
[]\T1/pcr/m/n/10 [,Matrix,logical,missing,ANY-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 3672--3674
[]\T1/pcr/m/n/10 [,Matrix,logical,missing,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 3674--3676
[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,ANY-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 3676--3678
[]\T1/pcr/m/n/10 [,Matrix,matrix,missing,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 3678--3680
[]\T1/pcr/m/n/10 [,Matrix,missing,index,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3680--3682
[]\T1/pcr/m/n/10 [,Matrix,missing,missing,ANY-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3682--3684
[]\T1/pcr/m/n/10 [,TsparseMatrix,index,index,logical-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3684--3686
[]\T1/pcr/m/n/10 [,TsparseMatrix,index,missing,logical-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3686--3688
[]\T1/pcr/m/n/10 [,TsparseMatrix,missing,index,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3690--3692
[]\T1/pcr/m/n/10 [,dMatrix,lMatrix,missing,ANY-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3692--3694
[]\T1/pcr/m/n/10 [,dMatrix,logical,missing,ANY-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 3694--3696
[]\T1/pcr/m/n/10 [,denseMatrix,index,index,logical-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3696--3698
[]\T1/pcr/m/n/10 [,denseMatrix,index,missing,logical-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 3698--3700
[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3700--3702
[]\T1/pcr/m/n/10 [,denseMatrix,matrix,missing,missing-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3702--3704
[]\T1/pcr/m/n/10 [,denseMatrix,missing,index,logical-method 
[3287]
Overfull \hbox (68.8567pt too wide) in paragraph at lines 3704--3706
[]\T1/pcr/m/n/10 [,diagonalMatrix,index,index,logical-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 3706--3708
[]\T1/pcr/m/n/10 [,diagonalMatrix,index,missing,logical-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 3708--3710
[]\T1/pcr/m/n/10 [,diagonalMatrix,missing,index,logical-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 3710--3712
[]\T1/pcr/m/n/10 [,indMatrix,index,missing,logical-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 3712--3714
[]\T1/pcr/m/n/10 [,sparseMatrix,index,index,logical-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3714--3716
[]\T1/pcr/m/n/10 [,sparseMatrix,index,missing,logical-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3716--3718
[]\T1/pcr/m/n/10 [,sparseMatrix,missing,index,logical-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 3718--3720
[]\T1/pcr/m/n/10 [,sparseVector,index,ANY,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3720--3722
[]\T1/pcr/m/n/10 [,sparseVector,lsparseVector,ANY,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3722--3724
[]\T1/pcr/m/n/10 [,sparseVector,nsparseVector,ANY,ANY-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3790--3792
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,Matrix,missing,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3792--3794
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3794--3796
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,index,sparseVector-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3796--3798
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3798--3800
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,index,missing,sparseVector-method 

Overfull \hbox (140.8567pt too wide) in paragraph at lines 3800--3802
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ldenseMatrix,missing,replValue-method 

Overfull \hbox (146.8567pt too wide) in paragraph at lines 3802--3804
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,lsparseMatrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3804--3806
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,matrix,missing,replValue-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3806--3808
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3808--3810
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,missing,index,sparseVector-method 

Overfull \hbox (140.8567pt too wide) in paragraph at lines 3810--3812
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,ndenseMatrix,missing,replValue-method 

Overfull \hbox (146.8567pt too wide) in paragraph at lines 3812--3814
[]\T1/pcr/m/n/10 [<-,CsparseMatrix,nsparseMatrix,missing,replValue-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 3816--3818
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,Matrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 3818--3820
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,ANY,matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3820--3822
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,missing,Matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3822--3824
[]\T1/pcr/m/n/10 [<-,Matrix,ANY,missing,matrix-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3824--3826
[]\T1/pcr/m/n/10 [<-,Matrix,ldenseMatrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3826--3828
[]\T1/pcr/m/n/10 [<-,Matrix,lsparseMatrix,missing,replValue-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3828--3830
[]\T1/pcr/m/n/10 [<-,Matrix,matrix,missing,replValue-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3830--3832
[]\T1/pcr/m/n/10 [<-,Matrix,missing,ANY,Matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 3832--3834
[]\T1/pcr/m/n/10 [<-,Matrix,missing,ANY,matrix-method 

Underfull \vbox (badness 1824) has occurred while \output is active [3288]
Overfull \hbox (98.8567pt too wide) in paragraph at lines 3834--3836
[]\T1/pcr/m/n/10 [<-,Matrix,ndenseMatrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3836--3838
[]\T1/pcr/m/n/10 [<-,Matrix,nsparseMatrix,missing,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3838--3840
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,index,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3840--3842
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,index,sparseVector-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3842--3844
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,missing,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3844--3846
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,index,missing,sparseVector-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3846--3848
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,matrix,missing,replValue-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3848--3850
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,missing,index,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3850--3852
[]\T1/pcr/m/n/10 [<-,RsparseMatrix,missing,index,sparseVector-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3852--3854
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,Matrix,missing,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3854--3856
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,index,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3856--3858
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,index,sparseVector-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3858--3860
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,missing,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3860--3862
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,index,missing,sparseVector-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3862--3864
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,lMatrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3864--3866
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,matrix,missing,replValue-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3866--3868
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,missing,index,replValue-method 

Overfull \hbox (116.8567pt too wide) in paragraph at lines 3868--3870
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,missing,index,sparseVector-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3870--3872
[]\T1/pcr/m/n/10 [<-,TsparseMatrix,nMatrix,missing,replValue-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3872--3874
[]\T1/pcr/m/n/10 [<-,denseMatrix,index,index,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3874--3876
[]\T1/pcr/m/n/10 [<-,denseMatrix,index,missing,replValue-method 

Overfull \hbox (92.8567pt too wide) in paragraph at lines 3876--3878
[]\T1/pcr/m/n/10 [<-,denseMatrix,matrix,missing,replValue-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 3878--3880
[]\T1/pcr/m/n/10 [<-,denseMatrix,missing,index,replValue-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 3880--3882
[]\T1/pcr/m/n/10 [<-,denseMatrix,missing,missing,ANY-method 

Overfull \hbox (92.8567pt too wide) in paragraph at lines 3882--3884
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,replValue-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3884--3886
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,sparseMatrix-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3886--3888
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,index,sparseVector-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3888--3890
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,replValue-method 

Overfull \hbox (122.8567pt too wide) in paragraph at lines 3890--3892
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,sparseMatrix-method 

Overfull \hbox (122.8567pt too wide) in paragraph at lines 3892--3894
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,index,missing,sparseVector-method 

Overfull \hbox (110.8567pt too wide) in paragraph at lines 3894--3896
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,matrix,missing,replValue-method 

Overfull \hbox (104.8567pt too wide) in paragraph at lines 3896--3898
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,replValue-method 

Overfull \hbox (122.8567pt too wide) in paragraph at lines 3898--3900
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,sparseMatrix-method 

Overfull \hbox (122.8567pt too wide) in paragraph at lines 3900--3902
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,index,sparseVector-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 3902--3904
[]\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,missing,ANY-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 3904--3906
[]\T1/pcr/m/n/10 [<-,indMatrix,index,ANY,ANY-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 3906--3908
[]\T1/pcr/m/n/10 [<-,indMatrix,missing,index,ANY-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 3908--3910
[]\T1/pcr/m/n/10 [<-,indMatrix,missing,missing,ANY-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 3910--3912
[]\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,ANY,sparseMatrix-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3912--3914
[]\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,missing,sparseMatrix-method 

Overfull \hbox (98.8567pt too wide) in paragraph at lines 3914--3916
[]\T1/pcr/m/n/10 [<-,sparseMatrix,missing,ANY,sparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 3916--3918
[]\T1/pcr/m/n/10 [<-,sparseMatrix,missing,missing,ANY-method 

Overfull \hbox (92.8567pt too wide) in paragraph at lines 3918--3920
[]\T1/pcr/m/n/10 [<-,sparseVector,index,missing,replValue-method 

Overfull \hbox (134.8567pt too wide) in paragraph at lines 3920--3922
[]\T1/pcr/m/n/10 [<-,sparseVector,sparseVector,missing,replValue-method 

Underfull \vbox (badness 1484) has occurred while \output is active [3289]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 3995--3997
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,CsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 3997--3999
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,ddenseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 3999--4001
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,diagonalMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4003--4005
[]\T1/pcr/m/n/10 %*%,CsparseMatrix,numLike-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4023--4025
[]\T1/pcr/m/n/10 %*%,TsparseMatrix,TsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4031--4033
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,CsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 4033--4035
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4035--4037
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4037--4039
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4039--4041
[]\T1/pcr/m/n/10 %*%,ddenseMatrix,dtrMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4041--4043
[]\T1/pcr/m/n/10 %*%,denseMatrix,diagonalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4045--4047
[]\T1/pcr/m/n/10 %*%,dgeMatrix,diagonalMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4047--4049
[]\T1/pcr/m/n/10 %*%,dgeMatrix,dsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 4055--4057
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,CsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4057--4059
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,denseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4059--4061
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,dgeMatrix-method 
[3290]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4061--4063
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,diagonalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4063--4065
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,lgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4065--4067
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,matrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4067--4069
[]\T1/pcr/m/n/10 %*%,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4069--4071
[]\T1/pcr/m/n/10 %*%,dspMatrix,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4073--4075
[]\T1/pcr/m/n/10 %*%,dsparseMatrix,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4075--4077
[]\T1/pcr/m/n/10 %*%,dsparseMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4077--4079
[]\T1/pcr/m/n/10 %*%,dsyMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4083--4085
[]\T1/pcr/m/n/10 %*%,dtpMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4087--4089
[]\T1/pcr/m/n/10 %*%,dtrMatrix,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4107--4109
[]\T1/pcr/m/n/10 %*%,ldenseMatrix,lsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4111--4113
[]\T1/pcr/m/n/10 %*%,lgeMatrix,diagonalMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4113--4115
[]\T1/pcr/m/n/10 %*%,lsparseMatrix,ldenseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4115--4117
[]\T1/pcr/m/n/10 %*%,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4123--4125
[]\T1/pcr/m/n/10 %*%,matrix,diagonalMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4141--4143
[]\T1/pcr/m/n/10 %*%,ndenseMatrix,nsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 4145--4147
[]\T1/pcr/m/n/10 %*%,nsparseMatrix,ndenseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4147--4149
[]\T1/pcr/m/n/10 %*%,nsparseMatrix,nsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4149--4151
[]\T1/pcr/m/n/10 %*%,numLike,CsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4161--4163
[]\T1/pcr/m/n/10 %*%,sparseMatrix,diagonalMatrix-method 
[3291]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 4165--4167
[]\T1/pcr/m/n/10 %*%,sparseVector,sparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4173--4175
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4175--4177
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4177--4179
[]\T1/pcr/m/n/10 %/%,ddiMatrix,ndenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4181--4183
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4183--4185
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4185--4187
[]\T1/pcr/m/n/10 %/%,ldiMatrix,ndenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4191--4193
[]\T1/pcr/m/n/10 %%,ddiMatrix,ddenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4193--4195
[]\T1/pcr/m/n/10 %%,ddiMatrix,ldenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4195--4197
[]\T1/pcr/m/n/10 %%,ddiMatrix,ndenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4199--4201
[]\T1/pcr/m/n/10 %%,ldiMatrix,ddenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4201--4203
[]\T1/pcr/m/n/10 %%,ldiMatrix,ldenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4203--4205
[]\T1/pcr/m/n/10 %%,ldiMatrix,ndenseMatrix-method 

Underfull \vbox (badness 5022) has occurred while \output is active [3292]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 4341--4343
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ad.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3293]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 4431--4433
[]\T1/pcr/m/n/10 all.equal,abIndex,abIndex-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4433--4435
[]\T1/pcr/m/n/10 all.equal,abIndex,numLike-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4437--4439
[]\T1/pcr/m/n/10 all.equal,ANY,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4439--4441
[]\T1/pcr/m/n/10 all.equal,ANY,sparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4445--4447
[]\T1/pcr/m/n/10 all.equal,numLike,abIndex-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4447--4449
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,ANY-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 4449--4451
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,sparseMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 4451--4453
[]\T1/pcr/m/n/10 all.equal,sparseMatrix,sparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4453--4455
[]\T1/pcr/m/n/10 all.equal,sparseVector,ANY-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 4455--4457
[]\T1/pcr/m/n/10 all.equal,sparseVector,sparseMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 4457--4459
[]\T1/pcr/m/n/10 all.equal,sparseVector,sparseVector-method 
[3294]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 4617--4619
[]\T1/pcr/m/n/10 Arith,CsparseMatrix,CsparseMatrix-method 
[3295]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 4619--4621
[]\T1/pcr/m/n/10 Arith,CsparseMatrix,numeric-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4621--4623
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4623--4625
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,logical-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4625--4627
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,numeric-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4627--4629
[]\T1/pcr/m/n/10 Arith,ddenseMatrix,sparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4633--4635
[]\T1/pcr/m/n/10 Arith,dgCMatrix,dgCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4639--4641
[]\T1/pcr/m/n/10 Arith,dgeMatrix,dgeMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4645--4647
[]\T1/pcr/m/n/10 Arith,dgeMatrix,sparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4657--4659
[]\T1/pcr/m/n/10 Arith,dsCMatrix,dsCMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4659--4661
[]\T1/pcr/m/n/10 Arith,dsparseMatrix,logical-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4661--4663
[]\T1/pcr/m/n/10 Arith,dsparseMatrix,numeric-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 4663--4665
[]\T1/pcr/m/n/10 Arith,dsparseVector,dsparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4665--4667
[]\T1/pcr/m/n/10 Arith,dtCMatrix,dtCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4671--4673
[]\T1/pcr/m/n/10 Arith,lgCMatrix,lgCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4673--4675
[]\T1/pcr/m/n/10 Arith,lgeMatrix,lgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4675--4677
[]\T1/pcr/m/n/10 Arith,lgTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4681--4683
[]\T1/pcr/m/n/10 Arith,logical,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4693--4695
[]\T1/pcr/m/n/10 Arith,logical,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4701--4703
[]\T1/pcr/m/n/10 Arith,lsparseMatrix,Matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4703--4705
[]\T1/pcr/m/n/10 Arith,Matrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4707--4709
[]\T1/pcr/m/n/10 Arith,Matrix,nsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 4709--4711
[]\T1/pcr/m/n/10 Arith,ngeMatrix,ngeMatrix-method 

Underfull \vbox (badness 5022) has occurred while \output is active [3296]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 4715--4717
[]\T1/pcr/m/n/10 Arith,nsparseMatrix,Matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4717--4719
[]\T1/pcr/m/n/10 Arith,numeric,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 4719--4721
[]\T1/pcr/m/n/10 Arith,numeric,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 4731--4733
[]\T1/pcr/m/n/10 Arith,numeric,dsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4741--4743
[]\T1/pcr/m/n/10 Arith,sparseVector,ddenseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 4743--4745
[]\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 4745--4747
[]\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 4747--4749
[]\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method 

Underfull \vbox (badness 3302) has occurred while \output is active [3297]
[3298]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 5028--5030
[]\T1/pcr/m/n/10 as.vector,abIndex,character-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5030--5032
[]\T1/pcr/m/n/10 as.vector,dgCMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5032--5034
[]\T1/pcr/m/n/10 as.vector,dgeMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 5034--5036
[]\T1/pcr/m/n/10 as.vector,diagonalMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5036--5038
[]\T1/pcr/m/n/10 as.vector,dsCMatrix,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5038--5040
[]\T1/pcr/m/n/10 as.vector,ldenseMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5040--5042
[]\T1/pcr/m/n/10 as.vector,lgeMatrix,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5044--5046
[]\T1/pcr/m/n/10 as.vector,ndenseMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5046--5048
[]\T1/pcr/m/n/10 as.vector,ngeMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 5048--5050
[]\T1/pcr/m/n/10 as.vector,sparseVector,character-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5050--5052
[]\T1/pcr/m/n/10 as.vector,sparseVector,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5076--5078
[]\T1/pcr/m/n/10 aspell_write_personal_dictionary_file 
[3299] [3300] [3301] [3302]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 5576--5578
[]\T1/pcr/m/n/10 cbind2,atomicVector,ddiMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 5578--5580
[]\T1/pcr/m/n/10 cbind2,atomicVector,ldiMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5580--5582
[]\T1/pcr/m/n/10 cbind2,atomicVector,Matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 5582--5584
[]\T1/pcr/m/n/10 cbind2,ddiMatrix,atomicVector-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 5586--5588
[]\T1/pcr/m/n/10 cbind2,denseMatrix,denseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 5588--5590
[]\T1/pcr/m/n/10 cbind2,denseMatrix,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5590--5592
[]\T1/pcr/m/n/10 cbind2,denseMatrix,numeric-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 5592--5594
[]\T1/pcr/m/n/10 cbind2,denseMatrix,sparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 5594--5596
[]\T1/pcr/m/n/10 cbind2,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 5596--5598
[]\T1/pcr/m/n/10 cbind2,ldiMatrix,atomicVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5602--5604
[]\T1/pcr/m/n/10 cbind2,Matrix,atomicVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 5606--5608
[]\T1/pcr/m/n/10 cbind2,matrix,denseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5616--5618
[]\T1/pcr/m/n/10 cbind2,matrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5620--5622
[]\T1/pcr/m/n/10 cbind2,numeric,denseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5622--5624
[]\T1/pcr/m/n/10 cbind2,numeric,sparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 5624--5626
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,denseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 5626--5628
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 5628--5630
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 5630--5632
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 5632--5634
[]\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method 
[3303]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 5789--5791
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 

Underfull \vbox (badness 1484) has occurred while \output is active [3304]
[3305]
Underfull \vbox (badness 1019) has occurred while \output is active [3306]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 6155--6157
[]\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6157--6159
[]\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6159--6161
[]\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6165--6167
[]\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6167--6169
[]\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6171--6173
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,denseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6173--6175
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,lMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6175--6177
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,lsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6177--6179
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.coo-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6179--6181
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.csc-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6181--6183
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix.csr-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6183--6185
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,nMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6185--6187
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,nsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6187--6189
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,sparseVector-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 6189--6191
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,symmetricMatrix-method 
[3307]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 6191--6193
[]\T1/pcr/m/n/10 coerce,CsparseMatrix,TsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6193--6195
[]\T1/pcr/m/n/10 coerce,ddenseMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6195--6197
[]\T1/pcr/m/n/10 coerce,ddenseMatrix,matrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6197--6199
[]\T1/pcr/m/n/10 coerce,ddiMatrix,CsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6199--6201
[]\T1/pcr/m/n/10 coerce,ddiMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6201--6203
[]\T1/pcr/m/n/10 coerce,ddiMatrix,dgeMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6203--6205
[]\T1/pcr/m/n/10 coerce,ddiMatrix,dsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6205--6207
[]\T1/pcr/m/n/10 coerce,ddiMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6207--6209
[]\T1/pcr/m/n/10 coerce,ddiMatrix,triangularMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6209--6211
[]\T1/pcr/m/n/10 coerce,ddiMatrix,TsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6211--6213
[]\T1/pcr/m/n/10 coerce,denseMatrix,CsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6213--6215
[]\T1/pcr/m/n/10 coerce,denseMatrix,generalMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6215--6217
[]\T1/pcr/m/n/10 coerce,denseMatrix,RsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6217--6219
[]\T1/pcr/m/n/10 coerce,denseMatrix,sparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6219--6221
[]\T1/pcr/m/n/10 coerce,denseMatrix,symmetricMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6221--6223
[]\T1/pcr/m/n/10 coerce,denseMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6223--6225
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6225--6227
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6227--6229
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6229--6231
[]\T1/pcr/m/n/10 coerce,dgCMatrix,dtCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6231--6233
[]\T1/pcr/m/n/10 coerce,dgCMatrix,lgCMatrix-method 

Underfull \vbox (badness 5022) has occurred while \output is active
Overfull \hbox (14.8567pt too wide) in paragraph at lines 6235--6237
[]\T1/pcr/m/n/10 coerce,dgCMatrix,matrix.csc-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6237--6239
[]\T1/pcr/m/n/10 coerce,dgCMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6241--6243
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6243--6245
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6245--6247
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6247--6249
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6249--6251
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6251--6253
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6253--6255
[]\T1/pcr/m/n/10 coerce,dgeMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6255--6257
[]\T1/pcr/m/n/10 coerce,dgeMatrix,lgeMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6259--6261
[]\T1/pcr/m/n/10 coerce,dgeMatrix,triangularMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6261--6263
[]\T1/pcr/m/n/10 coerce,dgRMatrix,matrix.csr-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6263--6265
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6265--6267
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6267--6269
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6269--6271
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dtCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6271--6273
[]\T1/pcr/m/n/10 coerce,dgTMatrix,dtTMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 6273--6275
[]\T1/pcr/m/n/10 coerce,dgTMatrix,graphNEL-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6277--6279
[]\T1/pcr/m/n/10 coerce,dgTMatrix,matrix.coo-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6279--6281
[]\T1/pcr/m/n/10 coerce,dgTMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6281--6283
[]\T1/pcr/m/n/10 coerce,dgTMatrix,triangularMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6283--6285
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,denseMatrix-method 
[3308]
Overfull \hbox (62.8567pt too wide) in paragraph at lines 6285--6287
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,generalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6287--6289
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6289--6291
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,nMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 6291--6293
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,nsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6293--6295
[]\T1/pcr/m/n/10 coerce,diagonalMatrix,sparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6299--6301
[]\T1/pcr/m/n/10 coerce,dpoMatrix,corMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6301--6303
[]\T1/pcr/m/n/10 coerce,dpoMatrix,dppMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6307--6309
[]\T1/pcr/m/n/10 coerce,dppMatrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6309--6311
[]\T1/pcr/m/n/10 coerce,dppMatrix,dpoMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6315--6317
[]\T1/pcr/m/n/10 coerce,dppMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6317--6319
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6319--6321
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6321--6323
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6323--6325
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsRMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6325--6327
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6327--6329
[]\T1/pcr/m/n/10 coerce,dsCMatrix,dsyMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6329--6331
[]\T1/pcr/m/n/10 coerce,dsCMatrix,generalMatrix-method 

Underfull \vbox (badness 3769) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6331--6333
[]\T1/pcr/m/n/10 coerce,dsCMatrix,lsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6335--6337
[]\T1/pcr/m/n/10 coerce,dsCMatrix,nsCMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6339--6341
[]\T1/pcr/m/n/10 coerce,dsparseMatrix,matrix.csr-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6341--6343
[]\T1/pcr/m/n/10 coerce,dspMatrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6343--6345
[]\T1/pcr/m/n/10 coerce,dspMatrix,dpoMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6345--6347
[]\T1/pcr/m/n/10 coerce,dspMatrix,dppMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6347--6349
[]\T1/pcr/m/n/10 coerce,dspMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6349--6351
[]\T1/pcr/m/n/10 coerce,dspMatrix,lspMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6353--6355
[]\T1/pcr/m/n/10 coerce,dspMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6355--6357
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6357--6359
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6359--6361
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6361--6363
[]\T1/pcr/m/n/10 coerce,dsTMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6363--6365
[]\T1/pcr/m/n/10 coerce,dsTMatrix,lsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6367--6369
[]\T1/pcr/m/n/10 coerce,dsyMatrix,corMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6369--6371
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dpoMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6371--6373
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6373--6375
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6375--6377
[]\T1/pcr/m/n/10 coerce,dsyMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6377--6379
[]\T1/pcr/m/n/10 coerce,dsyMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6381--6383
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgCMatrix-method 
[3309]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6383--6385
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6385--6387
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6387--6389
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6389--6391
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtRMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6391--6393
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6393--6395
[]\T1/pcr/m/n/10 coerce,dtCMatrix,dtTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6395--6397
[]\T1/pcr/m/n/10 coerce,dtCMatrix,ltCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6399--6401
[]\T1/pcr/m/n/10 coerce,dtCMatrix,ntCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6401--6403
[]\T1/pcr/m/n/10 coerce,dtCMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6403--6405
[]\T1/pcr/m/n/10 coerce,dtpMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6405--6407
[]\T1/pcr/m/n/10 coerce,dtpMatrix,dtTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6407--6409
[]\T1/pcr/m/n/10 coerce,dtpMatrix,ltpMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6411--6413
[]\T1/pcr/m/n/10 coerce,dtrMatrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6413--6415
[]\T1/pcr/m/n/10 coerce,dtrMatrix,dtpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6415--6417
[]\T1/pcr/m/n/10 coerce,dtrMatrix,ltrMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6419--6421
[]\T1/pcr/m/n/10 coerce,dtrMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6421--6423
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6423--6425
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6425--6427
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dtCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6427--6429
[]\T1/pcr/m/n/10 coerce,dtTMatrix,dtrMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6429--6431
[]\T1/pcr/m/n/10 coerce,dtTMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6435--6437
[]\T1/pcr/m/n/10 coerce,factor,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6437--6439
[]\T1/pcr/m/n/10 coerce,graph,CsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 6441--6443
[]\T1/pcr/m/n/10 coerce,graph,sparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6443--6445
[]\T1/pcr/m/n/10 coerce,graphAM,sparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6445--6447
[]\T1/pcr/m/n/10 coerce,graphNEL,CsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 6447--6449
[]\T1/pcr/m/n/10 coerce,graphNEL,dsCMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6449--6451
[]\T1/pcr/m/n/10 coerce,graphNEL,TsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6451--6453
[]\T1/pcr/m/n/10 coerce,indMatrix,CsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6455--6457
[]\T1/pcr/m/n/10 coerce,indMatrix,dsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6459--6461
[]\T1/pcr/m/n/10 coerce,indMatrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6463--6465
[]\T1/pcr/m/n/10 coerce,indMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6465--6467
[]\T1/pcr/m/n/10 coerce,indMatrix,ngTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6469--6471
[]\T1/pcr/m/n/10 coerce,indMatrix,nsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6471--6473
[]\T1/pcr/m/n/10 coerce,indMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6477--6479
[]\T1/pcr/m/n/10 coerce,ldenseMatrix,matrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6479--6481
[]\T1/pcr/m/n/10 coerce,ldiMatrix,CsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6481--6483
[]\T1/pcr/m/n/10 coerce,ldiMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6483--6485
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lgCMatrix-method 
[3310]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6485--6487
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lgTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6487--6489
[]\T1/pcr/m/n/10 coerce,ldiMatrix,lsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6489--6491
[]\T1/pcr/m/n/10 coerce,ldiMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6491--6493
[]\T1/pcr/m/n/10 coerce,ldiMatrix,triangularMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6493--6495
[]\T1/pcr/m/n/10 coerce,ldiMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6495--6497
[]\T1/pcr/m/n/10 coerce,lgCMatrix,dgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6497--6499
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6499--6501
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6501--6503
[]\T1/pcr/m/n/10 coerce,lgCMatrix,lsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6503--6505
[]\T1/pcr/m/n/10 coerce,lgCMatrix,ltCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6507--6509
[]\T1/pcr/m/n/10 coerce,lgeMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6509--6511
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6511--6513
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6513--6515
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6515--6517
[]\T1/pcr/m/n/10 coerce,lgeMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6517--6519
[]\T1/pcr/m/n/10 coerce,lgeMatrix,ltpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6519--6521
[]\T1/pcr/m/n/10 coerce,lgeMatrix,ltrMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6523--6525
[]\T1/pcr/m/n/10 coerce,lgeMatrix,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6525--6527
[]\T1/pcr/m/n/10 coerce,lgTMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6527--6529
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6529--6531
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6531--6533
[]\T1/pcr/m/n/10 coerce,lgTMatrix,lsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6533--6535
[]\T1/pcr/m/n/10 coerce,lgTMatrix,ltTMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6537--6539
[]\T1/pcr/m/n/10 coerce,lgTMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6539--6541
[]\T1/pcr/m/n/10 coerce,lgTMatrix,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6551--6553
[]\T1/pcr/m/n/10 coerce,lsCMatrix,dgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6553--6555
[]\T1/pcr/m/n/10 coerce,lsCMatrix,dsCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6555--6557
[]\T1/pcr/m/n/10 coerce,lsCMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6557--6559
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6559--6561
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6561--6563
[]\T1/pcr/m/n/10 coerce,lsCMatrix,lsTMatrix-method 
[3311]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 6565--6567
[]\T1/pcr/m/n/10 coerce,lsparseMatrix,dsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6567--6569
[]\T1/pcr/m/n/10 coerce,lsparseMatrix,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6569--6571
[]\T1/pcr/m/n/10 coerce,lspMatrix,dspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6571--6573
[]\T1/pcr/m/n/10 coerce,lspMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6573--6575
[]\T1/pcr/m/n/10 coerce,lspMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6575--6577
[]\T1/pcr/m/n/10 coerce,lsTMatrix,dsTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6577--6579
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6579--6581
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6581--6583
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6583--6585
[]\T1/pcr/m/n/10 coerce,lsTMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6587--6589
[]\T1/pcr/m/n/10 coerce,lsyMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6589--6591
[]\T1/pcr/m/n/10 coerce,lsyMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6591--6593
[]\T1/pcr/m/n/10 coerce,lsyMatrix,lspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6595--6597
[]\T1/pcr/m/n/10 coerce,ltCMatrix,dtCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6597--6599
[]\T1/pcr/m/n/10 coerce,ltCMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6599--6601
[]\T1/pcr/m/n/10 coerce,ltCMatrix,ltTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6603--6605
[]\T1/pcr/m/n/10 coerce,ltpMatrix,dtpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6605--6607
[]\T1/pcr/m/n/10 coerce,ltpMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6607--6609
[]\T1/pcr/m/n/10 coerce,ltpMatrix,ltrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6609--6611
[]\T1/pcr/m/n/10 coerce,ltrMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6611--6613
[]\T1/pcr/m/n/10 coerce,ltrMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6613--6615
[]\T1/pcr/m/n/10 coerce,ltrMatrix,ltpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6615--6617
[]\T1/pcr/m/n/10 coerce,ltTMatrix,dtTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6617--6619
[]\T1/pcr/m/n/10 coerce,ltTMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6619--6621
[]\T1/pcr/m/n/10 coerce,ltTMatrix,lgCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6621--6623
[]\T1/pcr/m/n/10 coerce,ltTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6623--6625
[]\T1/pcr/m/n/10 coerce,ltTMatrix,ltCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6625--6627
[]\T1/pcr/m/n/10 coerce,ltTMatrix,ltrMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6635--6637
[]\T1/pcr/m/n/10 coerce,Matrix,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6637--6639
[]\T1/pcr/m/n/10 coerce,matrix,CsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 6639--6641
[]\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method 
[3312]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 6649--6651
[]\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6651--6653
[]\T1/pcr/m/n/10 coerce,matrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6681--6683
[]\T1/pcr/m/n/10 coerce,matrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6711--6713
[]\T1/pcr/m/n/10 coerce,matrix,ndenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6737--6739
[]\T1/pcr/m/n/10 coerce,matrix,RsparseMatrix-method 

Underfull \vbox (badness 4328) has occurred while \output is active [3313]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6739--6741
[]\T1/pcr/m/n/10 coerce,Matrix,sparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 6741--6743
[]\T1/pcr/m/n/10 coerce,matrix,symmetricMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6743--6745
[]\T1/pcr/m/n/10 coerce,Matrix,TsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6745--6747
[]\T1/pcr/m/n/10 coerce,matrix,TsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6749--6751
[]\T1/pcr/m/n/10 coerce,matrix.coo,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6751--6753
[]\T1/pcr/m/n/10 coerce,matrix.coo,dgCMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6753--6755
[]\T1/pcr/m/n/10 coerce,matrix.coo,dgTMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6757--6759
[]\T1/pcr/m/n/10 coerce,matrix.coo,TsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6759--6761
[]\T1/pcr/m/n/10 coerce,matrix.csc,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6761--6763
[]\T1/pcr/m/n/10 coerce,matrix.csc,dgCMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6765--6767
[]\T1/pcr/m/n/10 coerce,matrix.csc,TsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6767--6769
[]\T1/pcr/m/n/10 coerce,matrix.csr,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6769--6771
[]\T1/pcr/m/n/10 coerce,matrix.csr,dgCMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 6771--6773
[]\T1/pcr/m/n/10 coerce,matrix.csr,dgRMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6775--6777
[]\T1/pcr/m/n/10 coerce,matrix.csr,RsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 6777--6779
[]\T1/pcr/m/n/10 coerce,matrix.csr,TsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6779--6781
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,CsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6781--6783
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6783--6785
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6785--6787
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,sparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6787--6789
[]\T1/pcr/m/n/10 coerce,ndenseMatrix,TsparseMatrix-method 

Underfull \vbox (badness 2903) has occurred while \output is active
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6789--6791
[]\T1/pcr/m/n/10 coerce,ngCMatrix,dgCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6793--6795
[]\T1/pcr/m/n/10 coerce,ngCMatrix,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6795--6797
[]\T1/pcr/m/n/10 coerce,ngCMatrix,lgCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6799--6801
[]\T1/pcr/m/n/10 coerce,ngCMatrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6803--6805
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6805--6807
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ngTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6807--6809
[]\T1/pcr/m/n/10 coerce,ngCMatrix,ntCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6809--6811
[]\T1/pcr/m/n/10 coerce,ngeMatrix,dgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6811--6813
[]\T1/pcr/m/n/10 coerce,ngeMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6815--6817
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6817--6819
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ngTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6819--6821
[]\T1/pcr/m/n/10 coerce,ngeMatrix,nspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6821--6823
[]\T1/pcr/m/n/10 coerce,ngeMatrix,nsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6823--6825
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ntpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6825--6827
[]\T1/pcr/m/n/10 coerce,ngeMatrix,ntrMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6827--6829
[]\T1/pcr/m/n/10 coerce,ngeMatrix,triangularMatrix-method 
[3314]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6829--6831
[]\T1/pcr/m/n/10 coerce,ngTMatrix,dgTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6833--6835
[]\T1/pcr/m/n/10 coerce,ngTMatrix,dsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6835--6837
[]\T1/pcr/m/n/10 coerce,ngTMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6837--6839
[]\T1/pcr/m/n/10 coerce,ngTMatrix,lgeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6839--6841
[]\T1/pcr/m/n/10 coerce,ngTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6845--6847
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6847--6849
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6849--6851
[]\T1/pcr/m/n/10 coerce,ngTMatrix,ntTMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 6851--6853
[]\T1/pcr/m/n/10 coerce,ngTMatrix,symmetricMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 6853--6855
[]\T1/pcr/m/n/10 coerce,ngTMatrix,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6867--6869
[]\T1/pcr/m/n/10 coerce,nsCMatrix,dsCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6869--6871
[]\T1/pcr/m/n/10 coerce,nsCMatrix,dsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6871--6873
[]\T1/pcr/m/n/10 coerce,nsCMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6875--6877
[]\T1/pcr/m/n/10 coerce,nsCMatrix,lsCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6877--6879
[]\T1/pcr/m/n/10 coerce,nsCMatrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6881--6883
[]\T1/pcr/m/n/10 coerce,nsCMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6883--6885
[]\T1/pcr/m/n/10 coerce,nsCMatrix,nsTMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6885--6887
[]\T1/pcr/m/n/10 coerce,nsparseMatrix,dsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6887--6889
[]\T1/pcr/m/n/10 coerce,nsparseVector,dsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6889--6891
[]\T1/pcr/m/n/10 coerce,nsparseVector,isparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6891--6893
[]\T1/pcr/m/n/10 coerce,nsparseVector,lsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 6893--6895
[]\T1/pcr/m/n/10 coerce,nsparseVector,zsparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6895--6897
[]\T1/pcr/m/n/10 coerce,nspMatrix,dspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6897--6899
[]\T1/pcr/m/n/10 coerce,nspMatrix,lspMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6899--6901
[]\T1/pcr/m/n/10 coerce,nspMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6901--6903
[]\T1/pcr/m/n/10 coerce,nspMatrix,nsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6903--6905
[]\T1/pcr/m/n/10 coerce,nsTMatrix,dsTMatrix-method 
[3315]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 6907--6909
[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6909--6911
[]\T1/pcr/m/n/10 coerce,nsTMatrix,ngTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6911--6913
[]\T1/pcr/m/n/10 coerce,nsTMatrix,nsCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6913--6915
[]\T1/pcr/m/n/10 coerce,nsTMatrix,nsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6915--6917
[]\T1/pcr/m/n/10 coerce,nsyMatrix,dsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6917--6919
[]\T1/pcr/m/n/10 coerce,nsyMatrix,lsyMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6919--6921
[]\T1/pcr/m/n/10 coerce,nsyMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6921--6923
[]\T1/pcr/m/n/10 coerce,nsyMatrix,nspMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6925--6927
[]\T1/pcr/m/n/10 coerce,ntCMatrix,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6927--6929
[]\T1/pcr/m/n/10 coerce,ntCMatrix,dtCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6931--6933
[]\T1/pcr/m/n/10 coerce,ntCMatrix,lsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6933--6935
[]\T1/pcr/m/n/10 coerce,ntCMatrix,ltCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6937--6939
[]\T1/pcr/m/n/10 coerce,ntCMatrix,ngCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6939--6941
[]\T1/pcr/m/n/10 coerce,ntCMatrix,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6941--6943
[]\T1/pcr/m/n/10 coerce,ntpMatrix,dtpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6943--6945
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ltpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6945--6947
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6947--6949
[]\T1/pcr/m/n/10 coerce,ntpMatrix,ntrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6949--6951
[]\T1/pcr/m/n/10 coerce,ntrMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6951--6953
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ltrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6953--6955
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6955--6957
[]\T1/pcr/m/n/10 coerce,ntrMatrix,ntpMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6957--6959
[]\T1/pcr/m/n/10 coerce,ntTMatrix,dtTMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 6959--6961
[]\T1/pcr/m/n/10 coerce,ntTMatrix,generalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6963--6965
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ngCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6965--6967
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ngTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6967--6969
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ntCMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 6969--6971
[]\T1/pcr/m/n/10 coerce,ntTMatrix,ntrMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6973--6975
[]\T1/pcr/m/n/10 coerce,numeric,CsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6981--6983
[]\T1/pcr/m/n/10 coerce,numeric,TsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6987--6989
[]\T1/pcr/m/n/10 coerce,pBunchKaufman,lMatrix-method 

Underfull \vbox (badness 4328) has occurred while \output is active [3316]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 6991--6993
[]\T1/pcr/m/n/10 coerce,pMatrix,CsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 6995--6997
[]\T1/pcr/m/n/10 coerce,pMatrix,dsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7007--7009
[]\T1/pcr/m/n/10 coerce,pMatrix,nsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7009--7011
[]\T1/pcr/m/n/10 coerce,pMatrix,TsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7011--7013
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,CsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7013--7015
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,denseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7015--7017
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dgeMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7017--7019
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7019--7021
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,dsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7021--7023
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,generalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7023--7025
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,lMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7025--7027
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,lsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7027--7029
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,matrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7029--7031
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,nMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7031--7033
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,nsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7033--7035
[]\T1/pcr/m/n/10 coerce,RsparseMatrix,TsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7039--7041
[]\T1/pcr/m/n/10 coerce,sparseMatrix,generalMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 7041--7043
[]\T1/pcr/m/n/10 coerce,sparseMatrix,graph-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7043--7045
[]\T1/pcr/m/n/10 coerce,sparseMatrix,graphNEL-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7045--7047
[]\T1/pcr/m/n/10 coerce,sparseMatrix,indMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7047--7049
[]\T1/pcr/m/n/10 coerce,sparseMatrix,pMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7049--7051
[]\T1/pcr/m/n/10 coerce,sparseMatrix,RsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7051--7053
[]\T1/pcr/m/n/10 coerce,sparseMatrix,sparseVector-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 7053--7055
[]\T1/pcr/m/n/10 coerce,sparseMatrix,symmetricMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7055--7057
[]\T1/pcr/m/n/10 coerce,sparseMatrix,triangularMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7057--7059
[]\T1/pcr/m/n/10 coerce,sparseVector,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7059--7061
[]\T1/pcr/m/n/10 coerce,sparseVector,integer-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7061--7063
[]\T1/pcr/m/n/10 coerce,sparseVector,logical-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7063--7065
[]\T1/pcr/m/n/10 coerce,sparseVector,Matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7065--7067
[]\T1/pcr/m/n/10 coerce,sparseVector,numeric-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7067--7069
[]\T1/pcr/m/n/10 coerce,sparseVector,sparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7069--7071
[]\T1/pcr/m/n/10 coerce,sparseVector,TsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7071--7073
[]\T1/pcr/m/n/10 coerce,sparseVector,vector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 7073--7075
[]\T1/pcr/m/n/10 coerce,table,sparseMatrix-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 7075--7077
[]\T1/pcr/m/n/10 coerce,triangularMatrix,symmetricMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7077--7079
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,CsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7079--7081
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,graphNEL-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7081--7083
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,lMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7083--7085
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,lsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7085--7087
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,matrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 7087--7089
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,nMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7089--7091
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,nsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7091--7093
[]\T1/pcr/m/n/10 coerce,TsparseMatrix,sparseVector-method 

Underfull \vbox (badness 2903) has occurred while \output is active [3317]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7093--7095
[]\T1/pcr/m/n/10 coerce,xsparseVector,dsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7095--7097
[]\T1/pcr/m/n/10 coerce,xsparseVector,isparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7097--7099
[]\T1/pcr/m/n/10 coerce,xsparseVector,lsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7099--7101
[]\T1/pcr/m/n/10 coerce,xsparseVector,nsparseVector-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7101--7103
[]\T1/pcr/m/n/10 coerce,xsparseVector,zsparseVector-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 7210--7212
[]\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method 
[3318]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7216--7218
[]\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 7228--7230
[]\T1/pcr/m/n/10 Compare,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7230--7232
[]\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 7244--7246
[]\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method 
[3319] [3320]
Overfull \hbox (14.8567pt too wide) in paragraph at lines 7570--7572
[]\T1/pcr/m/n/10 crossprod,ANY,TsparseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7572--7574
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7574--7576
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,ddenseMatrix-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 7576--7578
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,diagonalMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7578--7580
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,matrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7580--7582
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,missing-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7582--7584
[]\T1/pcr/m/n/10 crossprod,CsparseMatrix,numLike-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7584--7586
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,CsparseMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7586--7588
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,dgCMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7588--7590
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,dsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7590--7592
[]\T1/pcr/m/n/10 crossprod,ddenseMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7592--7594
[]\T1/pcr/m/n/10 crossprod,dgCMatrix,dgeMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7594--7596
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,dgeMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7596--7598
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,dsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7598--7600
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7600--7602
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7602--7604
[]\T1/pcr/m/n/10 crossprod,dgeMatrix,numLike-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 7604--7606
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,CsparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7606--7608
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,dgeMatrix-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 7608--7610
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,diagonalMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 7610--7612
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,lgeMatrix-method 
[3321]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 7612--7614
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7614--7616
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,missing-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7616--7618
[]\T1/pcr/m/n/10 crossprod,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7618--7620
[]\T1/pcr/m/n/10 crossprod,dsparseMatrix,ddenseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 7620--7622
[]\T1/pcr/m/n/10 crossprod,dsparseMatrix,dgeMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7622--7624
[]\T1/pcr/m/n/10 crossprod,dtpMatrix,ddenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7624--7626
[]\T1/pcr/m/n/10 crossprod,dtpMatrix,matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7626--7628
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,ddenseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7628--7630
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,dtrMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7630--7632
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7632--7634
[]\T1/pcr/m/n/10 crossprod,dtrMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7634--7636
[]\T1/pcr/m/n/10 crossprod,indMatrix,indMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7636--7638
[]\T1/pcr/m/n/10 crossprod,indMatrix,Matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7638--7640
[]\T1/pcr/m/n/10 crossprod,indMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7640--7642
[]\T1/pcr/m/n/10 crossprod,indMatrix,missing-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7642--7644
[]\T1/pcr/m/n/10 crossprod,ldenseMatrix,lsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7644--7646
[]\T1/pcr/m/n/10 crossprod,lgCMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7646--7648
[]\T1/pcr/m/n/10 crossprod,lgTMatrix,missing-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7648--7650
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,ldenseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7650--7652
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7652--7654
[]\T1/pcr/m/n/10 crossprod,lsparseMatrix,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7658--7660
[]\T1/pcr/m/n/10 crossprod,matrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 7660--7662
[]\T1/pcr/m/n/10 crossprod,matrix,dgeMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7672--7674
[]\T1/pcr/m/n/10 crossprod,Matrix,sparseVector-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7674--7676
[]\T1/pcr/m/n/10 crossprod,Matrix,TsparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7676--7678
[]\T1/pcr/m/n/10 crossprod,ndenseMatrix,nsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7678--7680
[]\T1/pcr/m/n/10 crossprod,ngCMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7680--7682
[]\T1/pcr/m/n/10 crossprod,ngTMatrix,missing-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7682--7684
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,missing-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 7684--7686
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,ndenseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7686--7688
[]\T1/pcr/m/n/10 crossprod,nsparseMatrix,nsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7690--7692
[]\T1/pcr/m/n/10 crossprod,numLike,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7692--7694
[]\T1/pcr/m/n/10 crossprod,numLike,dgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 7700--7702
[]\T1/pcr/m/n/10 crossprod,pMatrix,missing-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 7702--7704
[]\T1/pcr/m/n/10 crossprod,pMatrix,pMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7704--7706
[]\T1/pcr/m/n/10 crossprod,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7706--7708
[]\T1/pcr/m/n/10 crossprod,sparseVector,Matrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7708--7710
[]\T1/pcr/m/n/10 crossprod,sparseVector,missing-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 7710--7712
[]\T1/pcr/m/n/10 crossprod,sparseVector,sparseVector-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7712--7714
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,ANY-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7714--7716
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,Matrix-method 
[3322]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 7716--7718
[]\T1/pcr/m/n/10 crossprod,symmetricMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 7718--7720
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,ANY-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 7720--7722
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,Matrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 7722--7724
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,missing-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 7724--7726
[]\T1/pcr/m/n/10 crossprod,TsparseMatrix,TsparseMatrix-method 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 7741--7743
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 7788--7790
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 7792--7794
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3323]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 7967--7969
[]\T1/pcr/m/n/10 derivedDefaultMethodWithTrace-class 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7983--7985
[]\T1/pcr/m/n/10 determinant,CHMfactor,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7985--7987
[]\T1/pcr/m/n/10 determinant,CHMfactor,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7987--7989
[]\T1/pcr/m/n/10 determinant,ddenseMatrix,logical-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 7989--7991
[]\T1/pcr/m/n/10 determinant,ddenseMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7991--7993
[]\T1/pcr/m/n/10 determinant,dgCMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7993--7995
[]\T1/pcr/m/n/10 determinant,dgeMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7995--7997
[]\T1/pcr/m/n/10 determinant,dgeMatrix,missing-method 
[3324]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 7997--7999
[]\T1/pcr/m/n/10 determinant,diagonalMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 7999--8001
[]\T1/pcr/m/n/10 determinant,dpoMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8001--8003
[]\T1/pcr/m/n/10 determinant,dpoMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8003--8005
[]\T1/pcr/m/n/10 determinant,dppMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8005--8007
[]\T1/pcr/m/n/10 determinant,dppMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8007--8009
[]\T1/pcr/m/n/10 determinant,dsCMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8009--8011
[]\T1/pcr/m/n/10 determinant,dsCMatrix,missing-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 8011--8013
[]\T1/pcr/m/n/10 determinant,dsparseMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8013--8015
[]\T1/pcr/m/n/10 determinant,dtCMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8015--8017
[]\T1/pcr/m/n/10 determinant,dtpMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8017--8019
[]\T1/pcr/m/n/10 determinant,dtpMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8019--8021
[]\T1/pcr/m/n/10 determinant,dtrMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8021--8023
[]\T1/pcr/m/n/10 determinant,dtrMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 8023--8025
[]\T1/pcr/m/n/10 determinant,indMatrix,logical-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 8025--8027
[]\T1/pcr/m/n/10 determinant,Matrix,logical-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 8027--8029
[]\T1/pcr/m/n/10 determinant,Matrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 8029--8031
[]\T1/pcr/m/n/10 determinant,pMatrix,logical-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 8031--8033
[]\T1/pcr/m/n/10 determinant,sparseMatrix,logical-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 8033--8035
[]\T1/pcr/m/n/10 determinant,sparseMatrix,missing-method 
[3325] [3326]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 8249--8251
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 
[3327]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 8492--8494
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3328] [3329]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 8688--8690
[]\T1/pcr/m/n/10 expand,MatrixFactorization-method 

Overfull \hbox (10.01662pt too wide) in paragraph at lines 8688--8690
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 8802--8804
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3330] [3331]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 9003--9005
[]\T1/pcr/m/n/10 forceSymmetric,corMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9005--9007
[]\T1/pcr/m/n/10 forceSymmetric,corMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9007--9009
[]\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 9009--9011
[]\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9011--9013
[]\T1/pcr/m/n/10 forceSymmetric,denseMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9013--9015
[]\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9015--9017
[]\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9017--9019
[]\T1/pcr/m/n/10 forceSymmetric,dppMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9019--9021
[]\T1/pcr/m/n/10 forceSymmetric,dppMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9021--9023
[]\T1/pcr/m/n/10 forceSymmetric,dsCMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9023--9025
[]\T1/pcr/m/n/10 forceSymmetric,dsCMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9025--9027
[]\T1/pcr/m/n/10 forceSymmetric,dspMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9027--9029
[]\T1/pcr/m/n/10 forceSymmetric,dspMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9029--9031
[]\T1/pcr/m/n/10 forceSymmetric,dsRMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9031--9033
[]\T1/pcr/m/n/10 forceSymmetric,dsRMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9033--9035
[]\T1/pcr/m/n/10 forceSymmetric,dsTMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9035--9037
[]\T1/pcr/m/n/10 forceSymmetric,dsTMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9037--9039
[]\T1/pcr/m/n/10 forceSymmetric,dsyMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9039--9041
[]\T1/pcr/m/n/10 forceSymmetric,dsyMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9041--9043
[]\T1/pcr/m/n/10 forceSymmetric,lsCMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9043--9045
[]\T1/pcr/m/n/10 forceSymmetric,lsCMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9045--9047
[]\T1/pcr/m/n/10 forceSymmetric,lspMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9047--9049
[]\T1/pcr/m/n/10 forceSymmetric,lspMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9049--9051
[]\T1/pcr/m/n/10 forceSymmetric,lsRMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9051--9053
[]\T1/pcr/m/n/10 forceSymmetric,lsRMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9053--9055
[]\T1/pcr/m/n/10 forceSymmetric,lsTMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9055--9057
[]\T1/pcr/m/n/10 forceSymmetric,lsTMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9057--9059
[]\T1/pcr/m/n/10 forceSymmetric,lsyMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9059--9061
[]\T1/pcr/m/n/10 forceSymmetric,lsyMatrix,missing-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 9061--9063
[]\T1/pcr/m/n/10 forceSymmetric,matrix,ANY-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 9063--9065
[]\T1/pcr/m/n/10 forceSymmetric,Matrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9065--9067
[]\T1/pcr/m/n/10 forceSymmetric,nsCMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9067--9069
[]\T1/pcr/m/n/10 forceSymmetric,nsCMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9069--9071
[]\T1/pcr/m/n/10 forceSymmetric,nspMatrix,character-method 
[3332]
Overfull \hbox (44.8567pt too wide) in paragraph at lines 9071--9073
[]\T1/pcr/m/n/10 forceSymmetric,nspMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9073--9075
[]\T1/pcr/m/n/10 forceSymmetric,nsRMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9075--9077
[]\T1/pcr/m/n/10 forceSymmetric,nsRMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9077--9079
[]\T1/pcr/m/n/10 forceSymmetric,nsTMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9079--9081
[]\T1/pcr/m/n/10 forceSymmetric,nsTMatrix,missing-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 9081--9083
[]\T1/pcr/m/n/10 forceSymmetric,nsyMatrix,character-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 9083--9085
[]\T1/pcr/m/n/10 forceSymmetric,nsyMatrix,missing-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 9085--9087
[]\T1/pcr/m/n/10 forceSymmetric,sparseMatrix,ANY-method 
[3333] [3334] [3335] [3336]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 9792--9794
[]\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class 
[3337] [3338] [3339]
Underfull \vbox (badness 3769) has occurred while \output is active [3340]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 10270--10272
[]\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 10272--10274
[]\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 10280--10282
[]\T1/pcr/m/n/10 is.infinite,nsparseVector-method 
[3341]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 10412--10414
[]\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10418--10420
[]\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 10420--10422
[]\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10464--10466
[]\T1/pcr/m/n/10 isSymmetric,diagonalMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 10468--10470
[]\T1/pcr/m/n/10 isSymmetric,symmetricMatrix-method 
[3342]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 10470--10472
[]\T1/pcr/m/n/10 isSymmetric,triangularMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 10474--10476
[]\T1/pcr/m/n/10 isTriangular,BunchKaufman-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10478--10480
[]\T1/pcr/m/n/10 isTriangular,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 10482--10484
[]\T1/pcr/m/n/10 isTriangular,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10516--10518
[]\T1/pcr/m/n/10 isTriangular,pBunchKaufman-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10520--10522
[]\T1/pcr/m/n/10 isTriangular,triangularMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10522--10524
[]\T1/pcr/m/n/10 isTriangular,TsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 10586--10588
[]\T1/pcr/m/n/10 kronecker,ANY,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10590--10592
[]\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method 
[3343]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 10592--10594
[]\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10594--10596
[]\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 10596--10598
[]\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 10598--10600
[]\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 10600--10602
[]\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10602--10604
[]\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10604--10606
[]\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 10606--10608
[]\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 10610--10612
[]\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 10612--10614
[]\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 10614--10616
[]\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 10616--10618
[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 10618--10620
[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method 
[3344] [3345] [3346]
Overfull \hbox (50.8567pt too wide) in paragraph at lines 11055--11057
[]\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11061--11063
[]\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 11063--11065
[]\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11065--11067
[]\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11067--11069
[]\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11069--11071
[]\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11075--11077
[]\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11085--11087
[]\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 11087--11089
[]\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 11089--11091
[]\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 11091--11093
[]\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11093--11095
[]\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 11101--11103
[]\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11111--11113
[]\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 11113--11115
[]\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11121--11123
[]\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11123--11125
[]\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 11125--11127
[]\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 11127--11129
[]\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method 

Underfull \vbox (badness 3302) has occurred while \output is active [3347]
Overfull \hbox (74.8567pt too wide) in paragraph at lines 11129--11131
[]\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method 
[3348] [3349]
Underfull \vbox (badness 1348) has occurred while \output is active [3350]
[3351]
Overfull \hbox (52.01662pt too wide) in paragraph at lines 11713--11715
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
[3352] [3353]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 12025--12027
[]\T1/pcr/m/n/10 nonstandardGenericWithTrace-class 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 12036--12038
[]\T1/pcr/m/n/10 norm,ddenseMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 12038--12040
[]\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12044--12046
[]\T1/pcr/m/n/10 norm,diagonalMatrix,character-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 12062--12064
[]\T1/pcr/m/n/10 norm,ldenseMatrix,character-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 12068--12070
[]\T1/pcr/m/n/10 norm,ndenseMatrix,character-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 12070--12072
[]\T1/pcr/m/n/10 norm,sparseMatrix,character-method 
[3354] [3355]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 12240--12242
[]\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 12246--12248
[]\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 12258--12260
[]\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 12260--12262
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 12262--12264
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12264--12266
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method 

Underfull \vbox (badness 6876) has occurred while \output is active
Overfull \hbox (62.8567pt too wide) in paragraph at lines 12266--12268
[]\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12286--12288
[]\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12288--12290
[]\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 12304--12306
[]\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method 

Underfull \vbox (badness 5847) has occurred while \output is active [3356]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 12324--12326
[]\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12326--12328
[]\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12344--12346
[]\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method 

Underfull \vbox (badness 4328) has occurred while \output is active
Overfull \hbox (26.8567pt too wide) in paragraph at lines 12352--12354
[]\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12356--12358
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12358--12360
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 12360--12362
[]\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 12378--12380
[]\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 12380--12382
[]\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 12382--12384
[]\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 12384--12386
[]\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12388--12390
[]\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 12392--12394
[]\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method 
[3357]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 12396--12398
[]\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 12497--12499
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3358] [3359] [3360] [3361] [3362] [3363]
Overfull \hbox (4.01662pt too wide) in paragraph at lines 13320--13322
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13322--13324
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 13324--13326
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 13326--13328
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (52.01662pt too wide) in paragraph at lines 13328--13330
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13330--13332
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 13332--13334
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Underfull \vbox (badness 1484) has occurred while \output is active
Overfull \hbox (4.01662pt too wide) in paragraph at lines 13334--13336
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (52.01662pt too wide) in paragraph at lines 13338--13340
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13340--13342
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13342--13344
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13344--13346
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13346--13348
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13348--13350
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Underfull \vbox (badness 1824) has occurred while \output is active [3364]
[3365]
Overfull \hbox (4.01662pt too wide) in paragraph at lines 13578--13580
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 13641--13643
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3366] [3367] [3368]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 14015--14017
[]\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 14024--14026
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14026--14028
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14028--14030
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14030--14032
[]\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14040--14042
[]\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 14049--14051
[]\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 14063--14065
[]\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14069--14071
[]\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method 

Underfull \vbox (badness 1642) has occurred while \output is active [3369]
[3370]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 14308--14310
[]\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 14310--14312
[]\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14312--14314
[]\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 14314--14316
[]\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 14318--14320
[]\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14320--14322
[]\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14322--14324
[]\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 14324--14326
[]\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 14326--14328
[]\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14328--14330
[]\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 14330--14332
[]\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14336--14338
[]\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14340--14342
[]\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method 

Underfull \vbox (badness 5022) has occurred while \output is active [3371]
Overfull \hbox (8.8567pt too wide) in paragraph at lines 14350--14352
[]\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14354--14356
[]\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 14356--14358
[]\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 14358--14360
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method 

Overfull \hbox (56.8567pt too wide) in paragraph at lines 14360--14362
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14362--14364
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 14364--14366
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 14366--14368
[]\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14391--14393
[]\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 14393--14395
[]\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 14395--14397
[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14397--14399
[]\T1/pcr/m/n/10 rcond,dgeMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14401--14403
[]\T1/pcr/m/n/10 rcond,dpoMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14405--14407
[]\T1/pcr/m/n/10 rcond,dppMatrix,character-method 

Underfull \vbox (badness 1484) has occurred while \output is active
Overfull \hbox (2.8567pt too wide) in paragraph at lines 14409--14411
[]\T1/pcr/m/n/10 rcond,dspMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14413--14415
[]\T1/pcr/m/n/10 rcond,dsyMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14417--14419
[]\T1/pcr/m/n/10 rcond,dtpMatrix,character-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 14421--14423
[]\T1/pcr/m/n/10 rcond,dtrMatrix,character-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14425--14427
[]\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14429--14431
[]\T1/pcr/m/n/10 rcond,ndenseMatrix,character-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 14431--14433
[]\T1/pcr/m/n/10 rcond,sparseMatrix,character-method 
[3372] [3373] [3374] [3375] [3376]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 15066--15068
[]\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15068--15070
[]\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15072--15074
[]\T1/pcr/m/n/10 Schur,generalMatrix,logical-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15074--15076
[]\T1/pcr/m/n/10 Schur,generalMatrix,missing-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15080--15082
[]\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15082--15084
[]\T1/pcr/m/n/10 Schur,symmetricMatrix,missing-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 15084--15086
[]\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 15086--15088
[]\T1/pcr/m/n/10 Schur,triangularMatrix,missing-method 
[3377]
Overfull \hbox (26.8567pt too wide) in paragraph at lines 15318--15320
[]\T1/pcr/m/n/10 show,genericFunctionWithTrace-method 
[3378]
Overfull \hbox (10.01662pt too wide) in paragraph at lines 15322--15324
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/
ptm/m/n/10 , 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 15326--15328
[]\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15330--15332
[]\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15340--15342
[]\T1/pcr/m/n/10 show,refClassRepresentation-method 
[3379]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 15514--15516
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15516--15518
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15519--15521
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (5.3567pt too wide) in paragraph at lines 15523--15524
[]\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15528--15530
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (5.3567pt too wide) in paragraph at lines 15532--15533
[]\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15533--15535
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (23.3567pt too wide) in paragraph at lines 15536--15538
[]\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 

Overfull \hbox (46.01662pt too wide) in paragraph at lines 15539--15541
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 
[3380]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 15564--15566
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15584--15586
[]\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 15586--15588
[]\T1/pcr/m/n/10 solve,CHMfactor,diagonalMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15588--15590
[]\T1/pcr/m/n/10 solve,CHMfactor,dsparseMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15598--15600
[]\T1/pcr/m/n/10 solve,ddenseMatrix,Matrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15600--15602
[]\T1/pcr/m/n/10 solve,ddenseMatrix,matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 15602--15604
[]\T1/pcr/m/n/10 solve,ddenseMatrix,missing-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 15604--15606
[]\T1/pcr/m/n/10 solve,ddenseMatrix,numeric-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15608--15610
[]\T1/pcr/m/n/10 solve,dgCMatrix,ddenseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15610--15612
[]\T1/pcr/m/n/10 solve,dgCMatrix,dsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15616--15618
[]\T1/pcr/m/n/10 solve,dgeMatrix,ddenseMatrix-method 

Underfull \vbox (badness 2035) has occurred while \output is active
Overfull \hbox (20.8567pt too wide) in paragraph at lines 15622--15624
[]\T1/pcr/m/n/10 solve,dgeMatrix,sparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15624--15626
[]\T1/pcr/m/n/10 solve,diagonalMatrix,Matrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15626--15628
[]\T1/pcr/m/n/10 solve,diagonalMatrix,matrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15628--15630
[]\T1/pcr/m/n/10 solve,diagonalMatrix,missing-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15630--15632
[]\T1/pcr/m/n/10 solve,dpoMatrix,dgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15636--15638
[]\T1/pcr/m/n/10 solve,dppMatrix,dgeMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15644--15646
[]\T1/pcr/m/n/10 solve,dsCMatrix,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15646--15648
[]\T1/pcr/m/n/10 solve,dsCMatrix,denseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15648--15650
[]\T1/pcr/m/n/10 solve,dsCMatrix,dsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15656--15658
[]\T1/pcr/m/n/10 solve,dspMatrix,ddenseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15662--15664
[]\T1/pcr/m/n/10 solve,dsyMatrix,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15664--15666
[]\T1/pcr/m/n/10 solve,dsyMatrix,denseMatrix-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15670--15672
[]\T1/pcr/m/n/10 solve,dtCMatrix,CsparseMatrix-method 
[3381]
Overfull \hbox (2.8567pt too wide) in paragraph at lines 15672--15674
[]\T1/pcr/m/n/10 solve,dtCMatrix,dgeMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15680--15682
[]\T1/pcr/m/n/10 solve,dtpMatrix,ddenseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 15686--15688
[]\T1/pcr/m/n/10 solve,dtrMatrix,ddenseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15698--15700
[]\T1/pcr/m/n/10 solve,Matrix,diagonalMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 15710--15712
[]\T1/pcr/m/n/10 solve,Matrix,sparseVector-method 

Overfull \hbox (26.8567pt too wide) in paragraph at lines 15712--15714
[]\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 15714--15716
[]\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 15716--15718
[]\T1/pcr/m/n/10 solve,MatrixFactorization,numeric-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 15728--15730
[]\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method 
[3382]
Overfull \hbox (52.01662pt too wide) in paragraph at lines 15821--15823
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1
0 )\T1/ptm/m/n/10 , 
[3383]
Overfull \hbox (44.8567pt too wide) in paragraph at lines 16080--16082
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16082--16084
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_results 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16084--16086
[]\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings 
[3384]
Underfull \vbox (badness 2564) has occurred while \output is active [3385]
[3386] [3387] [3388]
Overfull \hbox (32.8567pt too wide) in paragraph at lines 16702--16704
[]\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16704--16706
[]\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 16706--16708
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 16708--16710
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 16710--16712
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,diagonalMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16712--16714
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16714--16716
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16716--16718
[]\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,numLike-method 

Overfull \hbox (74.8567pt too wide) in paragraph at lines 16718--16720
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,CsparseMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16720--16722
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dsCMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16722--16724
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dtrMatrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16724--16726
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,lsCMatrix-method 
[3389]
Overfull \hbox (38.8567pt too wide) in paragraph at lines 16726--16728
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,missing-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16728--16730
[]\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,nsCMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16730--16732
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,dgeMatrix-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 16732--16734
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,diagonalMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16734--16736
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,matrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16736--16738
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16738--16740
[]\T1/pcr/m/n/10 tcrossprod,dgeMatrix,numLike-method 

Overfull \hbox (86.8567pt too wide) in paragraph at lines 16740--16742
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,CsparseMatrix-method 

Overfull \hbox (92.8567pt too wide) in paragraph at lines 16742--16744
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,diagonalMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16744--16746
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,matrix-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16746--16748
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,missing-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 16748--16750
[]\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,sparseMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16750--16752
[]\T1/pcr/m/n/10 tcrossprod,dtrMatrix,dtrMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16752--16754
[]\T1/pcr/m/n/10 tcrossprod,indMatrix,indMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16754--16756
[]\T1/pcr/m/n/10 tcrossprod,indMatrix,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16756--16758
[]\T1/pcr/m/n/10 tcrossprod,lgCMatrix,missing-method 

Overfull \hbox (62.8567pt too wide) in paragraph at lines 16758--16760
[]\T1/pcr/m/n/10 tcrossprod,lgeMatrix,diagonalMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16760--16762
[]\T1/pcr/m/n/10 tcrossprod,lgTMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16762--16764
[]\T1/pcr/m/n/10 tcrossprod,lsparseMatrix,missing-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16766--16768
[]\T1/pcr/m/n/10 tcrossprod,matrix,CsparseMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16768--16770
[]\T1/pcr/m/n/10 tcrossprod,matrix,dgeMatrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16770--16772
[]\T1/pcr/m/n/10 tcrossprod,matrix,diagonalMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16772--16774
[]\T1/pcr/m/n/10 tcrossprod,matrix,dsCMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16774--16776
[]\T1/pcr/m/n/10 tcrossprod,matrix,dtrMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16776--16778
[]\T1/pcr/m/n/10 tcrossprod,Matrix,indMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16778--16780
[]\T1/pcr/m/n/10 tcrossprod,matrix,indMatrix-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16780--16782
[]\T1/pcr/m/n/10 tcrossprod,matrix,lsCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16788--16790
[]\T1/pcr/m/n/10 tcrossprod,Matrix,missing-method 

Overfull \hbox (14.8567pt too wide) in paragraph at lines 16790--16792
[]\T1/pcr/m/n/10 tcrossprod,matrix,nsCMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16792--16794
[]\T1/pcr/m/n/10 tcrossprod,Matrix,numLike-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16794--16796
[]\T1/pcr/m/n/10 tcrossprod,Matrix,pMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16796--16798
[]\T1/pcr/m/n/10 tcrossprod,matrix,pMatrix-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16798--16800
[]\T1/pcr/m/n/10 tcrossprod,Matrix,sparseVector-method 

Overfull \hbox (50.8567pt too wide) in paragraph at lines 16800--16802
[]\T1/pcr/m/n/10 tcrossprod,Matrix,symmetricMatrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16802--16804
[]\T1/pcr/m/n/10 tcrossprod,Matrix,TsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16804--16806
[]\T1/pcr/m/n/10 tcrossprod,ngCMatrix,missing-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16806--16808
[]\T1/pcr/m/n/10 tcrossprod,ngTMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16808--16810
[]\T1/pcr/m/n/10 tcrossprod,nsparseMatrix,missing-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16810--16812
[]\T1/pcr/m/n/10 tcrossprod,numLike,CsparseMatrix-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16812--16814
[]\T1/pcr/m/n/10 tcrossprod,numLike,dgeMatrix-method 

Overfull \hbox (2.8567pt too wide) in paragraph at lines 16814--16816
[]\T1/pcr/m/n/10 tcrossprod,numLike,Matrix-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 16816--16818
[]\T1/pcr/m/n/10 tcrossprod,pMatrix,missing-method 

Overfull \hbox (8.8567pt too wide) in paragraph at lines 16818--16820
[]\T1/pcr/m/n/10 tcrossprod,pMatrix,pMatrix-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 16820--16822
[]\T1/pcr/m/n/10 tcrossprod,sparseMatrix,diagonalMatrix-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 16822--16824
[]\T1/pcr/m/n/10 tcrossprod,sparseMatrix,sparseVector-method 

Overfull \hbox (32.8567pt too wide) in paragraph at lines 16824--16826
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,Matrix-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16826--16828
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,missing-method 

Overfull \hbox (68.8567pt too wide) in paragraph at lines 16828--16830
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,sparseMatrix-method 
[3390]
Overfull \hbox (68.8567pt too wide) in paragraph at lines 16830--16832
[]\T1/pcr/m/n/10 tcrossprod,sparseVector,sparseVector-method 

Overfull \hbox (20.8567pt too wide) in paragraph at lines 16832--16834
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,ANY-method 

Overfull \hbox (38.8567pt too wide) in paragraph at lines 16834--16836
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,Matrix-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 16836--16838
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,missing-method 

Overfull \hbox (80.8567pt too wide) in paragraph at lines 16838--16840
[]\T1/pcr/m/n/10 tcrossprod,TsparseMatrix,TsparseMatrix-method 

Overfull \hbox (4.01662pt too wide) in paragraph at lines 16860--16862
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 tensor.prod.model.matrix\T1/ptm/m/it/10 )\T1/p
tm/m/n/10 , 
[3391] [3392] [3393]
Overfull \hbox (46.01662pt too wide) in paragraph at lines 17379--17381
\T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10
 )\T1/ptm/m/n/10 , 

Underfull \vbox (badness 1348) has occurred while \output is active [3394]
[3395] [3396]
Overfull \hbox (56.8567pt too wide) in paragraph at lines 17848--17850
[]\T1/pcr/m/n/10 updown,character,mMatrix,CHMfactor-method 

Overfull \hbox (44.8567pt too wide) in paragraph at lines 17850--17852
[]\T1/pcr/m/n/10 updown,logical,mMatrix,CHMfactor-method 
[3397] [3398] [3399] [3400]) (./fullrefman.aux) )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.tree} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mem.limits} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced
 but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does 
not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.standardGeneric} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texlive
/fonts/type1/bluesky/ams/cmbsy7.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmbx10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmex10.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb></usr/share/texmf-tex
live/fonts/type1/bluesky/cm/cmmi5.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmmi7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmib10.pfb>
</usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb></usr/share/texmf-te
xlive/fonts/type1/bluesky/cm/cmr5.pfb></usr/share/texmf-texlive/fonts/type1/blu
esky/cm/cmr7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy10.pfb></
usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7.pfb></usr/share/texmf-texl
ive/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texmf-texlive/fonts/type1/ur
w/courier/ucrr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/courier/ucrro8a.
pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/t
exmf-texlive/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/t
ype1/urw/times/utmbi8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr
8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr8a.pfb></usr/share/t
exmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on fullrefman.pdf (3449 pages, 9032299 bytes).
Transcript written on fullrefman.log.
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2'
+ exit 0
Executing(%install): /bin/sh -e /usr/src/tmp/rpm-tmp.95971
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ /bin/chmod -Rf u+rwX -- /usr/src/tmp/R-base-buildroot
+ :
+ /bin/rm -rf -- /usr/src/tmp/R-base-buildroot
+ cd R-3.1.2
+ make 'INSTALL=/bin/install -p' install DESTDIR=/usr/src/tmp/R-base-buildroot install-pdf install-info
make: Entering directory `/usr/src/RPM/BUILD/R-3.1.2'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/m4'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/m4'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tools'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tools'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
installing doc ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/man/man1
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
installing doc/html ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/html
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/html'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
installing doc/manual ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/images
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/etc'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
installing etc ...
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/etc'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/share'
installing share ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/R
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/dictionaries
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/encodings
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/java
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/licenses
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/make
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/bibtex/bib
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/bibtex/bst
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/tex/latex
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/share'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/bin
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/scripts'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/include'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/include/R
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/include/R_ext'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/include/R_ext'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/include'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/blas'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/blas'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/bzip2'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/bzip2'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/pcre'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/pcre'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/tre'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/xdr'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/xdr'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/xz'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/xz'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/zlib'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/zlib'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/intl'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra/intl'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/extra'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/appl'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/nmath'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -pipe -Wall -g -O2 -fno-strict-aliasing  -L/usr/local/lib64 -DR_HOME='"/usr/lib64/R"' \
  -o Rscript ./Rscript.c
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/pkgconfig
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/unix'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/exec
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/main'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/internet'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/lapack'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/vfonts'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules/X11'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/modules'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/library
installing packages ...
  building HTML index ...
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src/library'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/src'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
installing R manuals in PDF format ...
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
ERROR: 'makeinfo' v4.7 or later needed but missing on your system.
make[1]: *** [R-FAQ.info] Error 1
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/doc/manual'
make: [install-info] Error 2 (ignored)
make: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2'
+ mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so
+ ln -s libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR-2.11.so
++ relative /usr/share/doc/R-3.1 /usr/lib64/R/doc
+ ln -s ../../share/doc/R-3.1 /usr/src/tmp/R-base-buildroot/usr/lib64/R/doc
++ relative /usr/include/R /usr/lib64/R/include
+ ln -s ../../include/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/include
+ cmp /usr/src/tmp/R-base-buildroot/usr/bin/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/R
++ relative /usr/lib64/R/bin/R /usr/bin/R
+ ln -snfv ../lib64/R/bin/R /usr/src/tmp/R-base-buildroot/usr/bin/R
'/usr/src/tmp/R-base-buildroot/usr/bin/R' -> '../lib64/R/bin/R'
+ cmp /usr/src/tmp/R-base-buildroot/usr/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/Rscript
++ relative /usr/lib64/R/bin/Rscript /usr/bin/Rscript
+ ln -snfv ../lib64/R/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/bin/Rscript
'/usr/src/tmp/R-base-buildroot/usr/bin/Rscript' -> '../lib64/R/bin/Rscript'
+ fgrep -r /usr/src/tmp/R-base-buildroot /usr/src/tmp/R-base-buildroot
+ mkdir -p /usr/src/tmp/R-base-buildroot/etc/R
+ mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Makeconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Renviron /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/javaconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/ldpaths /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/repositories /usr/src/tmp/R-base-buildroot/etc/R/
+ rmdir /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
++ relative /etc/R /usr/lib64/R/etc
+ ln -s ../../../etc/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
+ '[' -f /usr/src/tmp/R-base-buildroot/etc/R/ldpaths ']'
+ :
+ mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/applications
+ cat
+ '[' -f /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool ']'
++ relative /usr/bin/libtool /usr/lib64/R/bin/libtool
+ ln -snfv ../../../bin/libtool /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool
'/usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool' -> '../../../bin/libtool'
+ rm -fv '/usr/src/tmp/R-base-buildroot/usr/share/info/dir*'
+ /usr/lib/rpm/brp-alt
Cleaning files in /usr/src/tmp/R-base-buildroot (auto)
mode of './usr/lib64/libR.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/mgcv/libs/mgcv.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/class/libs/class.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/nlme/libs/nlme.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/cluster/libs/cluster.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/Matrix/libs/Matrix.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/nnet/libs/nnet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/KernSmooth/libs/KernSmooth.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/rpart/libs/rpart.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/MASS/libs/MASS.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/spatial/libs/spatial.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/foreign/libs/foreign.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/survival/libs/survival.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/lattice/libs/lattice.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/parallel/libs/parallel.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tcltk/libs/tcltk.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grid/libs/grid.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/utils/libs/utils.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/splines/libs/splines.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/cairo.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/grDevices.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/methods/libs/methods.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/stats/libs/stats.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/graphics/libs/graphics.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tools/libs/tools.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/R_de.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/R_X11.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/vfonts.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/lapack.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/internet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
Verifying and fixing files in /usr/src/tmp/R-base-buildroot (binconfig,pkgconfig,libtool,desktop)
/usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic  -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -L${rlibdir} -lR'
Compressing files in /usr/src/tmp/R-base-buildroot (auto)
Adjusting library links in /usr/src/tmp/R-base-buildroot
./usr/lib64:
	libR.so -> libR.so
./usr/lib64/R/lib:
Verifying ELF objects in /usr/src/tmp/R-base-buildroot (arch=normal,fhs=normal,lfs=relaxed,lint=relaxed,rpath=normal,stack=normal,textrel=normal,unresolved=normal)
Hardlinking identical .pyc and .pyo files
Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.67013
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.1.2
+ export TZ=GMT
+ TZ=GMT
+ make check
make: Entering directory `/usr/src/RPM/BUILD/R-3.1.2'
make[1]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests/Examples'
Testing examples for package 'base'
Testing examples for package 'tools'
  comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
Testing examples for package 'utils'
Testing examples for package 'grDevices'
  comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
Testing examples for package 'graphics'
  comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
Testing examples for package 'stats'
  comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ...
6484c6484
< Grand Mean: 291.5937
---
> Grand Mean: 291.5938
13041c13041
< 6  -0.5412  20.482886    -0.845157
---
> 6  -0.5412  20.482887    -0.845157
14625c14625
< Grand Mean: 291.5937
---
> Grand Mean: 291.5938
Testing examples for package 'datasets'
  comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
Testing examples for package 'methods'
Testing examples for package 'grid'
  comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
Testing examples for package 'splines'
  comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
Testing examples for package 'stats4'
  comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
Testing examples for package 'tcltk'
Testing examples for package 'compiler'
Testing examples for package 'parallel'
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests/Examples'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running strict specific tests
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'eval-etc.R' ... OK
  comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
running code in 'simple-true.R' ... OK
  comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK
running code in 'arith-true.R' ... OK
  comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK
running code in 'arith.R' ... OK
  comparing 'arith.Rout' to './arith.Rout.save' ... OK
running code in 'lm-tests.R' ... OK
  comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
running code in 'ok-errors.R' ... OK
  comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
running code in 'method-dispatch.R' ... OK
  comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'array-subset.R' ... OK
  comparing 'array-subset.Rout' to './array-subset.Rout.save' ... OK
running code in 'any-all.R' ... OK
  comparing 'any-all.Rout' to './any-all.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ... OK
  comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running sloppy specific tests
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'complex.R' ... OK
  comparing 'complex.Rout' to './complex.Rout.save' ... OK
running code in 'print-tests.R' ... OK
  comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK
running code in 'lapack.R' ... OK
  comparing 'lapack.Rout' to './lapack.Rout.save' ... OK
running code in 'datasets.R' ... OK
  comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
running code in 'datetime.R' ... OK
  comparing 'datetime.Rout' to './datetime.Rout.save' ... OK
running code in 'iec60559.R' ... OK
  comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running regression tests ...
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'reg-tests-1a.R' ... OK
running code in 'reg-tests-1b.R' ... OK
running code in 'reg-tests-1c.R' ... OK
running code in 'reg-tests-2.R' ... OK
  comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'reg-IO.R' ... OK
  comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK
running code in 'reg-IO2.R' ... OK
  comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK
running code in 'reg-plot.R' ... OK
  comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK
running code in 'reg-S4.R' ... OK
  comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK
running code in 'reg-BLAS.R' ... OK
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'reg-tests-3.R' ... OK
  comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK
running code in 'reg-examples3.R' ... OK
  comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ... OK
running tests of plotting Latin-1
  expect failure or some differences if not in a Latin-1 or UTF-8 locale
running code in 'reg-plot-latin1.R' ... FAILED
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running tests of Internet and socket functions
  expect some differences
make[3]: Entering directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
running code in 'internet.R' ... OK
  comparing 'internet.Rout' to './internet.Rout.save' ...14,16c14,355
< Warning message:
< In nsl("cran.r-project.org") :
<   nsl() was unable to resolve host 'cran.r-project.org'
---
> > 
> > # test do_download.
> > nrow(available.packages(contrib.url("http://cran.r-project.org")))
> [1] 5993
> > 
> > # test url connections on http
> > zz <- url("http://cran.r-project.org/")
> > readLines(zz)
>  [1] "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">"
>  [2] "<html>"                                                                                                   
>  [3] "<head>"                                                                                                   
>  [4] "<title>The Comprehensive R Archive Network</title>"                                                       
>  [5] "<META HTTP-EQUIV=\"content-type\" CONTENT=\"text/html; charset=utf-8\">"                                  
>  [6] "<link rel=\"icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                           
>  [7] "<link rel=\"shortcut icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                  
>  [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"                                               
>  [9] "</head>"                                                                                                  
> [10] ""                                                                                                         
> [11] "<FRAMESET cols=\"1*, 4*\" border=0>"                                                                      
> [12] "<FRAMESET rows=\"120, 1*\">"                                                                              
> [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>"                                                    
> [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>"                                              
> [15] "</FRAMESET>"                                                                                              
> [16] "<FRAME src=\"banner.shtml\" name=\"banner\" frameborder=0>"                                               
> [17] "<noframes>"                                                                                               
> [18] "<h1>The Comprehensive R Archive Network</h1>"                                                             
> [19] ""                                                                                                         
> [20] "Your browser seems not to support frames,"                                                                
> [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN."                                           
> [22] "</noframes>"                                                                                              
> [23] "</FRAMESET>"                                                                                              
> > close(zz)
> > 
> > ## check graceful failure:
> > try(zz <- url("http://foo.bar", "r"))
> Error in url("http://foo.bar", "r") : cannot open the connection
> In addition: Warning message:
> In url("http://foo.bar", "r") : unable to connect to 'foo.bar' on port 80.
> > 
> > # and via read.table, test http and ftp.
> > 
> > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
>      V1  V2   V3    V4 V5
> 1     1 307  930 36.58  0
> 2     2 307  940 36.73  0
> 3     3 307  950 36.93  0
> 4     4 307 1000 37.15  0
> 5     5 307 1010 37.23  0
> 6     6 307 1020 37.24  0
> 7     7 307 1030 37.24  0
> 8     8 307 1040 36.90  0
> 9     9 307 1050 36.95  0
> 10   10 307 1100 36.89  0
> 11   11 307 1110 36.95  0
> 12   12 307 1120 37.00  0
> 13   13 307 1130 36.90  0
> 14   14 307 1140 36.99  0
> 15   15 307 1150 36.99  0
> 16   16 307 1200 37.01  0
> 17   17 307 1210 37.04  0
> 18   18 307 1220 37.04  0
> 19   19 307 1230 37.14  0
> 20   20 307 1240 37.07  0
> 21   21 307 1250 36.98  0
> 22   22 307 1300 37.01  0
> 23   23 307 1310 36.97  0
> 24   24 307 1320 36.97  0
> 25   25 307 1330 37.12  0
> 26   26 307 1340 37.13  0
> 27   27 307 1350 37.14  0
> 28   28 307 1400 37.15  0
> 29   29 307 1410 37.17  0
> 30   30 307 1420 37.12  0
> 31   31 307 1430 37.12  0
> 32   32 307 1440 37.17  0
> 33   33 307 1450 37.28  0
> 34   34 307 1500 37.28  0
> 35   35 307 1510 37.44  0
> 36   36 307 1520 37.51  0
> 37   37 307 1530 37.64  0
> 38   38 307 1540 37.51  0
> 39   39 307 1550 37.98  1
> 40   40 307 1600 38.02  1
> 41   41 307 1610 38.00  1
> 42   42 307 1620 38.24  1
> 43   43 307 1630 38.10  1
> 44   44 307 1640 38.24  1
> 45   45 307 1650 38.11  1
> 46   46 307 1700 38.02  1
> 47   47 307 1710 38.11  1
> 48   48 307 1720 38.01  1
> 49   49 307 1730 37.91  1
> 50   50 307 1740 37.96  1
> 51   51 307 1750 38.03  1
> 52   52 307 1800 38.17  1
> 53   53 307 1810 38.19  1
> 54   54 307 1820 38.18  1
> 55   55 307 1830 38.15  1
> 56   56 307 1840 38.04  1
> 57   57 307 1850 37.96  1
> 58   58 307 1900 37.84  1
> 59   59 307 1910 37.83  1
> 60   60 307 1920 37.84  1
> 61   61 307 1930 37.74  1
> 62   62 307 1940 37.76  1
> 63   63 307 1950 37.76  1
> 64   64 307 2000 37.64  1
> 65   65 307 2010 37.63  1
> 66   66 307 2020 38.06  1
> 67   67 307 2030 38.19  1
> 68   68 307 2040 38.35  1
> 69   69 307 2050 38.25  1
> 70   70 307 2100 37.86  1
> 71   71 307 2110 37.95  1
> 72   72 307 2120 37.95  1
> 73   73 307 2130 37.76  1
> 74   74 307 2140 37.60  1
> 75   75 307 2150 37.89  1
> 76   76 307 2200 37.86  1
> 77   77 307 2210 37.71  1
> 78   78 307 2220 37.78  1
> 79   79 307 2230 37.82  1
> 80   80 307 2240 37.76  1
> 81   81 307 2250 37.81  1
> 82   82 307 2300 37.84  1
> 83   83 307 2310 38.01  1
> 84   84 307 2320 38.10  1
> 85   85 307 2330 38.15  1
> 86   86 307 2340 37.92  1
> 87   87 307 2350 37.64  1
> 88   88 308    0 37.70  1
> 89   89 308   10 37.46  1
> 90   90 308   20 37.41  1
> 91   91 308   30 37.46  1
> 92   92 308   40 37.56  1
> 93   93 308   50 37.55  1
> 94   94 308  100 37.75  1
> 95   95 308  110 37.76  1
> 96   96 308  120 37.73  1
> 97   97 308  130 37.77  1
> 98   98 308  140 38.01  1
> 99   99 308  150 38.04  1
> 100 100 308  200 38.07  1
> > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
>      V1  V2   V3    V4 V5
> 1     1 307  930 36.58  0
> 2     2 307  940 36.73  0
> 3     3 307  950 36.93  0
> 4     4 307 1000 37.15  0
> 5     5 307 1010 37.23  0
> 6     6 307 1020 37.24  0
> 7     7 307 1030 37.24  0
> 8     8 307 1040 36.90  0
> 9     9 307 1050 36.95  0
> 10   10 307 1100 36.89  0
> 11   11 307 1110 36.95  0
> 12   12 307 1120 37.00  0
> 13   13 307 1130 36.90  0
> 14   14 307 1140 36.99  0
> 15   15 307 1150 36.99  0
> 16   16 307 1200 37.01  0
> 17   17 307 1210 37.04  0
> 18   18 307 1220 37.04  0
> 19   19 307 1230 37.14  0
> 20   20 307 1240 37.07  0
> 21   21 307 1250 36.98  0
> 22   22 307 1300 37.01  0
> 23   23 307 1310 36.97  0
> 24   24 307 1320 36.97  0
> 25   25 307 1330 37.12  0
> 26   26 307 1340 37.13  0
> 27   27 307 1350 37.14  0
> 28   28 307 1400 37.15  0
> 29   29 307 1410 37.17  0
> 30   30 307 1420 37.12  0
> 31   31 307 1430 37.12  0
> 32   32 307 1440 37.17  0
> 33   33 307 1450 37.28  0
> 34   34 307 1500 37.28  0
> 35   35 307 1510 37.44  0
> 36   36 307 1520 37.51  0
> 37   37 307 1530 37.64  0
> 38   38 307 1540 37.51  0
> 39   39 307 1550 37.98  1
> 40   40 307 1600 38.02  1
> 41   41 307 1610 38.00  1
> 42   42 307 1620 38.24  1
> 43   43 307 1630 38.10  1
> 44   44 307 1640 38.24  1
> 45   45 307 1650 38.11  1
> 46   46 307 1700 38.02  1
> 47   47 307 1710 38.11  1
> 48   48 307 1720 38.01  1
> 49   49 307 1730 37.91  1
> 50   50 307 1740 37.96  1
> 51   51 307 1750 38.03  1
> 52   52 307 1800 38.17  1
> 53   53 307 1810 38.19  1
> 54   54 307 1820 38.18  1
> 55   55 307 1830 38.15  1
> 56   56 307 1840 38.04  1
> 57   57 307 1850 37.96  1
> 58   58 307 1900 37.84  1
> 59   59 307 1910 37.83  1
> 60   60 307 1920 37.84  1
> 61   61 307 1930 37.74  1
> 62   62 307 1940 37.76  1
> 63   63 307 1950 37.76  1
> 64   64 307 2000 37.64  1
> 65   65 307 2010 37.63  1
> 66   66 307 2020 38.06  1
> 67   67 307 2030 38.19  1
> 68   68 307 2040 38.35  1
> 69   69 307 2050 38.25  1
> 70   70 307 2100 37.86  1
> 71   71 307 2110 37.95  1
> 72   72 307 2120 37.95  1
> 73   73 307 2130 37.76  1
> 74   74 307 2140 37.60  1
> 75   75 307 2150 37.89  1
> 76   76 307 2200 37.86  1
> 77   77 307 2210 37.71  1
> 78   78 307 2220 37.78  1
> 79   79 307 2230 37.82  1
> 80   80 307 2240 37.76  1
> 81   81 307 2250 37.81  1
> 82   82 307 2300 37.84  1
> 83   83 307 2310 38.01  1
> 84   84 307 2320 38.10  1
> 85   85 307 2330 38.15  1
> 86   86 307 2340 37.92  1
> 87   87 307 2350 37.64  1
> 88   88 308    0 37.70  1
> 89   89 308   10 37.46  1
> 90   90 308   20 37.41  1
> 91   91 308   30 37.46  1
> 92   92 308   40 37.56  1
> 93   93 308   50 37.55  1
> 94   94 308  100 37.75  1
> 95   95 308  110 37.76  1
> 96   96 308  120 37.73  1
> 97   97 308  130 37.77  1
> 98   98 308  140 38.01  1
> 99   99 308  150 38.04  1
> 100 100 308  200 38.07  1
> > 
> > ## everything from here on is directly over sockets
> > if(!capabilities("sockets")) stop("no socket capabilities")
> > 
> > # do the same thing via sockets (cut-down httpclient)
> > httpget <- function (url, port = 80)
> + {
> +     urlel <- strsplit(url, "/")[[1]]
> +     if (urlel[1] != "http:") stop("Not an http:// URL")
> +     host <- urlel[3]
> +     rurl <- paste(c("", urlel[-(1:3)]), collapse = "/")
> +     a <- make.socket(host, port = port)
> +     on.exit(close.socket(a))
> +     headreq <- paste("HEAD", rurl, "HTTP/1.0\r\nConnection: Keep-Alive\r\nAccept: text/plain\r\n\r\n")
> +     write.socket(a, headreq)
> +     head <- read.socket(a, maxlen = 8000)
> +     b <- strsplit(head, "\n")[[1]]
> +     if (length(grep("200 OK", b[1])) == 0) stop(b[1])
> +     len <- as.numeric(strsplit(grep("Content-Length", b, value = TRUE),
> +                                ":")[[1]][2])
> +     getreq <- paste("GET", rurl, "HTTP/1.0\r\nConnection: Keep-Alive\r\nAccept: text/plain\r\n\r\n")
> +     write.socket(a, getreq)
> +     junk <- read.socket(a, maxlen = nchar(head))
> +     data <- ""
> +     b <- strsplit(c(head, junk), "\n")
> +     nn <- length(b[[1]])
> +     if (length(b[[2]]) > nn)
> +         data <- paste(b[[2]][-(1:nn)], collapse = "\n")
> +     while (nchar(data) < len) {
> +         data <- paste(data, read.socket(a, maxlen = len - nchar(data)),
> +                       sep = "")
> +     }
> +     strsplit(data, "\n")[[1]]
> + }
> > 
> > if(nzchar(Sys.getenv("http_proxy")) || nzchar(Sys.getenv("HTTP_PROXY"))) {
> +     cat("http proxy is set, so skip test of http over sockets\n")
> + } else {
> +     httpget("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
> + }
>   [1] "001 307 0930 36.58 0"  "002 307 0940 36.73 0"  "003 307 0950 36.93 0" 
>   [4] "004 307 1000 37.15 0"  "005 307 1010 37.23 0"  "006 307 1020 37.24 0" 
>   [7] "007 307 1030 37.24 0"  "008 307 1040 36.90 0"  "009 307 1050 36.95 0" 
>  [10] "010 307 1100 36.89 0"  "011 307 1110 36.95 0"  "012 307 1120 37.00 0" 
>  [13] "013 307 1130 36.90 0"  "014 307 1140 36.99 0"  "015 307 1150 36.99 0" 
>  [16] "016 307 1200 37.01 0"  "017 307 1210 37.04 0"  "018 307 1220 37.04 0" 
>  [19] "019 307 1230 37.14 0"  "020 307 1240 37.07 0"  "021 307 1250 36.98 0" 
>  [22] "022 307 1300 37.01 0"  "023 307 1310 36.97 0"  "024 307 1320 36.97 0" 
>  [25] "025 307 1330 37.12 0"  "026 307 1340 37.13 0"  "027 307 1350 37.14 0" 
>  [28] "028 307 1400 37.15 0"  "029 307 1410 37.17 0"  "030 307 1420 37.12 0" 
>  [31] "031 307 1430 37.12 0"  "032 307 1440 37.17 0"  "033 307 1450 37.28 0" 
>  [34] "034 307 1500 37.28 0"  "035 307 1510 37.44 0"  "036 307 1520 37.51 0" 
>  [37] "037 307 1530 37.64 0"  "038 307 1540 37.51 0"  "039 307 1550 37.98 1" 
>  [40] "040 307 1600 38.02 1"  "041 307 1610 38.00 1 " "042 307 1620 38.24 1 "
>  [43] "043 307 1630 38.10 1"  "044 307 1640 38.24 1"  "045 307 1650 38.11 1" 
>  [46] "046 307 1700 38.02 1"  "047 307 1710 38.11 1"  "048 307 1720 38.01 1" 
>  [49] "049 307 1730 37.91 1"  "050 307 1740 37.96 1"  "051 307 1750 38.03 1" 
>  [52] "052 307 1800 38.17 1"  "053 307 1810 38.19 1"  "054 307 1820 38.18 1" 
>  [55] "055 307 1830 38.15 1"  "056 307 1840 38.04 1"  "057 307 1850 37.96 1" 
>  [58] "058 307 1900 37.84 1"  "059 307 1910 37.83 1"  "060 307 1920 37.84 1" 
>  [61] "061 307 1930 37.74 1"  "062 307 1940 37.76 1"  "063 307 1950 37.76 1" 
>  [64] "064 307 2000 37.64 1"  "065 307 2010 37.63 1"  "066 307 2020 38.06 1" 
>  [67] "067 307 2030 38.19 1"  "068 307 2040 38.35 1"  "069 307 2050 38.25 1" 
>  [70] "070 307 2100 37.86 1"  "071 307 2110 37.95 1"  "072 307 2120 37.95 1" 
>  [73] "073 307 2130 37.76 1"  "074 307 2140 37.60 1"  "075 307 2150 37.89 1" 
>  [76] "076 307 2200 37.86 1"  "077 307 2210 37.71 1"  "078 307 2220 37.78 1" 
>  [79] "079 307 2230 37.82 1"  "080 307 2240 37.76 1"  "081 307 2250 37.81 1" 
>  [82] "082 307 2300 37.84 1"  "083 307 2310 38.01 1"  "084 307 2320 38.10 1" 
>  [85] "085 307 2330 38.15 1"  "086 307 2340 37.92 1"  "087 307 2350 37.64 1" 
>  [88] "088 308 0000 37.70 1"  "089 308 0010 37.46 1"  "090 308 0020 37.41 1" 
>  [91] "091 308 0030 37.46 1"  "092 308 0040 37.56 1"  "093 308 0050 37.55 1" 
>  [94] "094 308 0100 37.75 1"  "095 308 0110 37.76 1"  "096 308 0120 37.73 1" 
>  [97] "097 308 0130 37.77 1"  "098 308 0140 38.01 1"  "099 308 0150 38.04 1" 
> [100] "100 308 0200 38.07 1" 
> > 
> > finger <- function(user, host = "localhost", port = 79, print = TRUE)
> + {
> +     if (!is.character(user))
> +         stop("user name must be a string")
> +     user <- paste(user,"\r\n")
> +     socket <- make.socket(host, port)
> +     on.exit(close.socket(socket))
> +     write.socket(socket, user)
> +     output <- character(0)
> +     repeat{
> +         ss <- read.socket(socket)
> +         if (ss == "") break
> +         output <- paste(output, ss)
> +     }
> +     close.socket(socket)
> +     if (print) cat(output)
> +     invisible(output)
> + }
> > try(finger("root"))  ## only works if your site provides a finger daemon
> socket error: Connection refused
> Error in make.socket(host, port) : socket not established
> > 
 OK
make[3]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[2]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make[1]: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2/tests'
make: Leaving directory `/usr/src/RPM/BUILD/R-3.1.2'
+ exit 0
Processing files: R-base-3.1.2-alt1.1
Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.59333
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.1.2
+ DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ export DOCDIR
+ rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.1.2
+ exit 0
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/R.css
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde.html
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde2D.html
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkfe.html
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpih.html
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpik.html
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpill.html
warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/locpoly.html
warning: File listed twice: /usr/lib64/R/library/MASS/html
warning: File listed twice: /usr/lib64/R/library/MASS/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Aids2.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Animals.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Boston.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Cars93.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Cushings.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/DDT.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/GAGurine.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Insurance.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/MASS-internal.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Melanoma.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Null.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/OME.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Pima.tr.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/R.css
warning: File listed twice: /usr/lib64/R/library/MASS/html/Rabbit.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Rubber.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/SP500.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Sitka.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Sitka89.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Skye.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/Traffic.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/UScereal.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/UScrime.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/VA.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/abbey.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/accdeaths.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/addterm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/anorexia.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/anova.negbin.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/area.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/bacteria.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/bandwidth.nrd.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/bcv.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/beav1.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/beav2.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/biopsy.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/birthwt.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/boxcox.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/cabbages.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/caith.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/cats.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/cement.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/chem.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/con2tr.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/confint.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/contr.sdif.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/coop.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/corresp.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/cov.rob.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/cov.trob.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/cpus.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/crabs.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/deaths.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/denumerate.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/dose.p.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/drivers.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/dropterm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/eagles.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/epil.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/eqscplot.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/farms.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/fgl.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/fitdistr.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/forbes.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/fractions.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/galaxies.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/gamma.dispersion.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/gamma.shape.glm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/gehan.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/genotype.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/geyser.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/gilgais.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/ginv.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/glm.convert.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/glm.nb.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/glmmPQL.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/hills.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/hist.scott.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/housing.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/huber.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/hubers.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/immer.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/isoMDS.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/kde2d.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/lda.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/ldahist.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/leuk.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/lm.gls.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/lm.ridge.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/loglm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/loglm1.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/logtrans.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/lqs.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/mammals.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/mca.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/mcycle.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/menarche.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/michelson.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/minn38.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/motors.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/muscle.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/mvrnorm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/negative.binomial.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/newcomb.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/nlschools.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/npk.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/npr1.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/oats.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/painters.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/pairs.lda.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/parcoord.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/petrol.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/phones.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/plot.lda.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/plot.mca.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/plot.profile.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/polr.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/predict.glmmPQL.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/predict.lda.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/predict.lqs.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/predict.mca.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/predict.qda.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/profile.glm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/qda.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/quine.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/rational.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/renumerate.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/rlm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/rms.curv.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/rnegbin.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/road.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/rotifer.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/sammon.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/ships.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/shoes.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/shrimp.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/shuttle.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/snails.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/stdres.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/steam.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/stepAIC.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/stormer.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/studres.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/summary.loglm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/summary.negbin.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/summary.rlm.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/survey.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/synth.tr.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/theta.md.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/topo.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/truehist.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/ucv.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/waders.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/whiteside.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/width.SJ.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/write.matrix.html
warning: File listed twice: /usr/lib64/R/library/MASS/html/wtloss.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/BunchKaufman-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/CAex.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/CHMfactor-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Cholesky-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Cholesky.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/CsparseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Diagonal.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Hilbert.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/KNex.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/KhatriRao.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/LU-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Matrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Matrix.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/MatrixFactorization-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/R.css
warning: File listed twice: /usr/lib64/R/library/Matrix/html/RsparseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Schur-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Schur.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/SparseM-conv.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Subassign-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/TsparseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/USCounties.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/Xtrct-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/abIndex-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/abIseq.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/all-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/all.equal-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/atomicVector-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/band.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/bandSparse.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/bdiag.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/cBind.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/chol.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/chol2inv-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/colSums.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/compMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/condest.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/ddenseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/ddiMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/denseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dgCMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dgRMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dgTMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dgeMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/diagU2N.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/diagonalMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dpoMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/drop0.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dsCMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dsRMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dsparseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dsyMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dtCMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dtRMatrix-class-def.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dtpMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/dtrMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/expand.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/expm.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/externalFormats.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/facmul.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/forceSymmetric.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/formatSparseM.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/generalMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/graph2T.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/image-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/indMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/index-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/invPerm.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/is.na-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/is.null.DN.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/isSymmetric-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/isTriangular.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/kronecker-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/ldenseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/ldiMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/lgeMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/lsparseMatrix-classes.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/lsyMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/ltrMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/lu.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/matrix-products.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/nMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/ndenseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/nearPD.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/ngeMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/nnzero.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/norm.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/nsparseMatrix-classes.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/nsyMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/ntrMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/number-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/pMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/printSpMatrix.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/qr-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/rankMatrix.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/rcond.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/rep2abI.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/replValue-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/rleDiff-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/rsparsematrix.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/solve-methods.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/spMatrix.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/sparse.model.matrix.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/sparseLU-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/sparseMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/sparseMatrix.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/sparseQR-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/sparseVector-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/sparseVector.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/symmetricMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/symmpart.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/triangularMatrix-class.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/unpack.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/unused-classes.html
warning: File listed twice: /usr/lib64/R/library/Matrix/html/updown.html
warning: File listed twice: /usr/lib64/R/library/base/html
warning: File listed twice: /usr/lib64/R/library/base/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/base/html/Arithmetic.html
warning: File listed twice: /usr/lib64/R/library/base/html/AsIs.html
warning: File listed twice: /usr/lib64/R/library/base/html/Bessel.html
warning: File listed twice: /usr/lib64/R/library/base/html/CallExternal.html
warning: File listed twice: /usr/lib64/R/library/base/html/Colon.html
warning: File listed twice: /usr/lib64/R/library/base/html/Comparison.html
warning: File listed twice: /usr/lib64/R/library/base/html/Constants.html
warning: File listed twice: /usr/lib64/R/library/base/html/Control.html
warning: File listed twice: /usr/lib64/R/library/base/html/Cstack_info.html
warning: File listed twice: /usr/lib64/R/library/base/html/DateTimeClasses.html
warning: File listed twice: /usr/lib64/R/library/base/html/Dates.html
warning: File listed twice: /usr/lib64/R/library/base/html/Defunct.html
warning: File listed twice: /usr/lib64/R/library/base/html/Deprecated.html
warning: File listed twice: /usr/lib64/R/library/base/html/Encoding.html
warning: File listed twice: /usr/lib64/R/library/base/html/EnvVar.html
warning: File listed twice: /usr/lib64/R/library/base/html/Extract.data.frame.html
warning: File listed twice: /usr/lib64/R/library/base/html/Extract.factor.html
warning: File listed twice: /usr/lib64/R/library/base/html/Extract.html
warning: File listed twice: /usr/lib64/R/library/base/html/Extremes.html
warning: File listed twice: /usr/lib64/R/library/base/html/Foreign-internal.html
warning: File listed twice: /usr/lib64/R/library/base/html/Foreign.html
warning: File listed twice: /usr/lib64/R/library/base/html/Hyperbolic.html
warning: File listed twice: /usr/lib64/R/library/base/html/ISOdatetime.html
warning: File listed twice: /usr/lib64/R/library/base/html/Internal.html
warning: File listed twice: /usr/lib64/R/library/base/html/InternalMethods.html
warning: File listed twice: /usr/lib64/R/library/base/html/La_version.html
warning: File listed twice: /usr/lib64/R/library/base/html/Last.value.html
warning: File listed twice: /usr/lib64/R/library/base/html/Log.html
warning: File listed twice: /usr/lib64/R/library/base/html/Logic.html
warning: File listed twice: /usr/lib64/R/library/base/html/LongVectors.html
warning: File listed twice: /usr/lib64/R/library/base/html/MathFun.html
warning: File listed twice: /usr/lib64/R/library/base/html/Memory-limits.html
warning: File listed twice: /usr/lib64/R/library/base/html/Memory.html
warning: File listed twice: /usr/lib64/R/library/base/html/NA.html
warning: File listed twice: /usr/lib64/R/library/base/html/NULL.html
warning: File listed twice: /usr/lib64/R/library/base/html/NumericConstants.html
warning: File listed twice: /usr/lib64/R/library/base/html/Ops.Date.html
warning: File listed twice: /usr/lib64/R/library/base/html/Paren.html
warning: File listed twice: /usr/lib64/R/library/base/html/Platform.html
warning: File listed twice: /usr/lib64/R/library/base/html/Primitive.html
warning: File listed twice: /usr/lib64/R/library/base/html/Quotes.html
warning: File listed twice: /usr/lib64/R/library/base/html/R.css
warning: File listed twice: /usr/lib64/R/library/base/html/Random-user.html
warning: File listed twice: /usr/lib64/R/library/base/html/Random.html
warning: File listed twice: /usr/lib64/R/library/base/html/RdUtils.html
warning: File listed twice: /usr/lib64/R/library/base/html/Recall.html
warning: File listed twice: /usr/lib64/R/library/base/html/Reserved.html
warning: File listed twice: /usr/lib64/R/library/base/html/Rhome.html
warning: File listed twice: /usr/lib64/R/library/base/html/Round.html
warning: File listed twice: /usr/lib64/R/library/base/html/Signals.html
warning: File listed twice: /usr/lib64/R/library/base/html/Special.html
warning: File listed twice: /usr/lib64/R/library/base/html/Startup.html
warning: File listed twice: /usr/lib64/R/library/base/html/Syntax.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.getenv.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.getpid.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.glob.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.info.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.localeconv.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.readlink.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.setFileTime.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.setenv.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.sleep.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.time.html
warning: File listed twice: /usr/lib64/R/library/base/html/Sys.which.html
warning: File listed twice: /usr/lib64/R/library/base/html/Trig.html
warning: File listed twice: /usr/lib64/R/library/base/html/UseMethod.html
warning: File listed twice: /usr/lib64/R/library/base/html/Vectorize.html
warning: File listed twice: /usr/lib64/R/library/base/html/Version.html
warning: File listed twice: /usr/lib64/R/library/base/html/abbreviate.html
warning: File listed twice: /usr/lib64/R/library/base/html/agrep.html
warning: File listed twice: /usr/lib64/R/library/base/html/all.equal.html
warning: File listed twice: /usr/lib64/R/library/base/html/all.html
warning: File listed twice: /usr/lib64/R/library/base/html/allnames.html
warning: File listed twice: /usr/lib64/R/library/base/html/any.html
warning: File listed twice: /usr/lib64/R/library/base/html/aperm.html
warning: File listed twice: /usr/lib64/R/library/base/html/append.html
warning: File listed twice: /usr/lib64/R/library/base/html/apply.html
warning: File listed twice: /usr/lib64/R/library/base/html/args.html
warning: File listed twice: /usr/lib64/R/library/base/html/array.html
warning: File listed twice: /usr/lib64/R/library/base/html/as.Date.html
warning: File listed twice: /usr/lib64/R/library/base/html/as.POSIXlt.html
warning: File listed twice: /usr/lib64/R/library/base/html/as.data.frame.html
warning: File listed twice: /usr/lib64/R/library/base/html/as.environment.html
warning: File listed twice: /usr/lib64/R/library/base/html/as.function.html
warning: File listed twice: /usr/lib64/R/library/base/html/assign.html
warning: File listed twice: /usr/lib64/R/library/base/html/assignOps.html
warning: File listed twice: /usr/lib64/R/library/base/html/attach.html
warning: File listed twice: /usr/lib64/R/library/base/html/attr.html
warning: File listed twice: /usr/lib64/R/library/base/html/attributes.html
warning: File listed twice: /usr/lib64/R/library/base/html/autoload.html
warning: File listed twice: /usr/lib64/R/library/base/html/backsolve.html
warning: File listed twice: /usr/lib64/R/library/base/html/base-defunct.html
warning: File listed twice: /usr/lib64/R/library/base/html/base-deprecated.html
warning: File listed twice: /usr/lib64/R/library/base/html/base-internal.html
warning: File listed twice: /usr/lib64/R/library/base/html/base-package.html
warning: File listed twice: /usr/lib64/R/library/base/html/basename.html
warning: File listed twice: /usr/lib64/R/library/base/html/bincode.html
warning: File listed twice: /usr/lib64/R/library/base/html/bindenv.html
warning: File listed twice: /usr/lib64/R/library/base/html/bitwise.html
warning: File listed twice: /usr/lib64/R/library/base/html/body.html
warning: File listed twice: /usr/lib64/R/library/base/html/bquote.html
warning: File listed twice: /usr/lib64/R/library/base/html/browser.html
warning: File listed twice: /usr/lib64/R/library/base/html/browserText.html
warning: File listed twice: /usr/lib64/R/library/base/html/builtins.html
warning: File listed twice: /usr/lib64/R/library/base/html/by.html
warning: File listed twice: /usr/lib64/R/library/base/html/c.html
warning: File listed twice: /usr/lib64/R/library/base/html/call.html
warning: File listed twice: /usr/lib64/R/library/base/html/callCC.html
warning: File listed twice: /usr/lib64/R/library/base/html/capabilities.html
warning: File listed twice: /usr/lib64/R/library/base/html/cat.html
warning: File listed twice: /usr/lib64/R/library/base/html/cbind.html
warning: File listed twice: /usr/lib64/R/library/base/html/char.expand.html
warning: File listed twice: /usr/lib64/R/library/base/html/character.html
warning: File listed twice: /usr/lib64/R/library/base/html/charmatch.html
warning: File listed twice: /usr/lib64/R/library/base/html/chartr.html
warning: File listed twice: /usr/lib64/R/library/base/html/chol.html
warning: File listed twice: /usr/lib64/R/library/base/html/chol2inv.html
warning: File listed twice: /usr/lib64/R/library/base/html/class.html
warning: File listed twice: /usr/lib64/R/library/base/html/col.html
warning: File listed twice: /usr/lib64/R/library/base/html/colSums.html
warning: File listed twice: /usr/lib64/R/library/base/html/colnames.html
warning: File listed twice: /usr/lib64/R/library/base/html/commandArgs.html
warning: File listed twice: /usr/lib64/R/library/base/html/comment.html
warning: File listed twice: /usr/lib64/R/library/base/html/complex.html
warning: File listed twice: /usr/lib64/R/library/base/html/conditions.html
warning: File listed twice: /usr/lib64/R/library/base/html/conflicts.html
warning: File listed twice: /usr/lib64/R/library/base/html/connections.html
warning: File listed twice: /usr/lib64/R/library/base/html/contributors.html
warning: File listed twice: /usr/lib64/R/library/base/html/copyright.html
warning: File listed twice: /usr/lib64/R/library/base/html/crossprod.html
warning: File listed twice: /usr/lib64/R/library/base/html/cumsum.html
warning: File listed twice: /usr/lib64/R/library/base/html/cut.POSIXt.html
warning: File listed twice: /usr/lib64/R/library/base/html/cut.html
warning: File listed twice: /usr/lib64/R/library/base/html/data.class.html
warning: File listed twice: /usr/lib64/R/library/base/html/data.frame.html
warning: File listed twice: /usr/lib64/R/library/base/html/data.matrix.html
warning: File listed twice: /usr/lib64/R/library/base/html/dataframeHelpers.html
warning: File listed twice: /usr/lib64/R/library/base/html/date.html
warning: File listed twice: /usr/lib64/R/library/base/html/dcf.html
warning: File listed twice: /usr/lib64/R/library/base/html/debug.html
warning: File listed twice: /usr/lib64/R/library/base/html/delayedAssign.html
warning: File listed twice: /usr/lib64/R/library/base/html/deparse.html
warning: File listed twice: /usr/lib64/R/library/base/html/deparseOpts.html
warning: File listed twice: /usr/lib64/R/library/base/html/det.html
warning: File listed twice: /usr/lib64/R/library/base/html/detach.html
warning: File listed twice: /usr/lib64/R/library/base/html/dev.html
warning: File listed twice: /usr/lib64/R/library/base/html/diag.html
warning: File listed twice: /usr/lib64/R/library/base/html/diff.html
warning: File listed twice: /usr/lib64/R/library/base/html/difftime.html
warning: File listed twice: /usr/lib64/R/library/base/html/dim.html
warning: File listed twice: /usr/lib64/R/library/base/html/dimnames.html
warning: File listed twice: /usr/lib64/R/library/base/html/do.call.html
warning: File listed twice: /usr/lib64/R/library/base/html/dontCheck.html
warning: File listed twice: /usr/lib64/R/library/base/html/double.html
warning: File listed twice: /usr/lib64/R/library/base/html/dput.html
warning: File listed twice: /usr/lib64/R/library/base/html/drop.html
warning: File listed twice: /usr/lib64/R/library/base/html/droplevels.html
warning: File listed twice: /usr/lib64/R/library/base/html/dump.html
warning: File listed twice: /usr/lib64/R/library/base/html/duplicated.html
warning: File listed twice: /usr/lib64/R/library/base/html/dynload.html
warning: File listed twice: /usr/lib64/R/library/base/html/eapply.html
warning: File listed twice: /usr/lib64/R/library/base/html/eigen.html
warning: File listed twice: /usr/lib64/R/library/base/html/encodeString.html
warning: File listed twice: /usr/lib64/R/library/base/html/environment.html
warning: File listed twice: /usr/lib64/R/library/base/html/eval.html
warning: File listed twice: /usr/lib64/R/library/base/html/exists.html
warning: File listed twice: /usr/lib64/R/library/base/html/expand.grid.html
warning: File listed twice: /usr/lib64/R/library/base/html/expression.html
warning: File listed twice: /usr/lib64/R/library/base/html/factor.html
warning: File listed twice: /usr/lib64/R/library/base/html/file.access.html
warning: File listed twice: /usr/lib64/R/library/base/html/file.choose.html
warning: File listed twice: /usr/lib64/R/library/base/html/file.info.html
warning: File listed twice: /usr/lib64/R/library/base/html/file.path.html
warning: File listed twice: /usr/lib64/R/library/base/html/file.show.html
warning: File listed twice: /usr/lib64/R/library/base/html/files.html
warning: File listed twice: /usr/lib64/R/library/base/html/files2.html
warning: File listed twice: /usr/lib64/R/library/base/html/find.package.html
warning: File listed twice: /usr/lib64/R/library/base/html/findInterval.html
warning: File listed twice: /usr/lib64/R/library/base/html/force.html
warning: File listed twice: /usr/lib64/R/library/base/html/formals.html
warning: File listed twice: /usr/lib64/R/library/base/html/format.html
warning: File listed twice: /usr/lib64/R/library/base/html/format.info.html
warning: File listed twice: /usr/lib64/R/library/base/html/format.pval.html
warning: File listed twice: /usr/lib64/R/library/base/html/formatDL.html
warning: File listed twice: /usr/lib64/R/library/base/html/formatc.html
warning: File listed twice: /usr/lib64/R/library/base/html/function.html
warning: File listed twice: /usr/lib64/R/library/base/html/funprog.html
warning: File listed twice: /usr/lib64/R/library/base/html/gc.html
warning: File listed twice: /usr/lib64/R/library/base/html/gc.time.html
warning: File listed twice: /usr/lib64/R/library/base/html/gctorture.html
warning: File listed twice: /usr/lib64/R/library/base/html/get.html
warning: File listed twice: /usr/lib64/R/library/base/html/getCallingDLL.html
warning: File listed twice: /usr/lib64/R/library/base/html/getDLLRegisteredRoutines.html
warning: File listed twice: /usr/lib64/R/library/base/html/getLoadedDLLs.html
warning: File listed twice: /usr/lib64/R/library/base/html/getNativeSymbolInfo.html
warning: File listed twice: /usr/lib64/R/library/base/html/gettext.html
warning: File listed twice: /usr/lib64/R/library/base/html/getwd.html
warning: File listed twice: /usr/lib64/R/library/base/html/gl.html
warning: File listed twice: /usr/lib64/R/library/base/html/grep.html
warning: File listed twice: /usr/lib64/R/library/base/html/grepRaw.html
warning: File listed twice: /usr/lib64/R/library/base/html/groupGeneric.html
warning: File listed twice: /usr/lib64/R/library/base/html/gzcon.html
warning: File listed twice: /usr/lib64/R/library/base/html/hexmode.html
warning: File listed twice: /usr/lib64/R/library/base/html/iconv.html
warning: File listed twice: /usr/lib64/R/library/base/html/icuSetCollate.html
warning: File listed twice: /usr/lib64/R/library/base/html/identical.html
warning: File listed twice: /usr/lib64/R/library/base/html/identity.html
warning: File listed twice: /usr/lib64/R/library/base/html/ifelse.html
warning: File listed twice: /usr/lib64/R/library/base/html/integer.html
warning: File listed twice: /usr/lib64/R/library/base/html/interaction.html
warning: File listed twice: /usr/lib64/R/library/base/html/interactive.html
warning: File listed twice: /usr/lib64/R/library/base/html/invisible.html
warning: File listed twice: /usr/lib64/R/library/base/html/is.finite.html
warning: File listed twice: /usr/lib64/R/library/base/html/is.function.html
warning: File listed twice: /usr/lib64/R/library/base/html/is.language.html
warning: File listed twice: /usr/lib64/R/library/base/html/is.object.html
warning: File listed twice: /usr/lib64/R/library/base/html/is.recursive.html
warning: File listed twice: /usr/lib64/R/library/base/html/is.single.html
warning: File listed twice: /usr/lib64/R/library/base/html/is.unsorted.html
warning: File listed twice: /usr/lib64/R/library/base/html/isR.html
warning: File listed twice: /usr/lib64/R/library/base/html/isS4.html
warning: File listed twice: /usr/lib64/R/library/base/html/isSymmetric.html
warning: File listed twice: /usr/lib64/R/library/base/html/jitter.html
warning: File listed twice: /usr/lib64/R/library/base/html/kappa.html
warning: File listed twice: /usr/lib64/R/library/base/html/kronecker.html
warning: File listed twice: /usr/lib64/R/library/base/html/l10n_info.html
warning: File listed twice: /usr/lib64/R/library/base/html/labels.html
warning: File listed twice: /usr/lib64/R/library/base/html/lapply.html
warning: File listed twice: /usr/lib64/R/library/base/html/lazyload.html
warning: File listed twice: /usr/lib64/R/library/base/html/length.html
warning: File listed twice: /usr/lib64/R/library/base/html/levels.html
warning: File listed twice: /usr/lib64/R/library/base/html/libPaths.html
warning: File listed twice: /usr/lib64/R/library/base/html/library.dynam.html
warning: File listed twice: /usr/lib64/R/library/base/html/library.html
warning: File listed twice: /usr/lib64/R/library/base/html/license.html
warning: File listed twice: /usr/lib64/R/library/base/html/list.files.html
warning: File listed twice: /usr/lib64/R/library/base/html/list.html
warning: File listed twice: /usr/lib64/R/library/base/html/list2env.html
warning: File listed twice: /usr/lib64/R/library/base/html/load.html
warning: File listed twice: /usr/lib64/R/library/base/html/locales.html
warning: File listed twice: /usr/lib64/R/library/base/html/logical.html
warning: File listed twice: /usr/lib64/R/library/base/html/lower.tri.html
warning: File listed twice: /usr/lib64/R/library/base/html/ls.html
warning: File listed twice: /usr/lib64/R/library/base/html/make.names.html
warning: File listed twice: /usr/lib64/R/library/base/html/make.unique.html
warning: File listed twice: /usr/lib64/R/library/base/html/mapply.html
warning: File listed twice: /usr/lib64/R/library/base/html/margin.table.html
warning: File listed twice: /usr/lib64/R/library/base/html/mat.or.vec.html
warning: File listed twice: /usr/lib64/R/library/base/html/match.arg.html
warning: File listed twice: /usr/lib64/R/library/base/html/match.call.html
warning: File listed twice: /usr/lib64/R/library/base/html/match.fun.html
warning: File listed twice: /usr/lib64/R/library/base/html/match.html
warning: File listed twice: /usr/lib64/R/library/base/html/matmult.html
warning: File listed twice: /usr/lib64/R/library/base/html/matrix.html
warning: File listed twice: /usr/lib64/R/library/base/html/maxCol.html
warning: File listed twice: /usr/lib64/R/library/base/html/mean.html
warning: File listed twice: /usr/lib64/R/library/base/html/memCompress.html
warning: File listed twice: /usr/lib64/R/library/base/html/memory.profile.html
warning: File listed twice: /usr/lib64/R/library/base/html/merge.html
warning: File listed twice: /usr/lib64/R/library/base/html/message.html
warning: File listed twice: /usr/lib64/R/library/base/html/missing.html
warning: File listed twice: /usr/lib64/R/library/base/html/mode.html
warning: File listed twice: /usr/lib64/R/library/base/html/name.html
warning: File listed twice: /usr/lib64/R/library/base/html/names.html
warning: File listed twice: /usr/lib64/R/library/base/html/nargs.html
warning: File listed twice: /usr/lib64/R/library/base/html/nchar.html
warning: File listed twice: /usr/lib64/R/library/base/html/nlevels.html
warning: File listed twice: /usr/lib64/R/library/base/html/noquote.html
warning: File listed twice: /usr/lib64/R/library/base/html/norm.html
warning: File listed twice: /usr/lib64/R/library/base/html/normalizePath.html
warning: File listed twice: /usr/lib64/R/library/base/html/notyet.html
warning: File listed twice: /usr/lib64/R/library/base/html/nrow.html
warning: File listed twice: /usr/lib64/R/library/base/html/ns-dblcolon.html
warning: File listed twice: /usr/lib64/R/library/base/html/ns-hooks.html
warning: File listed twice: /usr/lib64/R/library/base/html/ns-internal.html
warning: File listed twice: /usr/lib64/R/library/base/html/ns-load.html
warning: File listed twice: /usr/lib64/R/library/base/html/ns-reflect.html
warning: File listed twice: /usr/lib64/R/library/base/html/ns-topenv.html
warning: File listed twice: /usr/lib64/R/library/base/html/numeric.html
warning: File listed twice: /usr/lib64/R/library/base/html/numeric_version.html
warning: File listed twice: /usr/lib64/R/library/base/html/octmode.html
warning: File listed twice: /usr/lib64/R/library/base/html/on.exit.html
warning: File listed twice: /usr/lib64/R/library/base/html/options.html
warning: File listed twice: /usr/lib64/R/library/base/html/order.html
warning: File listed twice: /usr/lib64/R/library/base/html/outer.html
warning: File listed twice: /usr/lib64/R/library/base/html/parse.html
warning: File listed twice: /usr/lib64/R/library/base/html/paste.html
warning: File listed twice: /usr/lib64/R/library/base/html/path.expand.html
warning: File listed twice: /usr/lib64/R/library/base/html/pmatch.html
warning: File listed twice: /usr/lib64/R/library/base/html/polyroot.html
warning: File listed twice: /usr/lib64/R/library/base/html/pos.to.env.html
warning: File listed twice: /usr/lib64/R/library/base/html/pretty.html
warning: File listed twice: /usr/lib64/R/library/base/html/print.dataframe.html
warning: File listed twice: /usr/lib64/R/library/base/html/print.default.html
warning: File listed twice: /usr/lib64/R/library/base/html/print.html
warning: File listed twice: /usr/lib64/R/library/base/html/prmatrix.html
warning: File listed twice: /usr/lib64/R/library/base/html/proc.time.html
warning: File listed twice: /usr/lib64/R/library/base/html/prod.html
warning: File listed twice: /usr/lib64/R/library/base/html/prop.table.html
warning: File listed twice: /usr/lib64/R/library/base/html/pushBack.html
warning: File listed twice: /usr/lib64/R/library/base/html/qr.html
warning: File listed twice: /usr/lib64/R/library/base/html/qraux.html
warning: File listed twice: /usr/lib64/R/library/base/html/quit.html
warning: File listed twice: /usr/lib64/R/library/base/html/range.html
warning: File listed twice: /usr/lib64/R/library/base/html/rank.html
warning: File listed twice: /usr/lib64/R/library/base/html/rapply.html
warning: File listed twice: /usr/lib64/R/library/base/html/raw.html
warning: File listed twice: /usr/lib64/R/library/base/html/rawConnection.html
warning: File listed twice: /usr/lib64/R/library/base/html/rawConversion.html
warning: File listed twice: /usr/lib64/R/library/base/html/readBin.html
warning: File listed twice: /usr/lib64/R/library/base/html/readChar.html
warning: File listed twice: /usr/lib64/R/library/base/html/readLines.html
warning: File listed twice: /usr/lib64/R/library/base/html/readRDS.html
warning: File listed twice: /usr/lib64/R/library/base/html/readRenviron.html
warning: File listed twice: /usr/lib64/R/library/base/html/readline.html
warning: File listed twice: /usr/lib64/R/library/base/html/reg.finalizer.html
warning: File listed twice: /usr/lib64/R/library/base/html/regex.html
warning: File listed twice: /usr/lib64/R/library/base/html/regmatches.html
warning: File listed twice: /usr/lib64/R/library/base/html/rep.html
warning: File listed twice: /usr/lib64/R/library/base/html/replace.html
warning: File listed twice: /usr/lib64/R/library/base/html/rev.html
warning: File listed twice: /usr/lib64/R/library/base/html/rle.html
warning: File listed twice: /usr/lib64/R/library/base/html/rm.html
warning: File listed twice: /usr/lib64/R/library/base/html/round.POSIXt.html
warning: File listed twice: /usr/lib64/R/library/base/html/row.html
warning: File listed twice: /usr/lib64/R/library/base/html/row.names.html
warning: File listed twice: /usr/lib64/R/library/base/html/rowsum.html
warning: File listed twice: /usr/lib64/R/library/base/html/sQuote.html
warning: File listed twice: /usr/lib64/R/library/base/html/sample.html
warning: File listed twice: /usr/lib64/R/library/base/html/save.html
warning: File listed twice: /usr/lib64/R/library/base/html/scale.html
warning: File listed twice: /usr/lib64/R/library/base/html/scan.html
warning: File listed twice: /usr/lib64/R/library/base/html/search.html
warning: File listed twice: /usr/lib64/R/library/base/html/seek.html
warning: File listed twice: /usr/lib64/R/library/base/html/seq.Date.html
warning: File listed twice: /usr/lib64/R/library/base/html/seq.POSIXt.html
warning: File listed twice: /usr/lib64/R/library/base/html/seq.html
warning: File listed twice: /usr/lib64/R/library/base/html/sequence.html
warning: File listed twice: /usr/lib64/R/library/base/html/serialize.html
warning: File listed twice: /usr/lib64/R/library/base/html/setTimeLimit.html
warning: File listed twice: /usr/lib64/R/library/base/html/sets.html
warning: File listed twice: /usr/lib64/R/library/base/html/shQuote.html
warning: File listed twice: /usr/lib64/R/library/base/html/showConnections.html
warning: File listed twice: /usr/lib64/R/library/base/html/sign.html
warning: File listed twice: /usr/lib64/R/library/base/html/sink.html
warning: File listed twice: /usr/lib64/R/library/base/html/slice.index.html
warning: File listed twice: /usr/lib64/R/library/base/html/slotOp.html
warning: File listed twice: /usr/lib64/R/library/base/html/socketSelect.html
warning: File listed twice: /usr/lib64/R/library/base/html/solve.html
warning: File listed twice: /usr/lib64/R/library/base/html/sort.html
warning: File listed twice: /usr/lib64/R/library/base/html/source.html
warning: File listed twice: /usr/lib64/R/library/base/html/split.html
warning: File listed twice: /usr/lib64/R/library/base/html/sprintf.html
warning: File listed twice: /usr/lib64/R/library/base/html/srcfile.html
warning: File listed twice: /usr/lib64/R/library/base/html/standardGeneric.html
warning: File listed twice: /usr/lib64/R/library/base/html/stop.html
warning: File listed twice: /usr/lib64/R/library/base/html/stopifnot.html
warning: File listed twice: /usr/lib64/R/library/base/html/strptime.html
warning: File listed twice: /usr/lib64/R/library/base/html/strsplit.html
warning: File listed twice: /usr/lib64/R/library/base/html/strtoi.html
warning: File listed twice: /usr/lib64/R/library/base/html/strtrim.html
warning: File listed twice: /usr/lib64/R/library/base/html/structure.html
warning: File listed twice: /usr/lib64/R/library/base/html/strwrap.html
warning: File listed twice: /usr/lib64/R/library/base/html/subset.html
warning: File listed twice: /usr/lib64/R/library/base/html/substitute.html
warning: File listed twice: /usr/lib64/R/library/base/html/substr.html
warning: File listed twice: /usr/lib64/R/library/base/html/sum.html
warning: File listed twice: /usr/lib64/R/library/base/html/summary.html
warning: File listed twice: /usr/lib64/R/library/base/html/svd.html
warning: File listed twice: /usr/lib64/R/library/base/html/sweep.html
warning: File listed twice: /usr/lib64/R/library/base/html/switch.html
warning: File listed twice: /usr/lib64/R/library/base/html/sys.parent.html
warning: File listed twice: /usr/lib64/R/library/base/html/sys.source.html
warning: File listed twice: /usr/lib64/R/library/base/html/system.file.html
warning: File listed twice: /usr/lib64/R/library/base/html/system.html
warning: File listed twice: /usr/lib64/R/library/base/html/system.time.html
warning: File listed twice: /usr/lib64/R/library/base/html/system2.html
warning: File listed twice: /usr/lib64/R/library/base/html/t.html
warning: File listed twice: /usr/lib64/R/library/base/html/table.html
warning: File listed twice: /usr/lib64/R/library/base/html/tabulate.html
warning: File listed twice: /usr/lib64/R/library/base/html/tapply.html
warning: File listed twice: /usr/lib64/R/library/base/html/taskCallback.html
warning: File listed twice: /usr/lib64/R/library/base/html/taskCallbackManager.html
warning: File listed twice: /usr/lib64/R/library/base/html/taskCallbackNames.html
warning: File listed twice: /usr/lib64/R/library/base/html/tempfile.html
warning: File listed twice: /usr/lib64/R/library/base/html/textconnections.html
warning: File listed twice: /usr/lib64/R/library/base/html/tilde.html
warning: File listed twice: /usr/lib64/R/library/base/html/timezones.html
warning: File listed twice: /usr/lib64/R/library/base/html/toString.html
warning: File listed twice: /usr/lib64/R/library/base/html/trace.html
warning: File listed twice: /usr/lib64/R/library/base/html/traceback.html
warning: File listed twice: /usr/lib64/R/library/base/html/tracemem.html
warning: File listed twice: /usr/lib64/R/library/base/html/transform.html
warning: File listed twice: /usr/lib64/R/library/base/html/try.html
warning: File listed twice: /usr/lib64/R/library/base/html/typeof.html
warning: File listed twice: /usr/lib64/R/library/base/html/unique.html
warning: File listed twice: /usr/lib64/R/library/base/html/unlink.html
warning: File listed twice: /usr/lib64/R/library/base/html/unlist.html
warning: File listed twice: /usr/lib64/R/library/base/html/unname.html
warning: File listed twice: /usr/lib64/R/library/base/html/userhooks.html
warning: File listed twice: /usr/lib64/R/library/base/html/utf8Conversion.html
warning: File listed twice: /usr/lib64/R/library/base/html/vector.html
warning: File listed twice: /usr/lib64/R/library/base/html/warning.html
warning: File listed twice: /usr/lib64/R/library/base/html/warnings.html
warning: File listed twice: /usr/lib64/R/library/base/html/weekday.POSIXt.html
warning: File listed twice: /usr/lib64/R/library/base/html/which.html
warning: File listed twice: /usr/lib64/R/library/base/html/which.min.html
warning: File listed twice: /usr/lib64/R/library/base/html/with.html
warning: File listed twice: /usr/lib64/R/library/base/html/withVisible.html
warning: File listed twice: /usr/lib64/R/library/base/html/write.html
warning: File listed twice: /usr/lib64/R/library/base/html/writeLines.html
warning: File listed twice: /usr/lib64/R/library/base/html/xtfrm.html
warning: File listed twice: /usr/lib64/R/library/base/html/zMachine.html
warning: File listed twice: /usr/lib64/R/library/base/html/zScript.html
warning: File listed twice: /usr/lib64/R/library/base/html/zapsmall.html
warning: File listed twice: /usr/lib64/R/library/base/html/zpackages.html
warning: File listed twice: /usr/lib64/R/library/base/html/zutils.html
warning: File listed twice: /usr/lib64/R/library/boot/html
warning: File listed twice: /usr/lib64/R/library/boot/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/boot/html/EEF.profile.html
warning: File listed twice: /usr/lib64/R/library/boot/html/Imp.Estimates.html
warning: File listed twice: /usr/lib64/R/library/boot/html/R.css
warning: File listed twice: /usr/lib64/R/library/boot/html/abc.ci.html
warning: File listed twice: /usr/lib64/R/library/boot/html/acme.html
warning: File listed twice: /usr/lib64/R/library/boot/html/aids.html
warning: File listed twice: /usr/lib64/R/library/boot/html/aircondit.html
warning: File listed twice: /usr/lib64/R/library/boot/html/amis.html
warning: File listed twice: /usr/lib64/R/library/boot/html/aml.html
warning: File listed twice: /usr/lib64/R/library/boot/html/beaver.html
warning: File listed twice: /usr/lib64/R/library/boot/html/bigcity.html
warning: File listed twice: /usr/lib64/R/library/boot/html/boot-practicals.html
warning: File listed twice: /usr/lib64/R/library/boot/html/boot.array.html
warning: File listed twice: /usr/lib64/R/library/boot/html/boot.ci.html
warning: File listed twice: /usr/lib64/R/library/boot/html/boot.html
warning: File listed twice: /usr/lib64/R/library/boot/html/brambles.html
warning: File listed twice: /usr/lib64/R/library/boot/html/breslow.html
warning: File listed twice: /usr/lib64/R/library/boot/html/calcium.html
warning: File listed twice: /usr/lib64/R/library/boot/html/cane.html
warning: File listed twice: /usr/lib64/R/library/boot/html/capability.html
warning: File listed twice: /usr/lib64/R/library/boot/html/catsM.html
warning: File listed twice: /usr/lib64/R/library/boot/html/cav.html
warning: File listed twice: /usr/lib64/R/library/boot/html/cd4.html
warning: File listed twice: /usr/lib64/R/library/boot/html/cd4.nested.html
warning: File listed twice: /usr/lib64/R/library/boot/html/censboot.html
warning: File listed twice: /usr/lib64/R/library/boot/html/channing.html
warning: File listed twice: /usr/lib64/R/library/boot/html/claridge.html
warning: File listed twice: /usr/lib64/R/library/boot/html/cloth.html
warning: File listed twice: /usr/lib64/R/library/boot/html/co.transfer.html
warning: File listed twice: /usr/lib64/R/library/boot/html/coal.html
warning: File listed twice: /usr/lib64/R/library/boot/html/control.html
warning: File listed twice: /usr/lib64/R/library/boot/html/corr.html
warning: File listed twice: /usr/lib64/R/library/boot/html/cum3.html
warning: File listed twice: /usr/lib64/R/library/boot/html/cv.glm.html
warning: File listed twice: /usr/lib64/R/library/boot/html/darwin.html
warning: File listed twice: /usr/lib64/R/library/boot/html/dogs.html
warning: File listed twice: /usr/lib64/R/library/boot/html/downs.bc.html
warning: File listed twice: /usr/lib64/R/library/boot/html/ducks.html
warning: File listed twice: /usr/lib64/R/library/boot/html/empinf.html
warning: File listed twice: /usr/lib64/R/library/boot/html/envelope.html
warning: File listed twice: /usr/lib64/R/library/boot/html/exp.tilt.html
warning: File listed twice: /usr/lib64/R/library/boot/html/fir.html
warning: File listed twice: /usr/lib64/R/library/boot/html/freq.array.html
warning: File listed twice: /usr/lib64/R/library/boot/html/frets.html
warning: File listed twice: /usr/lib64/R/library/boot/html/glm.diag.html
warning: File listed twice: /usr/lib64/R/library/boot/html/glm.diag.plots.html
warning: File listed twice: /usr/lib64/R/library/boot/html/gravity.html
warning: File listed twice: /usr/lib64/R/library/boot/html/hirose.html
warning: File listed twice: /usr/lib64/R/library/boot/html/imp.weights.html
warning: File listed twice: /usr/lib64/R/library/boot/html/inv.logit.html
warning: File listed twice: /usr/lib64/R/library/boot/html/islay.html
warning: File listed twice: /usr/lib64/R/library/boot/html/jack.after.boot.html
warning: File listed twice: /usr/lib64/R/library/boot/html/k3.linear.html
warning: File listed twice: /usr/lib64/R/library/boot/html/linear.approx.html
warning: File listed twice: /usr/lib64/R/library/boot/html/lines.saddle.distn.html
warning: File listed twice: /usr/lib64/R/library/boot/html/logit.html
warning: File listed twice: /usr/lib64/R/library/boot/html/manaus.html
warning: File listed twice: /usr/lib64/R/library/boot/html/melanoma.html
warning: File listed twice: /usr/lib64/R/library/boot/html/motor.html
warning: File listed twice: /usr/lib64/R/library/boot/html/neuro.html
warning: File listed twice: /usr/lib64/R/library/boot/html/nitrofen.html
warning: File listed twice: /usr/lib64/R/library/boot/html/nodal.html
warning: File listed twice: /usr/lib64/R/library/boot/html/norm.ci.html
warning: File listed twice: /usr/lib64/R/library/boot/html/nuclear.html
warning: File listed twice: /usr/lib64/R/library/boot/html/paulsen.html
warning: File listed twice: /usr/lib64/R/library/boot/html/plot.boot.html
warning: File listed twice: /usr/lib64/R/library/boot/html/poisons.html
warning: File listed twice: /usr/lib64/R/library/boot/html/polar.html
warning: File listed twice: /usr/lib64/R/library/boot/html/print.boot.html
warning: File listed twice: /usr/lib64/R/library/boot/html/print.bootci.html
warning: File listed twice: /usr/lib64/R/library/boot/html/print.saddle.distn.html
warning: File listed twice: /usr/lib64/R/library/boot/html/print.simplex.html
warning: File listed twice: /usr/lib64/R/library/boot/html/remission.html
warning: File listed twice: /usr/lib64/R/library/boot/html/saddle.distn.html
warning: File listed twice: /usr/lib64/R/library/boot/html/saddle.distn.object.html
warning: File listed twice: /usr/lib64/R/library/boot/html/saddle.html
warning: File listed twice: /usr/lib64/R/library/boot/html/salinity.html
warning: File listed twice: /usr/lib64/R/library/boot/html/simplex.html
warning: File listed twice: /usr/lib64/R/library/boot/html/simplex.object.html
warning: File listed twice: /usr/lib64/R/library/boot/html/smooth.f.html
warning: File listed twice: /usr/lib64/R/library/boot/html/sunspot.html
warning: File listed twice: /usr/lib64/R/library/boot/html/survival.html
warning: File listed twice: /usr/lib64/R/library/boot/html/tau.html
warning: File listed twice: /usr/lib64/R/library/boot/html/tilt.boot.html
warning: File listed twice: /usr/lib64/R/library/boot/html/tsboot.html
warning: File listed twice: /usr/lib64/R/library/boot/html/tuna.html
warning: File listed twice: /usr/lib64/R/library/boot/html/urine.html
warning: File listed twice: /usr/lib64/R/library/boot/html/var.linear.html
warning: File listed twice: /usr/lib64/R/library/boot/html/wool.html
warning: File listed twice: /usr/lib64/R/library/class/html
warning: File listed twice: /usr/lib64/R/library/class/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/class/html/R.css
warning: File listed twice: /usr/lib64/R/library/class/html/SOM.html
warning: File listed twice: /usr/lib64/R/library/class/html/batchSOM.html
warning: File listed twice: /usr/lib64/R/library/class/html/condense.html
warning: File listed twice: /usr/lib64/R/library/class/html/knn.cv.html
warning: File listed twice: /usr/lib64/R/library/class/html/knn.html
warning: File listed twice: /usr/lib64/R/library/class/html/knn1.html
warning: File listed twice: /usr/lib64/R/library/class/html/lvq1.html
warning: File listed twice: /usr/lib64/R/library/class/html/lvq2.html
warning: File listed twice: /usr/lib64/R/library/class/html/lvq3.html
warning: File listed twice: /usr/lib64/R/library/class/html/lvqinit.html
warning: File listed twice: /usr/lib64/R/library/class/html/lvqtest.html
warning: File listed twice: /usr/lib64/R/library/class/html/multiedit.html
warning: File listed twice: /usr/lib64/R/library/class/html/olvq1.html
warning: File listed twice: /usr/lib64/R/library/class/html/reduce.nn.html
warning: File listed twice: /usr/lib64/R/library/class/html/somgrid.html
warning: File listed twice: /usr/lib64/R/library/cluster/html
warning: File listed twice: /usr/lib64/R/library/cluster/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/R.css
warning: File listed twice: /usr/lib64/R/library/cluster/html/agnes.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/agnes.object.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/agriculture.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/animals.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/bannerplot.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/chorSub.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/clara.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/clara.object.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/clusGap.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/clusplot.default.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/clusplot.partition.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/cluster-internal.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/coef.hclust.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/daisy.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/diana.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/dissimilarity.object.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/ellipsoidhull.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/fanny.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/fanny.object.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/flower.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/lower.to.upper.tri.inds.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/mona.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/mona.object.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/pam.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/pam.object.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/partition.object.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/plantTraits.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/plot.agnes.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/plot.diana.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/plot.mona.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/plot.partition.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/pltree.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/pltree.twins.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/pluton.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/predict.ellipsoid.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/print.agnes.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/print.clara.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/print.diana.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/print.dissimilarity.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/print.fanny.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/print.mona.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/print.pam.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/ruspini.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/silhouette.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/sizeDiss.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/summary.agnes.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/summary.clara.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/summary.diana.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/summary.mona.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/summary.pam.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/twins.object.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/volume.ellipsoid.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/votes.repub.html
warning: File listed twice: /usr/lib64/R/library/cluster/html/xclara.html
warning: File listed twice: /usr/lib64/R/library/codetools/html
warning: File listed twice: /usr/lib64/R/library/codetools/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/codetools/html/R.css
warning: File listed twice: /usr/lib64/R/library/codetools/html/checkUsage.html
warning: File listed twice: /usr/lib64/R/library/codetools/html/codetools.html
warning: File listed twice: /usr/lib64/R/library/codetools/html/findGlobals.html
warning: File listed twice: /usr/lib64/R/library/codetools/html/showTree.html
warning: File listed twice: /usr/lib64/R/library/compiler/html
warning: File listed twice: /usr/lib64/R/library/compiler/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/compiler/html/R.css
warning: File listed twice: /usr/lib64/R/library/compiler/html/compile.html
warning: File listed twice: /usr/lib64/R/library/datasets/html
warning: File listed twice: /usr/lib64/R/library/datasets/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/AirPassengers.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/BJsales.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/BOD.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/ChickWeight.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/DNase.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/EuStockMarkets.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Formaldehyde.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/HairEyeColor.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Harman23.cor.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Harman74.cor.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Indometh.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/InsectSprays.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/JohnsonJohnson.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/LakeHuron.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/LifeCycleSavings.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Loblolly.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Nile.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Orange.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/OrchardSprays.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/PlantGrowth.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Puromycin.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/R.css
warning: File listed twice: /usr/lib64/R/library/datasets/html/Theoph.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/Titanic.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/ToothGrowth.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/UCBAdmissions.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/UKDriverDeaths.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/UKLungDeaths.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/UKgas.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/USAccDeaths.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/USArrests.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/USJudgeRatings.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/USPersonalExpenditure.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/VADeaths.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/WWWusage.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/WorldPhones.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/ability.cov.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/airmiles.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/airquality.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/anscombe.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/attenu.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/attitude.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/austres.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/beavers.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/cars.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/chickwts.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/co2.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/crimtab.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/datasets-package.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/discoveries.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/esoph.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/euro.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/eurodist.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/faithful.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/freeny.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/infert.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/iris.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/islands.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/lh.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/longley.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/lynx.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/morley.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/mtcars.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/nhtemp.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/nottem.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/npk.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/occupationalStatus.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/precip.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/presidents.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/pressure.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/quakes.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/randu.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/rivers.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/rock.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/sleep.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/stackloss.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/state.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/sunspot.month.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/sunspot.year.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/sunspots.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/swiss.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/treering.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/trees.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/uspop.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/volcano.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/warpbreaks.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/women.html
warning: File listed twice: /usr/lib64/R/library/datasets/html/zCO2.html
warning: File listed twice: /usr/lib64/R/library/foreign/html
warning: File listed twice: /usr/lib64/R/library/foreign/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/R.css
warning: File listed twice: /usr/lib64/R/library/foreign/html/lookup.xport.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.S.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.arff.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.dbf.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.dta.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.epiinfo.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.mtp.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.octave.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.spss.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.ssd.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.systat.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/read.xport.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/write.arff.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/write.dbf.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/write.dta.html
warning: File listed twice: /usr/lib64/R/library/foreign/html/write.foreign.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/Devices.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/Hershey.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/Japanese.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/R.css
warning: File listed twice: /usr/lib64/R/library/grDevices/html/Type1Font.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/adjustcolor.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/as.graphicsAnnot.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/as.raster.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/axisTicks.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/boxplot.stats.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/cairo.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/check.options.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/chull.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/cm.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/col2rgb.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/colorRamp.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/colors.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/contourLines.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/convertColor.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/densCols.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/dev.capabilities.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/dev.capture.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/dev.flush.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/dev.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/dev.interactive.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/dev.size.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/dev2.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/dev2bitmap.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/devAskNewPage.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/embedFonts.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/extendrange.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/getGraphicsEvent.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/grDevices-package.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/gray.colors.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/gray.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/hcl.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/hsv.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/make.rgb.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/n2mfrow.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/nclass.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/palette.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/palettes.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/pdf.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/pdf.options.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/pictex.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/plotmath.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/png.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/postscript.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/postscriptFonts.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/pretty.Date.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/ps.options.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/quartz.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/quartzFonts.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/recordGraphics.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/recordplot.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/rgb.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/rgb2hsv.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/savePlot.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/trans3d.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/x11.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/x11Fonts.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/xfig.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/xy.coords.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/xyTable.html
warning: File listed twice: /usr/lib64/R/library/grDevices/html/xyz.coords.html
warning: File listed twice: /usr/lib64/R/library/graphics/html
warning: File listed twice: /usr/lib64/R/library/graphics/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/R.css
warning: File listed twice: /usr/lib64/R/library/graphics/html/abline.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/arrows.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/assocplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/axTicks.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/axis.POSIXct.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/axis.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/barplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/box.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/boxplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/boxplot.matrix.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/bxp.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/cdplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/clip.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/contour.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/convertXY.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/coplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/curve.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/dotchart.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/filled.contour.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/fourfoldplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/frame.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/graphics-defunct.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/graphics-package.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/grid.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/hist.POSIXt.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/hist.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/identify.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/image.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/layout.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/legend.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/lines.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/locator.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/matplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/mosaicplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/mtext.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/pairs.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/panel.smooth.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/par.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/persp.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/pie.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.dataframe.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.default.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.design.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.factor.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.formula.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.table.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.window.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plot.xy.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/plothistogram.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/points.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/polygon.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/polypath.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/rasterImage.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/rect.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/rug.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/screen.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/segments.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/smoothScatter.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/spineplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/stars.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/stem.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/stripchart.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/strwidth.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/sunflowerplot.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/symbols.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/text.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/title.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/units.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/xspline.html
warning: File listed twice: /usr/lib64/R/library/graphics/html/zAxis.html
warning: File listed twice: /usr/lib64/R/library/grid/html
warning: File listed twice: /usr/lib64/R/library/grid/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/grid/html/Grid.html
warning: File listed twice: /usr/lib64/R/library/grid/html/R.css
warning: File listed twice: /usr/lib64/R/library/grid/html/absolute.size.html
warning: File listed twice: /usr/lib64/R/library/grid/html/arrow.html
warning: File listed twice: /usr/lib64/R/library/grid/html/calcStringMetric.html
warning: File listed twice: /usr/lib64/R/library/grid/html/current.viewport.html
warning: File listed twice: /usr/lib64/R/library/grid/html/dataViewport.html
warning: File listed twice: /usr/lib64/R/library/grid/html/depth.html
warning: File listed twice: /usr/lib64/R/library/grid/html/drawDetails.html
warning: File listed twice: /usr/lib64/R/library/grid/html/editDetails.html
warning: File listed twice: /usr/lib64/R/library/grid/html/explode.html
warning: File listed twice: /usr/lib64/R/library/grid/html/gEdit.html
warning: File listed twice: /usr/lib64/R/library/grid/html/gPath.html
warning: File listed twice: /usr/lib64/R/library/grid/html/getNames.html
warning: File listed twice: /usr/lib64/R/library/grid/html/gpar.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid-defunct.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid-internal.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid-package.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.DLapply.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.add.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.bezier.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.cap.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.circle.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.clip.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.convert.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.copy.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.curve.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.delay.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.display.list.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.draw.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.edit.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.force.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.frame.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.function.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.get.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.grab.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.grep.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.grill.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.grob.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.layout.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.lines.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.locator.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.ls.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.move.to.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.newpage.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.null.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.pack.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.path.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.place.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.plot.and.legend.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.points.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.polygon.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.pretty.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.raster.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.record.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.rect.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.refresh.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.remove.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.reorder.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.roundrect.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.segments.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.set.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.show.layout.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.show.viewport.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.text.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.xaxis.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.xspline.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grid.yaxis.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grobName.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grobWidth.html
warning: File listed twice: /usr/lib64/R/library/grid/html/grobX.html
warning: File listed twice: /usr/lib64/R/library/grid/html/legendGrob.html
warning: File listed twice: /usr/lib64/R/library/grid/html/makeContent.html
warning: File listed twice: /usr/lib64/R/library/grid/html/plotViewport.html
warning: File listed twice: /usr/lib64/R/library/grid/html/resolveRasterSize.html
warning: File listed twice: /usr/lib64/R/library/grid/html/showGrob.html
warning: File listed twice: /usr/lib64/R/library/grid/html/showViewport.html
warning: File listed twice: /usr/lib64/R/library/grid/html/stringWidth.html
warning: File listed twice: /usr/lib64/R/library/grid/html/unit.c.html
warning: File listed twice: /usr/lib64/R/library/grid/html/unit.html
warning: File listed twice: /usr/lib64/R/library/grid/html/unit.length.html
warning: File listed twice: /usr/lib64/R/library/grid/html/unit.pmin.html
warning: File listed twice: /usr/lib64/R/library/grid/html/unit.rep.html
warning: File listed twice: /usr/lib64/R/library/grid/html/valid.just.html
warning: File listed twice: /usr/lib64/R/library/grid/html/validDetails.html
warning: File listed twice: /usr/lib64/R/library/grid/html/viewport.html
warning: File listed twice: /usr/lib64/R/library/grid/html/viewports.html
warning: File listed twice: /usr/lib64/R/library/grid/html/vpPath.html
warning: File listed twice: /usr/lib64/R/library/grid/html/widthDetails.html
warning: File listed twice: /usr/lib64/R/library/grid/html/xDetails.html
warning: File listed twice: /usr/lib64/R/library/grid/html/xsplinePoints.html
warning: File listed twice: /usr/lib64/R/library/lattice/html
warning: File listed twice: /usr/lib64/R/library/lattice/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/Lattice.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/R.css
warning: File listed twice: /usr/lib64/R/library/lattice/html/Rows.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/axis.default.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/banking.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/barchart.table.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/barley.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/cloud.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/draw.colorkey.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/draw.key.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/environmental.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/ethanol.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/histogram.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/interaction.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/lattice.options.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/latticeParseFormula.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/level.colors.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/levelplot.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/llines.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/lset.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/make.groups.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/melanoma.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/oneway.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/packet.panel.default.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.axis.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.barchart.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.bwplot.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.cloud.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.densityplot.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.dotplot.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.functions.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.histogram.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.levelplot.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.loess.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.number.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.pairs.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.parallel.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.qqmath.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.qqmathline.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.smoothScatter.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.spline.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.stripplot.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.superpose.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.violin.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/panel.xyplot.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/prepanel.default.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/prepanel.functions.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/print.trellis.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/qq.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/qqmath.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/rfs.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/shingles.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/simpleKey.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/simpleTheme.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/singer.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/splom.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/strip.default.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/tmd.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/trellis.device.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/trellis.object.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/trellis.par.get.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/update.trellis.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/utilities.3d.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/xyplot.html
warning: File listed twice: /usr/lib64/R/library/lattice/html/xyplot.ts.html
warning: File listed twice: /usr/lib64/R/library/methods/html
warning: File listed twice: /usr/lib64/R/library/methods/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/methods/html/BasicClasses.html
warning: File listed twice: /usr/lib64/R/library/methods/html/Classes.html
warning: File listed twice: /usr/lib64/R/library/methods/html/Documentation.html
warning: File listed twice: /usr/lib64/R/library/methods/html/EmptyMethodsList-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/EnvironmentClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/GenericFunctions.html
warning: File listed twice: /usr/lib64/R/library/methods/html/LanguageClasses.html
warning: File listed twice: /usr/lib64/R/library/methods/html/LinearMethodsList-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/MethodDefinition-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/MethodSupport.html
warning: File listed twice: /usr/lib64/R/library/methods/html/MethodWithNext-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/Methods.html
warning: File listed twice: /usr/lib64/R/library/methods/html/MethodsList-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/MethodsList.html
warning: File listed twice: /usr/lib64/R/library/methods/html/NextMethod.html
warning: File listed twice: /usr/lib64/R/library/methods/html/ObjectsWithPackage-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/R.css
warning: File listed twice: /usr/lib64/R/library/methods/html/RClassUtils.html
warning: File listed twice: /usr/lib64/R/library/methods/html/RMethodUtils.html
warning: File listed twice: /usr/lib64/R/library/methods/html/S3Part.html
warning: File listed twice: /usr/lib64/R/library/methods/html/S4groupGeneric.html
warning: File listed twice: /usr/lib64/R/library/methods/html/SClassExtension-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/StructureClasses.html
warning: File listed twice: /usr/lib64/R/library/methods/html/TraceClasses.html
warning: File listed twice: /usr/lib64/R/library/methods/html/as.html
warning: File listed twice: /usr/lib64/R/library/methods/html/callGeneric.html
warning: File listed twice: /usr/lib64/R/library/methods/html/canCoerce.html
warning: File listed twice: /usr/lib64/R/library/methods/html/cbind2.html
warning: File listed twice: /usr/lib64/R/library/methods/html/className.html
warning: File listed twice: /usr/lib64/R/library/methods/html/classRepresentation-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/classesToAM.html
warning: File listed twice: /usr/lib64/R/library/methods/html/dotsMethods.html
warning: File listed twice: /usr/lib64/R/library/methods/html/evalSource.html
warning: File listed twice: /usr/lib64/R/library/methods/html/findClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/findMethods.html
warning: File listed twice: /usr/lib64/R/library/methods/html/fixPrevious.html
warning: File listed twice: /usr/lib64/R/library/methods/html/genericFunction-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/getClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/getMethod.html
warning: File listed twice: /usr/lib64/R/library/methods/html/getPackageName.html
warning: File listed twice: /usr/lib64/R/library/methods/html/hasArg.html
warning: File listed twice: /usr/lib64/R/library/methods/html/implicitGeneric.html
warning: File listed twice: /usr/lib64/R/library/methods/html/inheritedSlotNames.html
warning: File listed twice: /usr/lib64/R/library/methods/html/initialize-methods.html
warning: File listed twice: /usr/lib64/R/library/methods/html/is.html
warning: File listed twice: /usr/lib64/R/library/methods/html/isSealedMethod.html
warning: File listed twice: /usr/lib64/R/library/methods/html/languageEl.html
warning: File listed twice: /usr/lib64/R/library/methods/html/localRefClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/method.skeleton.html
warning: File listed twice: /usr/lib64/R/library/methods/html/methodUtilities.html
warning: File listed twice: /usr/lib64/R/library/methods/html/methods-defunct.html
warning: File listed twice: /usr/lib64/R/library/methods/html/methods-deprecated.html
warning: File listed twice: /usr/lib64/R/library/methods/html/methods-package.html
warning: File listed twice: /usr/lib64/R/library/methods/html/new.html
warning: File listed twice: /usr/lib64/R/library/methods/html/nonStructure-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/promptClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/promptMethods.html
warning: File listed twice: /usr/lib64/R/library/methods/html/refClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/representation.html
warning: File listed twice: /usr/lib64/R/library/methods/html/selectSuperClasses.html
warning: File listed twice: /usr/lib64/R/library/methods/html/setClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/setClassUnion.html
warning: File listed twice: /usr/lib64/R/library/methods/html/setGeneric.html
warning: File listed twice: /usr/lib64/R/library/methods/html/setLoadActions.html
warning: File listed twice: /usr/lib64/R/library/methods/html/setMethod.html
warning: File listed twice: /usr/lib64/R/library/methods/html/setOldClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/setSClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/show.html
warning: File listed twice: /usr/lib64/R/library/methods/html/showMethods.html
warning: File listed twice: /usr/lib64/R/library/methods/html/signature-class.html
warning: File listed twice: /usr/lib64/R/library/methods/html/slot.html
warning: File listed twice: /usr/lib64/R/library/methods/html/stdRefClass.html
warning: File listed twice: /usr/lib64/R/library/methods/html/substituteDirect.html
warning: File listed twice: /usr/lib64/R/library/methods/html/testInheritedMethods.html
warning: File listed twice: /usr/lib64/R/library/methods/html/validObject.html
warning: File listed twice: /usr/lib64/R/library/methods/html/zBasicFunsList.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/Beta.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/Predict.matrix.cr.smooth.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/Predict.matrix.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/Predict.matrix.soap.film.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/R.css
warning: File listed twice: /usr/lib64/R/library/mgcv/html/Rrank.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/Tweedie.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/anova.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/bam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/bam.update.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/cSplineDes.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/choose.k.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/columb.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/concurvity.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/coxph.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/exclude.too.far.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/extract.lme.cov.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/family.mgcv.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/fix.family.link.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/fixDependence.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/formXtViX.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/formula.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/fs.test.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/full.score.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.check.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.control.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.convergence.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.fit.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.fit3.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.models.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.outer.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.scale.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.selection.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.side.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam.vcomp.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gam2objective.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gamObject.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gamSim.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gamm.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/gaulss.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/get.var.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/in.out.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/inSide.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/influence.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/initial.sp.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/interpret.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/ldTweedie.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/linear.functional.terms.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/logLik.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/ls.size.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/magic.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/magic.post.proc.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/mgcv-FAQ.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/mgcv-package.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/mgcv-parallel.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/model.matrix.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/mono.con.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/mroot.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/mvn.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/negbin.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/new.name.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/notExp.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/notExp2.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/null.space.dimension.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/ocat.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/pcls.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/pdIdnot.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/pdTens.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/pen.edf.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/place.knots.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/plot.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/polys.plot.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/predict.bam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/predict.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/print.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/qq.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/rTweedie.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/random.effects.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/residuals.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/rig.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/s.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/scat.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/slanczos.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.ad.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.cr.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.ds.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.fs.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.mrf.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.ps.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.re.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.so.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.sos.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.t2.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.tensor.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.tp.smooth.spec.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smooth.terms.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/smoothCon.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/sp.vcov.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/spasm.construct.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/step.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/summary.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/t2.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/te.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/tensor.prod.model.matrix.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/uniquecombs.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/vcov.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/vis.gam.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/ziP.html
warning: File listed twice: /usr/lib64/R/library/mgcv/html/ziplss.html
warning: File listed twice: /usr/lib64/R/library/nlme/html
warning: File listed twice: /usr/lib64/R/library/nlme/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/ACF.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/ACF.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/ACF.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Alfalfa.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Assay.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/BodyWeight.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Cefamandole.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Coef.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Covariate.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Covariate.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Dialyzer.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Dim.corSpatial.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Dim.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Dim.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Dim.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Earthquake.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Extract.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Fatigue.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Gasoline.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Glucose.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Glucose2.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Gun.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/IGF.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Initialize.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Initialize.glsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Initialize.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Initialize.lmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Initialize.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Initialize.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/LDEsysMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Machines.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/MathAchSchool.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/MathAchieve.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Matrix.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Matrix.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Matrix.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Meat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Milk.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Muscle.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Names.formula.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Names.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Names.pdBlocked.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Names.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Names.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Nitrendipene.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Oats.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Orthodont.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Ovary.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Oxboys.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Oxide.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/PBG.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Phenobarb.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Pixel.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Quinidine.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/R.css
warning: File listed twice: /usr/lib64/R/library/nlme/html/Rail.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/RatPupWeight.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Relaxin.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Remifentanil.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Soybean.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Spruce.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Tetracycline1.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Tetracycline2.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/VarCorr.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corExp.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corGaus.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corLin.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corRatio.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corSpatial.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corSpher.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.default.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Variogram.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Wafer.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Wheat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/Wheat2.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/allCoef.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/anova.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/anova.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/as.matrix.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/as.matrix.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/as.matrix.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/asOneFormula.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/asTable.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/augPred.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/balancedGrouped.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/bdf.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/coef.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/coef.gnls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/coef.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/coef.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/coef.modelStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/coef.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/coef.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/coef.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/collapse.groupedData.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/collapse.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/compareFits.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/comparePred.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corAR1.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corARMA.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corCAR1.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corClasses.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corCompSymm.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corExp.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corFactor.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corFactor.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corGaus.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corLin.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corMatrix.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corMatrix.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corMatrix.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corMatrix.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corNatural.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corRatio.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corSpatial.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corSpher.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/corSymm.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/ergoStool.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fdHess.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fitted.glsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fitted.gnlsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fitted.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fitted.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fitted.lmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fitted.nlmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fixed.effects.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/fixef.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/formula.pdBlocked.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/formula.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/formula.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/gapply.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getCovariate.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getCovariate.data.frame.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getCovariate.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getCovariate.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getCovariateFormula.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getData.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getData.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getData.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getData.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getGroups.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getGroups.data.frame.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getGroups.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getGroups.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getGroups.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getGroups.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getGroups.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getGroupsFormula.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getResponse.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getResponseFormula.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/getVarCov.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/gls-internal.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/glsControl.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/glsObject.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/glsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/gnls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/gnlsControl.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/gnlsObject.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/gnlsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/groupedData.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/gsummary.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/intervals.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/intervals.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/intervals.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/intervals.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/isBalanced.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/isInitialized.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/lmList.groupedData.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/lme.groupedData.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/lme.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/lmeControl.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/lmeObject.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/lmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logDet.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logDet.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logDet.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logDet.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.glsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.gnls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.gnlsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.lmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/logLik.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/model.matrix.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/needUpdate.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/needUpdate.modelStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/nlme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/nlme.nlsList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/nlmeControl.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/nlmeObject.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/nlmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/nlsList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/nlsList.selfStart.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pairs.compareFits.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pairs.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pairs.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdBlocked.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdClasses.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdCompSymm.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdConstruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdConstruct.pdBlocked.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdDiag.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdFactor.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdFactor.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdIdent.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdLogChol.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdMatrix.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdMatrix.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdNatural.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pdSymm.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/phenoModel.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.ACF.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.Variogram.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.augPred.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.compareFits.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.intervals.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.nffGroupedData.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.nfnGroupedData.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.nmGroupedData.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.ranef.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/plot.ranef.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/pooledSD.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/predict.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/predict.gnls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/predict.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/predict.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/predict.nlme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/print.summary.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/print.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/qqnorm.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/qqnorm.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/quinModel.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/random.effects.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/ranef.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/ranef.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/recalc.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/recalc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/recalc.modelStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/recalc.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/recalc.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/residuals.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/residuals.glsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/residuals.gnlsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/residuals.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/residuals.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/residuals.lmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/residuals.nlmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/simulate.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/solve.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/solve.reStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/splitFormula.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/summary.corStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/summary.gls.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/summary.lmList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/summary.lme.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/summary.modelStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/summary.nlsList.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/summary.pdMat.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/summary.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/update.modelStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/update.varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varClasses.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varComb.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varConstPower.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varExp.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varFixed.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varFunc.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varIdent.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varPower.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varWeights.glsStruct.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varWeights.html
warning: File listed twice: /usr/lib64/R/library/nlme/html/varWeights.lmeStruct.html
warning: File listed twice: /usr/lib64/R/library/nnet/html
warning: File listed twice: /usr/lib64/R/library/nnet/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/nnet/html/R.css
warning: File listed twice: /usr/lib64/R/library/nnet/html/class.ind.html
warning: File listed twice: /usr/lib64/R/library/nnet/html/multinom.html
warning: File listed twice: /usr/lib64/R/library/nnet/html/nnet.Hess.html
warning: File listed twice: /usr/lib64/R/library/nnet/html/nnet.html
warning: File listed twice: /usr/lib64/R/library/nnet/html/predict.nnet.html
warning: File listed twice: /usr/lib64/R/library/nnet/html/which.is.max.html
warning: File listed twice: /usr/lib64/R/library/parallel/html
warning: File listed twice: /usr/lib64/R/library/parallel/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/R.css
warning: File listed twice: /usr/lib64/R/library/parallel/html/RngStream.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/children.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/clusterApply.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/detectCores.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/makeCluster.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/mcaffinity.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/mcfork.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/mclapply.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/mcparallel.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/parallel-package.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/pvec.html
warning: File listed twice: /usr/lib64/R/library/parallel/html/splitIndices.html
warning: File listed twice: /usr/lib64/R/library/rpart/html
warning: File listed twice: /usr/lib64/R/library/rpart/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/R.css
warning: File listed twice: /usr/lib64/R/library/rpart/html/car.test.frame.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/car90.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/cu.summary.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/kyphosis.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/labels.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/meanvar.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/na.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/path.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/plot.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/plotcp.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/post.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/predict.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/print.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/printcp.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/prune.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/residuals.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/rpart-internal.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/rpart.control.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/rpart.exp.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/rpart.object.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/rsq.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/snip.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/solder.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/stagec.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/summary.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/text.rpart.html
warning: File listed twice: /usr/lib64/R/library/rpart/html/xpred.rpart.html
warning: File listed twice: /usr/lib64/R/library/spatial/html
warning: File listed twice: /usr/lib64/R/library/spatial/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/Kaver.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/Kenvl.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/Kfn.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/Psim.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/R.css
warning: File listed twice: /usr/lib64/R/library/spatial/html/SSI.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/Strauss.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/anova.trls.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/correlogram.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/expcov.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/ppgetregion.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/ppinit.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/pplik.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/ppregion.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/predict.trls.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/prmat.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/semat.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/surf.gls.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/surf.ls.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/trls.influence.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/trmat.html
warning: File listed twice: /usr/lib64/R/library/spatial/html/variogram.html
warning: File listed twice: /usr/lib64/R/library/splines/html
warning: File listed twice: /usr/lib64/R/library/splines/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/splines/html/R.css
warning: File listed twice: /usr/lib64/R/library/splines/html/asVector.html
warning: File listed twice: /usr/lib64/R/library/splines/html/backSpline.html
warning: File listed twice: /usr/lib64/R/library/splines/html/bs.html
warning: File listed twice: /usr/lib64/R/library/splines/html/interpSpline.html
warning: File listed twice: /usr/lib64/R/library/splines/html/ns.html
warning: File listed twice: /usr/lib64/R/library/splines/html/periodicSpline.html
warning: File listed twice: /usr/lib64/R/library/splines/html/polySpline.html
warning: File listed twice: /usr/lib64/R/library/splines/html/predict.bSpline.html
warning: File listed twice: /usr/lib64/R/library/splines/html/predict.bs.html
warning: File listed twice: /usr/lib64/R/library/splines/html/splineDesign.html
warning: File listed twice: /usr/lib64/R/library/splines/html/splineKnots.html
warning: File listed twice: /usr/lib64/R/library/splines/html/splineOrder.html
warning: File listed twice: /usr/lib64/R/library/splines/html/splines-package.html
warning: File listed twice: /usr/lib64/R/library/splines/html/xyVector.html
warning: File listed twice: /usr/lib64/R/library/stats/html
warning: File listed twice: /usr/lib64/R/library/stats/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/stats/html/AIC.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ARMAacf.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ARMAtoMA.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Beta.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Binomial.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Cauchy.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Chisquare.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Distributions.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Exponential.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Fdist.html
warning: File listed twice: /usr/lib64/R/library/stats/html/GammaDist.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Geometric.html
warning: File listed twice: /usr/lib64/R/library/stats/html/HoltWinters.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Hypergeometric.html
warning: File listed twice: /usr/lib64/R/library/stats/html/IQR.html
warning: File listed twice: /usr/lib64/R/library/stats/html/KalmanLike.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Logistic.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Lognormal.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Multinom.html
warning: File listed twice: /usr/lib64/R/library/stats/html/NLSstAsymptotic.html
warning: File listed twice: /usr/lib64/R/library/stats/html/NLSstClosestX.html
warning: File listed twice: /usr/lib64/R/library/stats/html/NLSstLfAsymptote.html
warning: File listed twice: /usr/lib64/R/library/stats/html/NLSstRtAsymptote.html
warning: File listed twice: /usr/lib64/R/library/stats/html/NegBinomial.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Normal.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Poisson.html
warning: File listed twice: /usr/lib64/R/library/stats/html/R.css
warning: File listed twice: /usr/lib64/R/library/stats/html/SSD.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSasymp.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSasympOff.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSasympOrig.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSbiexp.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSfol.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSfpl.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSgompertz.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSlogis.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSmicmen.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SSweibull.html
warning: File listed twice: /usr/lib64/R/library/stats/html/SignRank.html
warning: File listed twice: /usr/lib64/R/library/stats/html/StructTS.html
warning: File listed twice: /usr/lib64/R/library/stats/html/TDist.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Tukey.html
warning: File listed twice: /usr/lib64/R/library/stats/html/TukeyHSD.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Uniform.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Weibull.html
warning: File listed twice: /usr/lib64/R/library/stats/html/Wilcoxon.html
warning: File listed twice: /usr/lib64/R/library/stats/html/acf.html
warning: File listed twice: /usr/lib64/R/library/stats/html/acf2AR.html
warning: File listed twice: /usr/lib64/R/library/stats/html/add1.html
warning: File listed twice: /usr/lib64/R/library/stats/html/addmargins.html
warning: File listed twice: /usr/lib64/R/library/stats/html/aggregate.html
warning: File listed twice: /usr/lib64/R/library/stats/html/alias.html
warning: File listed twice: /usr/lib64/R/library/stats/html/anova.glm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/anova.html
warning: File listed twice: /usr/lib64/R/library/stats/html/anova.lm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/anova.mlm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ansari.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/aov.html
warning: File listed twice: /usr/lib64/R/library/stats/html/approxfun.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ar.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ar.ols.html
warning: File listed twice: /usr/lib64/R/library/stats/html/arima.html
warning: File listed twice: /usr/lib64/R/library/stats/html/arima.sim.html
warning: File listed twice: /usr/lib64/R/library/stats/html/arima0.html
warning: File listed twice: /usr/lib64/R/library/stats/html/as.hclust.html
warning: File listed twice: /usr/lib64/R/library/stats/html/asOneSidedFormula.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ave.html
warning: File listed twice: /usr/lib64/R/library/stats/html/bandwidth.html
warning: File listed twice: /usr/lib64/R/library/stats/html/bartlett.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/binom.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/biplot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/biplot.princomp.html
warning: File listed twice: /usr/lib64/R/library/stats/html/birthday.html
warning: File listed twice: /usr/lib64/R/library/stats/html/box.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/cancor.html
warning: File listed twice: /usr/lib64/R/library/stats/html/case.names.html
warning: File listed twice: /usr/lib64/R/library/stats/html/checkMFClasses.html
warning: File listed twice: /usr/lib64/R/library/stats/html/chisq.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/cmdscale.html
warning: File listed twice: /usr/lib64/R/library/stats/html/coef.html
warning: File listed twice: /usr/lib64/R/library/stats/html/complete.cases.html
warning: File listed twice: /usr/lib64/R/library/stats/html/confint.html
warning: File listed twice: /usr/lib64/R/library/stats/html/constrOptim.html
warning: File listed twice: /usr/lib64/R/library/stats/html/contrast.html
warning: File listed twice: /usr/lib64/R/library/stats/html/contrasts.html
warning: File listed twice: /usr/lib64/R/library/stats/html/convolve.html
warning: File listed twice: /usr/lib64/R/library/stats/html/cophenetic.html
warning: File listed twice: /usr/lib64/R/library/stats/html/cor.html
warning: File listed twice: /usr/lib64/R/library/stats/html/cor.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/cov.wt.html
warning: File listed twice: /usr/lib64/R/library/stats/html/cpgram.html
warning: File listed twice: /usr/lib64/R/library/stats/html/cutree.html
warning: File listed twice: /usr/lib64/R/library/stats/html/decompose.html
warning: File listed twice: /usr/lib64/R/library/stats/html/delete.response.html
warning: File listed twice: /usr/lib64/R/library/stats/html/dendrapply.html
warning: File listed twice: /usr/lib64/R/library/stats/html/dendrogram.html
warning: File listed twice: /usr/lib64/R/library/stats/html/density.html
warning: File listed twice: /usr/lib64/R/library/stats/html/deriv.html
warning: File listed twice: /usr/lib64/R/library/stats/html/deviance.html
warning: File listed twice: /usr/lib64/R/library/stats/html/df.residual.html
warning: File listed twice: /usr/lib64/R/library/stats/html/diffinv.html
warning: File listed twice: /usr/lib64/R/library/stats/html/dist.html
warning: File listed twice: /usr/lib64/R/library/stats/html/dummy.coef.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ecdf.html
warning: File listed twice: /usr/lib64/R/library/stats/html/eff.aovlist.html
warning: File listed twice: /usr/lib64/R/library/stats/html/effects.html
warning: File listed twice: /usr/lib64/R/library/stats/html/embed.html
warning: File listed twice: /usr/lib64/R/library/stats/html/expand.model.frame.html
warning: File listed twice: /usr/lib64/R/library/stats/html/extractAIC.html
warning: File listed twice: /usr/lib64/R/library/stats/html/factanal.html
warning: File listed twice: /usr/lib64/R/library/stats/html/factor.scope.html
warning: File listed twice: /usr/lib64/R/library/stats/html/family.html
warning: File listed twice: /usr/lib64/R/library/stats/html/fft.html
warning: File listed twice: /usr/lib64/R/library/stats/html/filter.html
warning: File listed twice: /usr/lib64/R/library/stats/html/fisher.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/fitted.values.html
warning: File listed twice: /usr/lib64/R/library/stats/html/fivenum.html
warning: File listed twice: /usr/lib64/R/library/stats/html/fligner.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/formula.html
warning: File listed twice: /usr/lib64/R/library/stats/html/formula.nls.html
warning: File listed twice: /usr/lib64/R/library/stats/html/friedman.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ftable.formula.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ftable.html
warning: File listed twice: /usr/lib64/R/library/stats/html/getInitial.html
warning: File listed twice: /usr/lib64/R/library/stats/html/glm.control.html
warning: File listed twice: /usr/lib64/R/library/stats/html/glm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/glm.summaries.html
warning: File listed twice: /usr/lib64/R/library/stats/html/hclust.html
warning: File listed twice: /usr/lib64/R/library/stats/html/heatmap.html
warning: File listed twice: /usr/lib64/R/library/stats/html/identify.hclust.html
warning: File listed twice: /usr/lib64/R/library/stats/html/influence.measures.html
warning: File listed twice: /usr/lib64/R/library/stats/html/integrate.html
warning: File listed twice: /usr/lib64/R/library/stats/html/interaction.plot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/is.empty.html
warning: File listed twice: /usr/lib64/R/library/stats/html/isoreg.html
warning: File listed twice: /usr/lib64/R/library/stats/html/kernapply.html
warning: File listed twice: /usr/lib64/R/library/stats/html/kernel.html
warning: File listed twice: /usr/lib64/R/library/stats/html/kmeans.html
warning: File listed twice: /usr/lib64/R/library/stats/html/kruskal.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ks.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ksmooth.html
warning: File listed twice: /usr/lib64/R/library/stats/html/lag.html
warning: File listed twice: /usr/lib64/R/library/stats/html/lag.plot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/line.html
warning: File listed twice: /usr/lib64/R/library/stats/html/listof.html
warning: File listed twice: /usr/lib64/R/library/stats/html/lm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/lm.influence.html
warning: File listed twice: /usr/lib64/R/library/stats/html/lm.summaries.html
warning: File listed twice: /usr/lib64/R/library/stats/html/lmfit.html
warning: File listed twice: /usr/lib64/R/library/stats/html/loadings.html
warning: File listed twice: /usr/lib64/R/library/stats/html/loess.control.html
warning: File listed twice: /usr/lib64/R/library/stats/html/loess.html
warning: File listed twice: /usr/lib64/R/library/stats/html/logLik.html
warning: File listed twice: /usr/lib64/R/library/stats/html/loglin.html
warning: File listed twice: /usr/lib64/R/library/stats/html/lowess.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ls.diag.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ls.print.html
warning: File listed twice: /usr/lib64/R/library/stats/html/lsfit.html
warning: File listed twice: /usr/lib64/R/library/stats/html/mad.html
warning: File listed twice: /usr/lib64/R/library/stats/html/mahalanobis.html
warning: File listed twice: /usr/lib64/R/library/stats/html/make.link.html
warning: File listed twice: /usr/lib64/R/library/stats/html/makepredictcall.html
warning: File listed twice: /usr/lib64/R/library/stats/html/manova.html
warning: File listed twice: /usr/lib64/R/library/stats/html/mantelhaen.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/mauchly.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/mcnemar.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/median.html
warning: File listed twice: /usr/lib64/R/library/stats/html/medpolish.html
warning: File listed twice: /usr/lib64/R/library/stats/html/model.extract.html
warning: File listed twice: /usr/lib64/R/library/stats/html/model.frame.html
warning: File listed twice: /usr/lib64/R/library/stats/html/model.matrix.html
warning: File listed twice: /usr/lib64/R/library/stats/html/model.tables.html
warning: File listed twice: /usr/lib64/R/library/stats/html/monthplot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/mood.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/na.action.html
warning: File listed twice: /usr/lib64/R/library/stats/html/na.contiguous.html
warning: File listed twice: /usr/lib64/R/library/stats/html/na.fail.html
warning: File listed twice: /usr/lib64/R/library/stats/html/nafns.html
warning: File listed twice: /usr/lib64/R/library/stats/html/naprint.html
warning: File listed twice: /usr/lib64/R/library/stats/html/nextn.html
warning: File listed twice: /usr/lib64/R/library/stats/html/nlm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/nlminb.html
warning: File listed twice: /usr/lib64/R/library/stats/html/nls.control.html
warning: File listed twice: /usr/lib64/R/library/stats/html/nls.html
warning: File listed twice: /usr/lib64/R/library/stats/html/nobs.html
warning: File listed twice: /usr/lib64/R/library/stats/html/numericDeriv.html
warning: File listed twice: /usr/lib64/R/library/stats/html/offset.html
warning: File listed twice: /usr/lib64/R/library/stats/html/oneway.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/optim.html
warning: File listed twice: /usr/lib64/R/library/stats/html/optimize.html
warning: File listed twice: /usr/lib64/R/library/stats/html/order.dendrogram.html
warning: File listed twice: /usr/lib64/R/library/stats/html/p.adjust.html
warning: File listed twice: /usr/lib64/R/library/stats/html/pairwise.prop.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/pairwise.t.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/pairwise.table.html
warning: File listed twice: /usr/lib64/R/library/stats/html/pairwise.wilcox.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.HoltWinters.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.acf.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.density.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.isoreg.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.lm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.ppr.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.profile.nls.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.spec.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.stepfun.html
warning: File listed twice: /usr/lib64/R/library/stats/html/plot.ts.html
warning: File listed twice: /usr/lib64/R/library/stats/html/poisson.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/poly.html
warning: File listed twice: /usr/lib64/R/library/stats/html/power.anova.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/power.html
warning: File listed twice: /usr/lib64/R/library/stats/html/power.prop.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/power.t.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/pp.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ppoints.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ppr.html
warning: File listed twice: /usr/lib64/R/library/stats/html/prcomp.html
warning: File listed twice: /usr/lib64/R/library/stats/html/predict.HoltWinters.html
warning: File listed twice: /usr/lib64/R/library/stats/html/predict.arima.html
warning: File listed twice: /usr/lib64/R/library/stats/html/predict.glm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/predict.html
warning: File listed twice: /usr/lib64/R/library/stats/html/predict.lm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/predict.loess.html
warning: File listed twice: /usr/lib64/R/library/stats/html/predict.nls.html
warning: File listed twice: /usr/lib64/R/library/stats/html/predict.smooth.spline.html
warning: File listed twice: /usr/lib64/R/library/stats/html/preplot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/princomp.html
warning: File listed twice: /usr/lib64/R/library/stats/html/print.power.htest.html
warning: File listed twice: /usr/lib64/R/library/stats/html/print.ts.html
warning: File listed twice: /usr/lib64/R/library/stats/html/printCoefmat.html
warning: File listed twice: /usr/lib64/R/library/stats/html/profile.html
warning: File listed twice: /usr/lib64/R/library/stats/html/profile.nls.html
warning: File listed twice: /usr/lib64/R/library/stats/html/proj.html
warning: File listed twice: /usr/lib64/R/library/stats/html/prop.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/prop.trend.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/qqnorm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/quade.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/quantile.html
warning: File listed twice: /usr/lib64/R/library/stats/html/r2dtable.html
warning: File listed twice: /usr/lib64/R/library/stats/html/rWishart.html
warning: File listed twice: /usr/lib64/R/library/stats/html/read.ftable.html
warning: File listed twice: /usr/lib64/R/library/stats/html/rect.hclust.html
warning: File listed twice: /usr/lib64/R/library/stats/html/relevel.html
warning: File listed twice: /usr/lib64/R/library/stats/html/reorder.dendrogram.html
warning: File listed twice: /usr/lib64/R/library/stats/html/reorder.factor.html
warning: File listed twice: /usr/lib64/R/library/stats/html/replications.html
warning: File listed twice: /usr/lib64/R/library/stats/html/reshape.html
warning: File listed twice: /usr/lib64/R/library/stats/html/residuals.html
warning: File listed twice: /usr/lib64/R/library/stats/html/runmed.html
warning: File listed twice: /usr/lib64/R/library/stats/html/scatter.smooth.html
warning: File listed twice: /usr/lib64/R/library/stats/html/screeplot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/sd.html
warning: File listed twice: /usr/lib64/R/library/stats/html/se.contrast.html
warning: File listed twice: /usr/lib64/R/library/stats/html/selfStart.html
warning: File listed twice: /usr/lib64/R/library/stats/html/setNames.html
warning: File listed twice: /usr/lib64/R/library/stats/html/shapiro.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/simulate.html
warning: File listed twice: /usr/lib64/R/library/stats/html/smooth.html
warning: File listed twice: /usr/lib64/R/library/stats/html/smooth.spline.html
warning: File listed twice: /usr/lib64/R/library/stats/html/smoothEnds.html
warning: File listed twice: /usr/lib64/R/library/stats/html/sortedXyData.html
warning: File listed twice: /usr/lib64/R/library/stats/html/spec.ar.html
warning: File listed twice: /usr/lib64/R/library/stats/html/spec.pgram.html
warning: File listed twice: /usr/lib64/R/library/stats/html/spec.taper.html
warning: File listed twice: /usr/lib64/R/library/stats/html/spectrum.html
warning: File listed twice: /usr/lib64/R/library/stats/html/splinefun.html
warning: File listed twice: /usr/lib64/R/library/stats/html/start.html
warning: File listed twice: /usr/lib64/R/library/stats/html/stat.anova.html
warning: File listed twice: /usr/lib64/R/library/stats/html/stats-defunct.html
warning: File listed twice: /usr/lib64/R/library/stats/html/stats-deprecated.html
warning: File listed twice: /usr/lib64/R/library/stats/html/stats-package.html
warning: File listed twice: /usr/lib64/R/library/stats/html/step.html
warning: File listed twice: /usr/lib64/R/library/stats/html/stepfun.html
warning: File listed twice: /usr/lib64/R/library/stats/html/stl.html
warning: File listed twice: /usr/lib64/R/library/stats/html/stlmethods.html
warning: File listed twice: /usr/lib64/R/library/stats/html/summary.aov.html
warning: File listed twice: /usr/lib64/R/library/stats/html/summary.glm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/summary.lm.html
warning: File listed twice: /usr/lib64/R/library/stats/html/summary.manova.html
warning: File listed twice: /usr/lib64/R/library/stats/html/summary.nls.html
warning: File listed twice: /usr/lib64/R/library/stats/html/summary.princomp.html
warning: File listed twice: /usr/lib64/R/library/stats/html/supsmu.html
warning: File listed twice: /usr/lib64/R/library/stats/html/symnum.html
warning: File listed twice: /usr/lib64/R/library/stats/html/t.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/termplot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/terms.formula.html
warning: File listed twice: /usr/lib64/R/library/stats/html/terms.html
warning: File listed twice: /usr/lib64/R/library/stats/html/terms.object.html
warning: File listed twice: /usr/lib64/R/library/stats/html/time.html
warning: File listed twice: /usr/lib64/R/library/stats/html/toeplitz.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ts-methods.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ts.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ts.plot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/ts.union.html
warning: File listed twice: /usr/lib64/R/library/stats/html/tsSmooth.html
warning: File listed twice: /usr/lib64/R/library/stats/html/tsdiag.html
warning: File listed twice: /usr/lib64/R/library/stats/html/tsp.html
warning: File listed twice: /usr/lib64/R/library/stats/html/uniroot.html
warning: File listed twice: /usr/lib64/R/library/stats/html/update.formula.html
warning: File listed twice: /usr/lib64/R/library/stats/html/update.html
warning: File listed twice: /usr/lib64/R/library/stats/html/var.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/varimax.html
warning: File listed twice: /usr/lib64/R/library/stats/html/vcov.html
warning: File listed twice: /usr/lib64/R/library/stats/html/weighted.mean.html
warning: File listed twice: /usr/lib64/R/library/stats/html/weighted.residuals.html
warning: File listed twice: /usr/lib64/R/library/stats/html/weights.html
warning: File listed twice: /usr/lib64/R/library/stats/html/wilcox.test.html
warning: File listed twice: /usr/lib64/R/library/stats/html/window.html
warning: File listed twice: /usr/lib64/R/library/stats/html/xtabs.html
warning: File listed twice: /usr/lib64/R/library/stats/html/zC.html
warning: File listed twice: /usr/lib64/R/library/stats4/html
warning: File listed twice: /usr/lib64/R/library/stats4/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/R.css
warning: File listed twice: /usr/lib64/R/library/stats4/html/coef-methods.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/confint-methods.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/logLik-methods.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/mle-class.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/mle.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/plot-methods.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/profile-methods.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/profile.mle-class.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/show-methods.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/stats4-package.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/summary-methods.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/summary.mle-class.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/update-methods.html
warning: File listed twice: /usr/lib64/R/library/stats4/html/vcov-methods.html
warning: File listed twice: /usr/lib64/R/library/survival/html
warning: File listed twice: /usr/lib64/R/library/survival/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/survival/html/R.css
warning: File listed twice: /usr/lib64/R/library/survival/html/Surv.html
warning: File listed twice: /usr/lib64/R/library/survival/html/aareg.html
warning: File listed twice: /usr/lib64/R/library/survival/html/agreg.fit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/aml.html
warning: File listed twice: /usr/lib64/R/library/survival/html/anova.coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/attrassign.html
warning: File listed twice: /usr/lib64/R/library/survival/html/basehaz.html
warning: File listed twice: /usr/lib64/R/library/survival/html/bladder.html
warning: File listed twice: /usr/lib64/R/library/survival/html/cch.html
warning: File listed twice: /usr/lib64/R/library/survival/html/cgd.html
warning: File listed twice: /usr/lib64/R/library/survival/html/clogit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/cluster.html
warning: File listed twice: /usr/lib64/R/library/survival/html/colon.html
warning: File listed twice: /usr/lib64/R/library/survival/html/cox.zph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/coxph.control.html
warning: File listed twice: /usr/lib64/R/library/survival/html/coxph.detail.html
warning: File listed twice: /usr/lib64/R/library/survival/html/coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/coxph.object.html
warning: File listed twice: /usr/lib64/R/library/survival/html/coxph.wtest.html
warning: File listed twice: /usr/lib64/R/library/survival/html/dsurvreg.html
warning: File listed twice: /usr/lib64/R/library/survival/html/flchain.html
warning: File listed twice: /usr/lib64/R/library/survival/html/frailty.html
warning: File listed twice: /usr/lib64/R/library/survival/html/heart.html
warning: File listed twice: /usr/lib64/R/library/survival/html/is.ratetable.html
warning: File listed twice: /usr/lib64/R/library/survival/html/kidney.html
warning: File listed twice: /usr/lib64/R/library/survival/html/lines.survfit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/logan.html
warning: File listed twice: /usr/lib64/R/library/survival/html/lung.html
warning: File listed twice: /usr/lib64/R/library/survival/html/mgus.html
warning: File listed twice: /usr/lib64/R/library/survival/html/model.frame.coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/model.matrix.coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/nwtco.html
warning: File listed twice: /usr/lib64/R/library/survival/html/ovarian.html
warning: File listed twice: /usr/lib64/R/library/survival/html/pbc.html
warning: File listed twice: /usr/lib64/R/library/survival/html/pbcseq.html
warning: File listed twice: /usr/lib64/R/library/survival/html/plot.aareg.html
warning: File listed twice: /usr/lib64/R/library/survival/html/plot.cox.zph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/plot.survfit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/predict.coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/predict.survreg.html
warning: File listed twice: /usr/lib64/R/library/survival/html/print.aareg.html
warning: File listed twice: /usr/lib64/R/library/survival/html/print.summary.coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/print.summary.survexp.html
warning: File listed twice: /usr/lib64/R/library/survival/html/print.summary.survfit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/print.survfit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/pspline.html
warning: File listed twice: /usr/lib64/R/library/survival/html/pyears.html
warning: File listed twice: /usr/lib64/R/library/survival/html/quantile.survfit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/ratetable.html
warning: File listed twice: /usr/lib64/R/library/survival/html/ratetableDate.html
warning: File listed twice: /usr/lib64/R/library/survival/html/rats.html
warning: File listed twice: /usr/lib64/R/library/survival/html/rats2.html
warning: File listed twice: /usr/lib64/R/library/survival/html/residuals.coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/residuals.survreg.html
warning: File listed twice: /usr/lib64/R/library/survival/html/ridge.html
warning: File listed twice: /usr/lib64/R/library/survival/html/stanford2.html
warning: File listed twice: /usr/lib64/R/library/survival/html/strata.html
warning: File listed twice: /usr/lib64/R/library/survival/html/summary.aareg.html
warning: File listed twice: /usr/lib64/R/library/survival/html/summary.coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/summary.survexp.html
warning: File listed twice: /usr/lib64/R/library/survival/html/summary.survfit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survConcordance.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survSplit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survdiff.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survexp.fit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survexp.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survexp.us.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survfit.coxph.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survfit.formula.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survfit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survfit.object.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survfitcoxph.fit.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survival-internal.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survobrien.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survreg.control.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survreg.distributions.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survreg.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survreg.object.html
warning: File listed twice: /usr/lib64/R/library/survival/html/survregDtest.html
warning: File listed twice: /usr/lib64/R/library/survival/html/tcut.html
warning: File listed twice: /usr/lib64/R/library/survival/html/tobin.html
warning: File listed twice: /usr/lib64/R/library/survival/html/untangle.specials.html
warning: File listed twice: /usr/lib64/R/library/survival/html/uspop2.html
warning: File listed twice: /usr/lib64/R/library/survival/html/veteran.html
warning: File listed twice: /usr/lib64/R/library/tools/html
warning: File listed twice: /usr/lib64/R/library/tools/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/tools/html/HTMLheader.html
warning: File listed twice: /usr/lib64/R/library/tools/html/HTMLlinks.html
warning: File listed twice: /usr/lib64/R/library/tools/html/QC.html
warning: File listed twice: /usr/lib64/R/library/tools/html/R.css
warning: File listed twice: /usr/lib64/R/library/tools/html/Rd2HTML.html
warning: File listed twice: /usr/lib64/R/library/tools/html/Rd2txt_options.html
warning: File listed twice: /usr/lib64/R/library/tools/html/RdTextFilter.html
warning: File listed twice: /usr/lib64/R/library/tools/html/Rdiff.html
warning: File listed twice: /usr/lib64/R/library/tools/html/Rdindex.html
warning: File listed twice: /usr/lib64/R/library/tools/html/Rdutils.html
warning: File listed twice: /usr/lib64/R/library/tools/html/SweaveTeXFilter.html
warning: File listed twice: /usr/lib64/R/library/tools/html/add_datalist.html
warning: File listed twice: /usr/lib64/R/library/tools/html/assertCondition.html
warning: File listed twice: /usr/lib64/R/library/tools/html/bibstyle.html
warning: File listed twice: /usr/lib64/R/library/tools/html/buildVignette.html
warning: File listed twice: /usr/lib64/R/library/tools/html/buildVignettes.html
warning: File listed twice: /usr/lib64/R/library/tools/html/charsets.html
warning: File listed twice: /usr/lib64/R/library/tools/html/checkFF.html
warning: File listed twice: /usr/lib64/R/library/tools/html/checkMD5sums.html
warning: File listed twice: /usr/lib64/R/library/tools/html/checkPoFiles.html
warning: File listed twice: /usr/lib64/R/library/tools/html/checkRd.html
warning: File listed twice: /usr/lib64/R/library/tools/html/checkRdaFiles.html
warning: File listed twice: /usr/lib64/R/library/tools/html/checkTnF.html
warning: File listed twice: /usr/lib64/R/library/tools/html/checkVignettes.html
warning: File listed twice: /usr/lib64/R/library/tools/html/check_packages_in_dir.html
warning: File listed twice: /usr/lib64/R/library/tools/html/codoc.html
warning: File listed twice: /usr/lib64/R/library/tools/html/compactPDF.html
warning: File listed twice: /usr/lib64/R/library/tools/html/delimMatch.html
warning: File listed twice: /usr/lib64/R/library/tools/html/dependsOnPkgs.html
warning: File listed twice: /usr/lib64/R/library/tools/html/encoded.html
warning: File listed twice: /usr/lib64/R/library/tools/html/fileutils.html
warning: File listed twice: /usr/lib64/R/library/tools/html/find_gs_cmd.html
warning: File listed twice: /usr/lib64/R/library/tools/html/getDepList.html
warning: File listed twice: /usr/lib64/R/library/tools/html/getVignetteInfo.html
warning: File listed twice: /usr/lib64/R/library/tools/html/installFoundDepends.html
warning: File listed twice: /usr/lib64/R/library/tools/html/makeLazyLoading.html
warning: File listed twice: /usr/lib64/R/library/tools/html/make_translations_pkg.html
warning: File listed twice: /usr/lib64/R/library/tools/html/md5sum.html
warning: File listed twice: /usr/lib64/R/library/tools/html/package.dependencies.html
warning: File listed twice: /usr/lib64/R/library/tools/html/package_dependencies.html
warning: File listed twice: /usr/lib64/R/library/tools/html/parseLatex.html
warning: File listed twice: /usr/lib64/R/library/tools/html/parse_Rd.html
warning: File listed twice: /usr/lib64/R/library/tools/html/print.via.format.html
warning: File listed twice: /usr/lib64/R/library/tools/html/pskill.html
warning: File listed twice: /usr/lib64/R/library/tools/html/psnice.html
warning: File listed twice: /usr/lib64/R/library/tools/html/read.00Index.html
warning: File listed twice: /usr/lib64/R/library/tools/html/showNonASCII.html
warning: File listed twice: /usr/lib64/R/library/tools/html/startDynamicHelp.html
warning: File listed twice: /usr/lib64/R/library/tools/html/testInstalledPackage.html
warning: File listed twice: /usr/lib64/R/library/tools/html/texi2dvi.html
warning: File listed twice: /usr/lib64/R/library/tools/html/toHTML.html
warning: File listed twice: /usr/lib64/R/library/tools/html/toRd.html
warning: File listed twice: /usr/lib64/R/library/tools/html/tools-defunct.html
warning: File listed twice: /usr/lib64/R/library/tools/html/tools-deprecated.html
warning: File listed twice: /usr/lib64/R/library/tools/html/tools-package.html
warning: File listed twice: /usr/lib64/R/library/tools/html/undoc.html
warning: File listed twice: /usr/lib64/R/library/tools/html/update_pkg_po.html
warning: File listed twice: /usr/lib64/R/library/tools/html/vignetteDepends.html
warning: File listed twice: /usr/lib64/R/library/tools/html/vignetteEngine.html
warning: File listed twice: /usr/lib64/R/library/tools/html/writePACKAGES.html
warning: File listed twice: /usr/lib64/R/library/tools/html/xgettext.html
warning: File listed twice: /usr/lib64/R/library/utils/html
warning: File listed twice: /usr/lib64/R/library/utils/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/utils/html/BATCH.html
warning: File listed twice: /usr/lib64/R/library/utils/html/COMPILE.html
warning: File listed twice: /usr/lib64/R/library/utils/html/INSTALL.html
warning: File listed twice: /usr/lib64/R/library/utils/html/LINK.html
warning: File listed twice: /usr/lib64/R/library/utils/html/PkgUtils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Question.html
warning: File listed twice: /usr/lib64/R/library/utils/html/R.css
warning: File listed twice: /usr/lib64/R/library/utils/html/REMOVE.html
warning: File listed twice: /usr/lib64/R/library/utils/html/RHOME.html
warning: File listed twice: /usr/lib64/R/library/utils/html/RShowDoc.html
warning: File listed twice: /usr/lib64/R/library/utils/html/RSiteSearch.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rprof.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rprofmem.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rscript.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rtangle.html
warning: File listed twice: /usr/lib64/R/library/utils/html/RweaveLatex.html
warning: File listed twice: /usr/lib64/R/library/utils/html/SHLIB.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Sweave.html
warning: File listed twice: /usr/lib64/R/library/utils/html/SweaveSyntConv.html
warning: File listed twice: /usr/lib64/R/library/utils/html/SweaveUtils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/URLencode.html
warning: File listed twice: /usr/lib64/R/library/utils/html/View.html
warning: File listed twice: /usr/lib64/R/library/utils/html/adist.html
warning: File listed twice: /usr/lib64/R/library/utils/html/alarm.html
warning: File listed twice: /usr/lib64/R/library/utils/html/apropos.html
warning: File listed twice: /usr/lib64/R/library/utils/html/aregexec.html
warning: File listed twice: /usr/lib64/R/library/utils/html/aspell-utils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/aspell.html
warning: File listed twice: /usr/lib64/R/library/utils/html/available.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/bibentry.html
warning: File listed twice: /usr/lib64/R/library/utils/html/browseEnv.html
warning: File listed twice: /usr/lib64/R/library/utils/html/browseURL.html
warning: File listed twice: /usr/lib64/R/library/utils/html/browseVignettes.html
warning: File listed twice: /usr/lib64/R/library/utils/html/bug.report.html
warning: File listed twice: /usr/lib64/R/library/utils/html/capture.output.html
warning: File listed twice: /usr/lib64/R/library/utils/html/changedFiles.html
warning: File listed twice: /usr/lib64/R/library/utils/html/chooseBioCmirror.html
warning: File listed twice: /usr/lib64/R/library/utils/html/chooseCRANmirror.html
warning: File listed twice: /usr/lib64/R/library/utils/html/citEntry.html
warning: File listed twice: /usr/lib64/R/library/utils/html/citation.html
warning: File listed twice: /usr/lib64/R/library/utils/html/cite.html
warning: File listed twice: /usr/lib64/R/library/utils/html/close.socket.html
warning: File listed twice: /usr/lib64/R/library/utils/html/combn.html
warning: File listed twice: /usr/lib64/R/library/utils/html/compareVersion.html
warning: File listed twice: /usr/lib64/R/library/utils/html/contrib.url.html
warning: File listed twice: /usr/lib64/R/library/utils/html/count.fields.html
warning: File listed twice: /usr/lib64/R/library/utils/html/create.post.html
warning: File listed twice: /usr/lib64/R/library/utils/html/data.html
warning: File listed twice: /usr/lib64/R/library/utils/html/dataentry.html
warning: File listed twice: /usr/lib64/R/library/utils/html/debugger.html
warning: File listed twice: /usr/lib64/R/library/utils/html/demo.html
warning: File listed twice: /usr/lib64/R/library/utils/html/download.file.html
warning: File listed twice: /usr/lib64/R/library/utils/html/download.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/edit.data.frame.html
warning: File listed twice: /usr/lib64/R/library/utils/html/edit.html
warning: File listed twice: /usr/lib64/R/library/utils/html/example.html
warning: File listed twice: /usr/lib64/R/library/utils/html/file.edit.html
warning: File listed twice: /usr/lib64/R/library/utils/html/filetest.html
warning: File listed twice: /usr/lib64/R/library/utils/html/findLineNum.html
warning: File listed twice: /usr/lib64/R/library/utils/html/fix.html
warning: File listed twice: /usr/lib64/R/library/utils/html/flush.console.html
warning: File listed twice: /usr/lib64/R/library/utils/html/format.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getAnywhere.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getFromNamespace.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getParseData.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getS3method.html
warning: File listed twice: /usr/lib64/R/library/utils/html/glob2rx.html
warning: File listed twice: /usr/lib64/R/library/utils/html/globalVariables.html
warning: File listed twice: /usr/lib64/R/library/utils/html/head.html
warning: File listed twice: /usr/lib64/R/library/utils/html/help.html
warning: File listed twice: /usr/lib64/R/library/utils/html/help.request.html
warning: File listed twice: /usr/lib64/R/library/utils/html/help.search.html
warning: File listed twice: /usr/lib64/R/library/utils/html/help.start.html
warning: File listed twice: /usr/lib64/R/library/utils/html/install.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/installed.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/localeToCharset.html
warning: File listed twice: /usr/lib64/R/library/utils/html/ls_str.html
warning: File listed twice: /usr/lib64/R/library/utils/html/maintainer.html
warning: File listed twice: /usr/lib64/R/library/utils/html/make.packages.html.html
warning: File listed twice: /usr/lib64/R/library/utils/html/make.socket.html
warning: File listed twice: /usr/lib64/R/library/utils/html/memory.size.html
warning: File listed twice: /usr/lib64/R/library/utils/html/menu.html
warning: File listed twice: /usr/lib64/R/library/utils/html/methods.html
warning: File listed twice: /usr/lib64/R/library/utils/html/mirrorAdmin.html
warning: File listed twice: /usr/lib64/R/library/utils/html/modifyList.html
warning: File listed twice: /usr/lib64/R/library/utils/html/news.html
warning: File listed twice: /usr/lib64/R/library/utils/html/nsl.html
warning: File listed twice: /usr/lib64/R/library/utils/html/object.size.html
warning: File listed twice: /usr/lib64/R/library/utils/html/package.skeleton.html
warning: File listed twice: /usr/lib64/R/library/utils/html/packageDescription.html
warning: File listed twice: /usr/lib64/R/library/utils/html/packageName.html
warning: File listed twice: /usr/lib64/R/library/utils/html/packageStatus.html
warning: File listed twice: /usr/lib64/R/library/utils/html/page.html
warning: File listed twice: /usr/lib64/R/library/utils/html/person.html
warning: File listed twice: /usr/lib64/R/library/utils/html/process.events.html
warning: File listed twice: /usr/lib64/R/library/utils/html/prompt.html
warning: File listed twice: /usr/lib64/R/library/utils/html/promptData.html
warning: File listed twice: /usr/lib64/R/library/utils/html/promptPackage.html
warning: File listed twice: /usr/lib64/R/library/utils/html/rcompgen.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.DIF.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.fortran.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.fwf.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.socket.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.table.html
warning: File listed twice: /usr/lib64/R/library/utils/html/recover.html
warning: File listed twice: /usr/lib64/R/library/utils/html/relist.html
warning: File listed twice: /usr/lib64/R/library/utils/html/remove.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/removeSource.html
warning: File listed twice: /usr/lib64/R/library/utils/html/roman.html
warning: File listed twice: /usr/lib64/R/library/utils/html/rtags.html
warning: File listed twice: /usr/lib64/R/library/utils/html/savehistory.html
warning: File listed twice: /usr/lib64/R/library/utils/html/select.list.html
warning: File listed twice: /usr/lib64/R/library/utils/html/sessionInfo.html
warning: File listed twice: /usr/lib64/R/library/utils/html/setRepositories.html
warning: File listed twice: /usr/lib64/R/library/utils/html/sourceutils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/stack.html
warning: File listed twice: /usr/lib64/R/library/utils/html/str.html
warning: File listed twice: /usr/lib64/R/library/utils/html/summaryRprof.html
warning: File listed twice: /usr/lib64/R/library/utils/html/tar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/toLatex.html
warning: File listed twice: /usr/lib64/R/library/utils/html/txtProgressBar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/type.convert.html
warning: File listed twice: /usr/lib64/R/library/utils/html/untar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/unzip.html
warning: File listed twice: /usr/lib64/R/library/utils/html/update.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/url.show.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-defunct.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-deprecated.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-package.html
warning: File listed twice: /usr/lib64/R/library/utils/html/vignette.html
warning: File listed twice: /usr/lib64/R/library/utils/html/write.table.html
warning: File listed twice: /usr/lib64/R/library/utils/html/zip.html
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.aZijxB
find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,shell,tcl,typelib)
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
--- find-provides-deps	2015-12-11 12:41:49.784974777 +0000
+++ filter-provides-deps	2015-12-11 12:41:49.788974776 +0000
@@ -1 +1,2 @@
 libR.so()(64bit) = set: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
+libR-2.11.so()(64bit) = set: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
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.oYN8Bw
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,tcl,typelib)
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/MASS/libs/MASS.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/foreign/libs/foreign.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grDevices/libs/grDevices.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/graphics/libs/graphics.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grid/libs/grid.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/lattice/libs/lattice.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/nnet/libs/nnet.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/rpart/libs/rpart.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/spatial/libs/spatial.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/survival/libs/survival.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/utils/libs/utils.so: underlinked libraries: /lib64/liblzma.so.5 /lib64/libm.so.6
shebang.req.files: executable script /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh/echo.sh is not executable
find-requires: FINDPACKAGE-COMMANDS: cat grep sh
Provides: libR.so()(64bit) = set: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, libR-2.11.so()(64bit) = set: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
Requires: /bin/sh, /lib64/ld-linux-x86-64.so.2, coreutils, grep, ld-linux-x86-64.so.2()(64bit) >= set:ihbW3, ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit), libX11.so.6()(64bit) >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426Dgj994wsONU8RZq4ZjETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQZtURAFElDl8totXyLZkjPS80tH2, libXmu.so.6()(64bit) >= set:ljat5WdZ0, libXt.so.6()(64bit) >= set:miBmG8bmWeKY1r3A0IpjGJmzcnuk4L1fZ82d, libbz2.so.1()(64bit) >= set:ieU4cq8R9SL02Pd7T6CQAbuVPJL2, libc.so.6(GLIBC_2.11)(64bit), libc.so.6(GLIBC_2.14)(64bit), libc.so.6(GLIBC_2.15)(64bit), libc.so.6(GLIBC_2.16)(64bit), libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libc.so.6(GLIBC_2.6)(64bit), libc.so.6(GLIBC_2.7)(64bit), libc.so.6(GLIBC_2.8)(64bit), libcairo.so.2()(64bit) >= set:mgBeCp25NOIyrlQHFS7nAegwnSqIIeytSyjemApNcNsUClh1Z3fji718UL5HMxPMkimVZpVN9h6QFUdKO6OFjNsjitz641ARaZ5HZAmxdD86kgBnSaNq3ZAVlemZpcoP0tsFeDiZfuQuf3, libdl.so.2(GLIBC_2.2.5)(64bit), libgobject-2.0.so.0()(64bit) >= set:ml6W90, libicui18n.so.50()(64bit) >= set:qnzoOwLhMIix4mUiJaHPcrq7, libicuuc.so.50()(64bit) >= set:pnTfJo5ss, libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQ6Ly73P71OXgQjXcEVpBpZdQN0du6bEemIGcwvkRUyfGzE7kPRWTAeHIPYhIl5W1Y695GSMOChpvZBbtwQPBftLjrj750B9wOLQMqCw2WsWFYAb4WY6oiJ3rgT0C7giNl5FM20Ezc0060tUk1, liblzma.so.5()(64bit) >= set:kgIy0DJFZFQ2NtZsOqIUpfV9l2, libm.so.6(GLIBC_2.2.5)(64bit), libopenblas.so.0()(64bit) >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQ6cD75j31i4ky6SMMCoRQ1, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgd5, libpcre.so.3()(64bit) >= set:jgZdsEZ2sgNXHHLwc1, libpng15.so.15()(64bit) >= set:lhHMixNA5RSP1K7ShG9w7fCPfx2bPUEiWED20, libpng15.so.15(PNG15_0)(64bit), libreadline.so.6()(64bit) >= set:nioSWGipM22fZzwThmVscM35BWrboE0sZwI3SqZmoz0XZu0BVGKnVqw4lr, librt.so.1()(64bit) >= set:jiq20, librt.so.1(GLIBC_2.2.5)(64bit), libtiff.so.5()(64bit) >= set:lihRIYpxQTgnDIeRTSwCs2, libz.so.1()(64bit) >= set:kgb6dgbWdAhpAO8J7FmJCZm37ST4, rtld(GNU_HASH), sh
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.GoSVO4
Creating R-base-debuginfo package
Processing files: R-devel-3.1.2-alt1.1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.9JygaI
find-provides: broken symbolic link /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool -> ../../../bin/libtool is not going to provide anything
find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,shell,tcl,typelib)
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.TJYkgp
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,tcl,typelib)
/usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:39:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header
 #  error R_ext/GraphicsEngine.h must be included first, and includes this header
    ^
cpp.req: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed, trying c++ mode
/usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:39:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header
 #  error R_ext/GraphicsEngine.h must be included first, and includes this header
    ^
cpp.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed
find-requires: FINDPACKAGE-COMMANDS: chmod mkdir rm rmdir
Provides: pkgconfig(libR) = 3.1.2
PreReq: R-base = 3.1.2-alt1.1
Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/libR.so, /usr/lib64/pkgconfig, coreutils
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.X3pGRd
Processing files: R-tcltk-3.1.2-alt1.1
warning: File listed twice: /usr/lib64/R/library/tcltk/html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/R.css
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TclInterface.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkCommands.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgetcmds.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgets.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tclServiceMode.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-defunct.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-package.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkProgressBar.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkStartGUI.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.dir.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.files.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_messageBox.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_select.list.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkpager.html
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.zcdve6
find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,shell,tcl,typelib)
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.faeMl2
find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,tcl,typelib)
Provides: tcl(::Utility) = 1.0, tcl(::Utility::dump) = 1.0, tcl(::Utility::expand) = 1.0, tcl(::Utility::number) = 1.0, tcl(::Utility::string) = 1.0, tcl(::Utility::tk) = 1.0, tcl(Hierarchy) = 2.0, tcl(PBar) = 1.0, tcl(Widget) = 2.0
Requires: R-base = 3.1.2-alt1.1, libR.so()(64bit) >= set:ng3YhoVZ7zG1yRZ5FTWvS3cZe7GN2bQlckaUP3hGPQZ9ZDUD4rZrfNE7wbgoIdtiz5VnwW3HABLzZbEsM4Ch8s6gQMWD7416FVYn9zdqood7g7fgCwK9Giw5JBqEyOof0MFnhEpT9X5JupXdGI6VXZGYdo0iIJYXNsqzxXD0veJIrUzULDPywvN1, libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libtcl8.5.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.5.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk)
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.P4t8c2
Creating R-tcltk-debuginfo package
Processing files: R-doc-html-3.1.2-alt1.1
error: File not found by glob: /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/*.html


RPM build errors:
    File listed twice: /usr/lib64/R/library/KernSmooth/html
    File listed twice: /usr/lib64/R/library/KernSmooth/html/00Index.html
    File listed twice: /usr/lib64/R/library/KernSmooth/html/R.css
    File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde.html
    File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde2D.html
    File listed twice: /usr/lib64/R/library/KernSmooth/html/bkfe.html
    File listed twice: /usr/lib64/R/library/KernSmooth/html/dpih.html
    File listed twice: /usr/lib64/R/library/KernSmooth/html/dpik.html
    File listed twice: /usr/lib64/R/library/KernSmooth/html/dpill.html
    File listed twice: /usr/lib64/R/library/KernSmooth/html/locpoly.html
    File listed twice: /usr/lib64/R/library/MASS/html
    File listed twice: /usr/lib64/R/library/MASS/html/00Index.html
    File listed twice: /usr/lib64/R/library/MASS/html/Aids2.html
    File listed twice: /usr/lib64/R/library/MASS/html/Animals.html
    File listed twice: /usr/lib64/R/library/MASS/html/Boston.html
    File listed twice: /usr/lib64/R/library/MASS/html/Cars93.html
    File listed twice: /usr/lib64/R/library/MASS/html/Cushings.html
    File listed twice: /usr/lib64/R/library/MASS/html/DDT.html
    File listed twice: /usr/lib64/R/library/MASS/html/GAGurine.html
    File listed twice: /usr/lib64/R/library/MASS/html/Insurance.html
    File listed twice: /usr/lib64/R/library/MASS/html/MASS-internal.html
    File listed twice: /usr/lib64/R/library/MASS/html/Melanoma.html
    File listed twice: /usr/lib64/R/library/MASS/html/Null.html
    File listed twice: /usr/lib64/R/library/MASS/html/OME.html
    File listed twice: /usr/lib64/R/library/MASS/html/Pima.tr.html
    File listed twice: /usr/lib64/R/library/MASS/html/R.css
    File listed twice: /usr/lib64/R/library/MASS/html/Rabbit.html
    File listed twice: /usr/lib64/R/library/MASS/html/Rubber.html
    File listed twice: /usr/lib64/R/library/MASS/html/SP500.html
    File listed twice: /usr/lib64/R/library/MASS/html/Sitka.html
    File listed twice: /usr/lib64/R/library/MASS/html/Sitka89.html
    File listed twice: /usr/lib64/R/library/MASS/html/Skye.html
    File listed twice: /usr/lib64/R/library/MASS/html/Traffic.html
    File listed twice: /usr/lib64/R/library/MASS/html/UScereal.html
    File listed twice: /usr/lib64/R/library/MASS/html/UScrime.html
    File listed twice: /usr/lib64/R/library/MASS/html/VA.html
    File listed twice: /usr/lib64/R/library/MASS/html/abbey.html
    File listed twice: /usr/lib64/R/library/MASS/html/accdeaths.html
    File listed twice: /usr/lib64/R/library/MASS/html/addterm.html
    File listed twice: /usr/lib64/R/library/MASS/html/anorexia.html
    File listed twice: /usr/lib64/R/library/MASS/html/anova.negbin.html
    File listed twice: /usr/lib64/R/library/MASS/html/area.html
    File listed twice: /usr/lib64/R/library/MASS/html/bacteria.html
    File listed twice: /usr/lib64/R/library/MASS/html/bandwidth.nrd.html
    File listed twice: /usr/lib64/R/library/MASS/html/bcv.html
    File listed twice: /usr/lib64/R/library/MASS/html/beav1.html
    File listed twice: /usr/lib64/R/library/MASS/html/beav2.html
    File listed twice: /usr/lib64/R/library/MASS/html/biopsy.html
    File listed twice: /usr/lib64/R/library/MASS/html/birthwt.html
    File listed twice: /usr/lib64/R/library/MASS/html/boxcox.html
    File listed twice: /usr/lib64/R/library/MASS/html/cabbages.html
    File listed twice: /usr/lib64/R/library/MASS/html/caith.html
    File listed twice: /usr/lib64/R/library/MASS/html/cats.html
    File listed twice: /usr/lib64/R/library/MASS/html/cement.html
    File listed twice: /usr/lib64/R/library/MASS/html/chem.html
    File listed twice: /usr/lib64/R/library/MASS/html/con2tr.html
    File listed twice: /usr/lib64/R/library/MASS/html/confint.html
    File listed twice: /usr/lib64/R/library/MASS/html/contr.sdif.html
    File listed twice: /usr/lib64/R/library/MASS/html/coop.html
    File listed twice: /usr/lib64/R/library/MASS/html/corresp.html
    File listed twice: /usr/lib64/R/library/MASS/html/cov.rob.html
    File listed twice: /usr/lib64/R/library/MASS/html/cov.trob.html
    File listed twice: /usr/lib64/R/library/MASS/html/cpus.html
    File listed twice: /usr/lib64/R/library/MASS/html/crabs.html
    File listed twice: /usr/lib64/R/library/MASS/html/deaths.html
    File listed twice: /usr/lib64/R/library/MASS/html/denumerate.html
    File listed twice: /usr/lib64/R/library/MASS/html/dose.p.html
    File listed twice: /usr/lib64/R/library/MASS/html/drivers.html
    File listed twice: /usr/lib64/R/library/MASS/html/dropterm.html
    File listed twice: /usr/lib64/R/library/MASS/html/eagles.html
    File listed twice: /usr/lib64/R/library/MASS/html/epil.html
    File listed twice: /usr/lib64/R/library/MASS/html/eqscplot.html
    File listed twice: /usr/lib64/R/library/MASS/html/farms.html
    File listed twice: /usr/lib64/R/library/MASS/html/fgl.html
    File listed twice: /usr/lib64/R/library/MASS/html/fitdistr.html
    File listed twice: /usr/lib64/R/library/MASS/html/forbes.html
    File listed twice: /usr/lib64/R/library/MASS/html/fractions.html
    File listed twice: /usr/lib64/R/library/MASS/html/galaxies.html
    File listed twice: /usr/lib64/R/library/MASS/html/gamma.dispersion.html
    File listed twice: /usr/lib64/R/library/MASS/html/gamma.shape.glm.html
    File listed twice: /usr/lib64/R/library/MASS/html/gehan.html
    File listed twice: /usr/lib64/R/library/MASS/html/genotype.html
    File listed twice: /usr/lib64/R/library/MASS/html/geyser.html
    File listed twice: /usr/lib64/R/library/MASS/html/gilgais.html
    File listed twice: /usr/lib64/R/library/MASS/html/ginv.html
    File listed twice: /usr/lib64/R/library/MASS/html/glm.convert.html
    File listed twice: /usr/lib64/R/library/MASS/html/glm.nb.html
    File listed twice: /usr/lib64/R/library/MASS/html/glmmPQL.html
    File listed twice: /usr/lib64/R/library/MASS/html/hills.html
    File listed twice: /usr/lib64/R/library/MASS/html/hist.scott.html
    File listed twice: /usr/lib64/R/library/MASS/html/housing.html
    File listed twice: /usr/lib64/R/library/MASS/html/huber.html
    File listed twice: /usr/lib64/R/library/MASS/html/hubers.html
    File listed twice: /usr/lib64/R/library/MASS/html/immer.html
    File listed twice: /usr/lib64/R/library/MASS/html/isoMDS.html
    File listed twice: /usr/lib64/R/library/MASS/html/kde2d.html
    File listed twice: /usr/lib64/R/library/MASS/html/lda.html
    File listed twice: /usr/lib64/R/library/MASS/html/ldahist.html
    File listed twice: /usr/lib64/R/library/MASS/html/leuk.html
    File listed twice: /usr/lib64/R/library/MASS/html/lm.gls.html
    File listed twice: /usr/lib64/R/library/MASS/html/lm.ridge.html
    File listed twice: /usr/lib64/R/library/MASS/html/loglm.html
    File listed twice: /usr/lib64/R/library/MASS/html/loglm1.html
    File listed twice: /usr/lib64/R/library/MASS/html/logtrans.html
    File listed twice: /usr/lib64/R/library/MASS/html/lqs.html
    File listed twice: /usr/lib64/R/library/MASS/html/mammals.html
    File listed twice: /usr/lib64/R/library/MASS/html/mca.html
    File listed twice: /usr/lib64/R/library/MASS/html/mcycle.html
    File listed twice: /usr/lib64/R/library/MASS/html/menarche.html
    File listed twice: /usr/lib64/R/library/MASS/html/michelson.html
    File listed twice: /usr/lib64/R/library/MASS/html/minn38.html
    File listed twice: /usr/lib64/R/library/MASS/html/motors.html
    File listed twice: /usr/lib64/R/library/MASS/html/muscle.html
    File listed twice: /usr/lib64/R/library/MASS/html/mvrnorm.html
    File listed twice: /usr/lib64/R/library/MASS/html/negative.binomial.html
    File listed twice: /usr/lib64/R/library/MASS/html/newcomb.html
    File listed twice: /usr/lib64/R/library/MASS/html/nlschools.html
    File listed twice: /usr/lib64/R/library/MASS/html/npk.html
    File listed twice: /usr/lib64/R/library/MASS/html/npr1.html
    File listed twice: /usr/lib64/R/library/MASS/html/oats.html
    File listed twice: /usr/lib64/R/library/MASS/html/painters.html
    File listed twice: /usr/lib64/R/library/MASS/html/pairs.lda.html
    File listed twice: /usr/lib64/R/library/MASS/html/parcoord.html
    File listed twice: /usr/lib64/R/library/MASS/html/petrol.html
    File listed twice: /usr/lib64/R/library/MASS/html/phones.html
    File listed twice: /usr/lib64/R/library/MASS/html/plot.lda.html
    File listed twice: /usr/lib64/R/library/MASS/html/plot.mca.html
    File listed twice: /usr/lib64/R/library/MASS/html/plot.profile.html
    File listed twice: /usr/lib64/R/library/MASS/html/polr.html
    File listed twice: /usr/lib64/R/library/MASS/html/predict.glmmPQL.html
    File listed twice: /usr/lib64/R/library/MASS/html/predict.lda.html
    File listed twice: /usr/lib64/R/library/MASS/html/predict.lqs.html
    File listed twice: /usr/lib64/R/library/MASS/html/predict.mca.html
    File listed twice: /usr/lib64/R/library/MASS/html/predict.qda.html
    File listed twice: /usr/lib64/R/library/MASS/html/profile.glm.html
    File listed twice: /usr/lib64/R/library/MASS/html/qda.html
    File listed twice: /usr/lib64/R/library/MASS/html/quine.html
    File listed twice: /usr/lib64/R/library/MASS/html/rational.html
    File listed twice: /usr/lib64/R/library/MASS/html/renumerate.html
    File listed twice: /usr/lib64/R/library/MASS/html/rlm.html
    File listed twice: /usr/lib64/R/library/MASS/html/rms.curv.html
    File listed twice: /usr/lib64/R/library/MASS/html/rnegbin.html
    File listed twice: /usr/lib64/R/library/MASS/html/road.html
    File listed twice: /usr/lib64/R/library/MASS/html/rotifer.html
    File listed twice: /usr/lib64/R/library/MASS/html/sammon.html
    File listed twice: /usr/lib64/R/library/MASS/html/ships.html
    File listed twice: /usr/lib64/R/library/MASS/html/shoes.html
    File listed twice: /usr/lib64/R/library/MASS/html/shrimp.html
    File listed twice: /usr/lib64/R/library/MASS/html/shuttle.html
    File listed twice: /usr/lib64/R/library/MASS/html/snails.html
    File listed twice: /usr/lib64/R/library/MASS/html/stdres.html
    File listed twice: /usr/lib64/R/library/MASS/html/steam.html
    File listed twice: /usr/lib64/R/library/MASS/html/stepAIC.html
    File listed twice: /usr/lib64/R/library/MASS/html/stormer.html
    File listed twice: /usr/lib64/R/library/MASS/html/studres.html
    File listed twice: /usr/lib64/R/library/MASS/html/summary.loglm.html
    File listed twice: /usr/lib64/R/library/MASS/html/summary.negbin.html
    File listed twice: /usr/lib64/R/library/MASS/html/summary.rlm.html
    File listed twice: /usr/lib64/R/library/MASS/html/survey.html
    File listed twice: /usr/lib64/R/library/MASS/html/synth.tr.html
    File listed twice: /usr/lib64/R/library/MASS/html/theta.md.html
    File listed twice: /usr/lib64/R/library/MASS/html/topo.html
    File listed twice: /usr/lib64/R/library/MASS/html/truehist.html
    File listed twice: /usr/lib64/R/library/MASS/html/ucv.html
    File listed twice: /usr/lib64/R/library/MASS/html/waders.html
    File listed twice: /usr/lib64/R/library/MASS/html/whiteside.html
    File listed twice: /usr/lib64/R/library/MASS/html/width.SJ.html
    File listed twice: /usr/lib64/R/library/MASS/html/write.matrix.html
    File listed twice: /usr/lib64/R/library/MASS/html/wtloss.html
    File listed twice: /usr/lib64/R/library/Matrix/html
    File listed twice: /usr/lib64/R/library/Matrix/html/00Index.html
    File listed twice: /usr/lib64/R/library/Matrix/html/BunchKaufman-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/CAex.html
    File listed twice: /usr/lib64/R/library/Matrix/html/CHMfactor-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Cholesky-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Cholesky.html
    File listed twice: /usr/lib64/R/library/Matrix/html/CsparseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Diagonal.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Hilbert.html
    File listed twice: /usr/lib64/R/library/Matrix/html/KNex.html
    File listed twice: /usr/lib64/R/library/Matrix/html/KhatriRao.html
    File listed twice: /usr/lib64/R/library/Matrix/html/LU-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Matrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Matrix.html
    File listed twice: /usr/lib64/R/library/Matrix/html/MatrixFactorization-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/R.css
    File listed twice: /usr/lib64/R/library/Matrix/html/RsparseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Schur-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Schur.html
    File listed twice: /usr/lib64/R/library/Matrix/html/SparseM-conv.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Subassign-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/TsparseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/USCounties.html
    File listed twice: /usr/lib64/R/library/Matrix/html/Xtrct-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/abIndex-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/abIseq.html
    File listed twice: /usr/lib64/R/library/Matrix/html/all-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/all.equal-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/atomicVector-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/band.html
    File listed twice: /usr/lib64/R/library/Matrix/html/bandSparse.html
    File listed twice: /usr/lib64/R/library/Matrix/html/bdiag.html
    File listed twice: /usr/lib64/R/library/Matrix/html/cBind.html
    File listed twice: /usr/lib64/R/library/Matrix/html/chol.html
    File listed twice: /usr/lib64/R/library/Matrix/html/chol2inv-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/colSums.html
    File listed twice: /usr/lib64/R/library/Matrix/html/compMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/condest.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/ddenseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/ddiMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/denseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dgCMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dgRMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dgTMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dgeMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/diagU2N.html
    File listed twice: /usr/lib64/R/library/Matrix/html/diagonalMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dpoMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/drop0.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dsCMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dsRMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dsparseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dsyMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dtCMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dtRMatrix-class-def.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dtpMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/dtrMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/expand.html
    File listed twice: /usr/lib64/R/library/Matrix/html/expm.html
    File listed twice: /usr/lib64/R/library/Matrix/html/externalFormats.html
    File listed twice: /usr/lib64/R/library/Matrix/html/facmul.html
    File listed twice: /usr/lib64/R/library/Matrix/html/forceSymmetric.html
    File listed twice: /usr/lib64/R/library/Matrix/html/formatSparseM.html
    File listed twice: /usr/lib64/R/library/Matrix/html/generalMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/graph2T.html
    File listed twice: /usr/lib64/R/library/Matrix/html/image-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/indMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/index-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/invPerm.html
    File listed twice: /usr/lib64/R/library/Matrix/html/is.na-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/is.null.DN.html
    File listed twice: /usr/lib64/R/library/Matrix/html/isSymmetric-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/isTriangular.html
    File listed twice: /usr/lib64/R/library/Matrix/html/kronecker-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/ldenseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/ldiMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/lgeMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/lsparseMatrix-classes.html
    File listed twice: /usr/lib64/R/library/Matrix/html/lsyMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/ltrMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/lu.html
    File listed twice: /usr/lib64/R/library/Matrix/html/matrix-products.html
    File listed twice: /usr/lib64/R/library/Matrix/html/nMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/ndenseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/nearPD.html
    File listed twice: /usr/lib64/R/library/Matrix/html/ngeMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/nnzero.html
    File listed twice: /usr/lib64/R/library/Matrix/html/norm.html
    File listed twice: /usr/lib64/R/library/Matrix/html/nsparseMatrix-classes.html
    File listed twice: /usr/lib64/R/library/Matrix/html/nsyMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/ntrMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/number-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/pMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/printSpMatrix.html
    File listed twice: /usr/lib64/R/library/Matrix/html/qr-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/rankMatrix.html
    File listed twice: /usr/lib64/R/library/Matrix/html/rcond.html
    File listed twice: /usr/lib64/R/library/Matrix/html/rep2abI.html
    File listed twice: /usr/lib64/R/library/Matrix/html/replValue-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/rleDiff-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/rsparsematrix.html
    File listed twice: /usr/lib64/R/library/Matrix/html/solve-methods.html
    File listed twice: /usr/lib64/R/library/Matrix/html/spMatrix.html
    File listed twice: /usr/lib64/R/library/Matrix/html/sparse.model.matrix.html
    File listed twice: /usr/lib64/R/library/Matrix/html/sparseLU-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/sparseMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/sparseMatrix.html
    File listed twice: /usr/lib64/R/library/Matrix/html/sparseQR-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/sparseVector-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/sparseVector.html
    File listed twice: /usr/lib64/R/library/Matrix/html/symmetricMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/symmpart.html
    File listed twice: /usr/lib64/R/library/Matrix/html/triangularMatrix-class.html
    File listed twice: /usr/lib64/R/library/Matrix/html/unpack.html
    File listed twice: /usr/lib64/R/library/Matrix/html/unused-classes.html
    File listed twice: /usr/lib64/R/library/Matrix/html/updown.html
    File listed twice: /usr/lib64/R/library/base/html
    File listed twice: /usr/lib64/R/library/base/html/00Index.html
    File listed twice: /usr/lib64/R/library/base/html/Arithmetic.html
    File listed twice: /usr/lib64/R/library/base/html/AsIs.html
    File listed twice: /usr/lib64/R/library/base/html/Bessel.html
    File listed twice: /usr/lib64/R/library/base/html/CallExternal.html
    File listed twice: /usr/lib64/R/library/base/html/Colon.html
    File listed twice: /usr/lib64/R/library/base/html/Comparison.html
    File listed twice: /usr/lib64/R/library/base/html/Constants.html
    File listed twice: /usr/lib64/R/library/base/html/Control.html
    File listed twice: /usr/lib64/R/library/base/html/Cstack_info.html
    File listed twice: /usr/lib64/R/library/base/html/DateTimeClasses.html
    File listed twice: /usr/lib64/R/library/base/html/Dates.html
    File listed twice: /usr/lib64/R/library/base/html/Defunct.html
    File listed twice: /usr/lib64/R/library/base/html/Deprecated.html
    File listed twice: /usr/lib64/R/library/base/html/Encoding.html
    File listed twice: /usr/lib64/R/library/base/html/EnvVar.html
    File listed twice: /usr/lib64/R/library/base/html/Extract.data.frame.html
    File listed twice: /usr/lib64/R/library/base/html/Extract.factor.html
    File listed twice: /usr/lib64/R/library/base/html/Extract.html
    File listed twice: /usr/lib64/R/library/base/html/Extremes.html
    File listed twice: /usr/lib64/R/library/base/html/Foreign-internal.html
    File listed twice: /usr/lib64/R/library/base/html/Foreign.html
    File listed twice: /usr/lib64/R/library/base/html/Hyperbolic.html
    File listed twice: /usr/lib64/R/library/base/html/ISOdatetime.html
    File listed twice: /usr/lib64/R/library/base/html/Internal.html
    File listed twice: /usr/lib64/R/library/base/html/InternalMethods.html
    File listed twice: /usr/lib64/R/library/base/html/La_version.html
    File listed twice: /usr/lib64/R/library/base/html/Last.value.html
    File listed twice: /usr/lib64/R/library/base/html/Log.html
    File listed twice: /usr/lib64/R/library/base/html/Logic.html
    File listed twice: /usr/lib64/R/library/base/html/LongVectors.html
    File listed twice: /usr/lib64/R/library/base/html/MathFun.html
    File listed twice: /usr/lib64/R/library/base/html/Memory-limits.html
    File listed twice: /usr/lib64/R/library/base/html/Memory.html
    File listed twice: /usr/lib64/R/library/base/html/NA.html
    File listed twice: /usr/lib64/R/library/base/html/NULL.html
    File listed twice: /usr/lib64/R/library/base/html/NumericConstants.html
    File listed twice: /usr/lib64/R/library/base/html/Ops.Date.html
    File listed twice: /usr/lib64/R/library/base/html/Paren.html
    File listed twice: /usr/lib64/R/library/base/html/Platform.html
    File listed twice: /usr/lib64/R/library/base/html/Primitive.html
    File listed twice: /usr/lib64/R/library/base/html/Quotes.html
    File listed twice: /usr/lib64/R/library/base/html/R.css
    File listed twice: /usr/lib64/R/library/base/html/Random-user.html
    File listed twice: /usr/lib64/R/library/base/html/Random.html
    File listed twice: /usr/lib64/R/library/base/html/RdUtils.html
    File listed twice: /usr/lib64/R/library/base/html/Recall.html
    File listed twice: /usr/lib64/R/library/base/html/Reserved.html
    File listed twice: /usr/lib64/R/library/base/html/Rhome.html
    File listed twice: /usr/lib64/R/library/base/html/Round.html
    File listed twice: /usr/lib64/R/library/base/html/Signals.html
    File listed twice: /usr/lib64/R/library/base/html/Special.html
    File listed twice: /usr/lib64/R/library/base/html/Startup.html
    File listed twice: /usr/lib64/R/library/base/html/Syntax.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.getenv.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.getpid.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.glob.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.info.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.localeconv.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.readlink.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.setFileTime.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.setenv.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.sleep.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.time.html
    File listed twice: /usr/lib64/R/library/base/html/Sys.which.html
    File listed twice: /usr/lib64/R/library/base/html/Trig.html
    File listed twice: /usr/lib64/R/library/base/html/UseMethod.html
    File listed twice: /usr/lib64/R/library/base/html/Vectorize.html
    File listed twice: /usr/lib64/R/library/base/html/Version.html
    File listed twice: /usr/lib64/R/library/base/html/abbreviate.html
    File listed twice: /usr/lib64/R/library/base/html/agrep.html
    File listed twice: /usr/lib64/R/library/base/html/all.equal.html
    File listed twice: /usr/lib64/R/library/base/html/all.html
    File listed twice: /usr/lib64/R/library/base/html/allnames.html
    File listed twice: /usr/lib64/R/library/base/html/any.html
    File listed twice: /usr/lib64/R/library/base/html/aperm.html
    File listed twice: /usr/lib64/R/library/base/html/append.html
    File listed twice: /usr/lib64/R/library/base/html/apply.html
    File listed twice: /usr/lib64/R/library/base/html/args.html
    File listed twice: /usr/lib64/R/library/base/html/array.html
    File listed twice: /usr/lib64/R/library/base/html/as.Date.html
    File listed twice: /usr/lib64/R/library/base/html/as.POSIXlt.html
    File listed twice: /usr/lib64/R/library/base/html/as.data.frame.html
    File listed twice: /usr/lib64/R/library/base/html/as.environment.html
    File listed twice: /usr/lib64/R/library/base/html/as.function.html
    File listed twice: /usr/lib64/R/library/base/html/assign.html
    File listed twice: /usr/lib64/R/library/base/html/assignOps.html
    File listed twice: /usr/lib64/R/library/base/html/attach.html
    File listed twice: /usr/lib64/R/library/base/html/attr.html
    File listed twice: /usr/lib64/R/library/base/html/attributes.html
    File listed twice: /usr/lib64/R/library/base/html/autoload.html
    File listed twice: /usr/lib64/R/library/base/html/backsolve.html
    File listed twice: /usr/lib64/R/library/base/html/base-defunct.html
    File listed twice: /usr/lib64/R/library/base/html/base-deprecated.html
    File listed twice: /usr/lib64/R/library/base/html/base-internal.html
    File listed twice: /usr/lib64/R/library/base/html/base-package.html
    File listed twice: /usr/lib64/R/library/base/html/basename.html
    File listed twice: /usr/lib64/R/library/base/html/bincode.html
    File listed twice: /usr/lib64/R/library/base/html/bindenv.html
    File listed twice: /usr/lib64/R/library/base/html/bitwise.html
    File listed twice: /usr/lib64/R/library/base/html/body.html
    File listed twice: /usr/lib64/R/library/base/html/bquote.html
    File listed twice: /usr/lib64/R/library/base/html/browser.html
    File listed twice: /usr/lib64/R/library/base/html/browserText.html
    File listed twice: /usr/lib64/R/library/base/html/builtins.html
    File listed twice: /usr/lib64/R/library/base/html/by.html
    File listed twice: /usr/lib64/R/library/base/html/c.html
    File listed twice: /usr/lib64/R/library/base/html/call.html
    File listed twice: /usr/lib64/R/library/base/html/callCC.html
    File listed twice: /usr/lib64/R/library/base/html/capabilities.html
    File listed twice: /usr/lib64/R/library/base/html/cat.html
    File listed twice: /usr/lib64/R/library/base/html/cbind.html
    File listed twice: /usr/lib64/R/library/base/html/char.expand.html
    File listed twice: /usr/lib64/R/library/base/html/character.html
    File listed twice: /usr/lib64/R/library/base/html/charmatch.html
    File listed twice: /usr/lib64/R/library/base/html/chartr.html
    File listed twice: /usr/lib64/R/library/base/html/chol.html
    File listed twice: /usr/lib64/R/library/base/html/chol2inv.html
    File listed twice: /usr/lib64/R/library/base/html/class.html
    File listed twice: /usr/lib64/R/library/base/html/col.html
    File listed twice: /usr/lib64/R/library/base/html/colSums.html
    File listed twice: /usr/lib64/R/library/base/html/colnames.html
    File listed twice: /usr/lib64/R/library/base/html/commandArgs.html
    File listed twice: /usr/lib64/R/library/base/html/comment.html
    File listed twice: /usr/lib64/R/library/base/html/complex.html
    File listed twice: /usr/lib64/R/library/base/html/conditions.html
    File listed twice: /usr/lib64/R/library/base/html/conflicts.html
    File listed twice: /usr/lib64/R/library/base/html/connections.html
    File listed twice: /usr/lib64/R/library/base/html/contributors.html
    File listed twice: /usr/lib64/R/library/base/html/copyright.html
    File listed twice: /usr/lib64/R/library/base/html/crossprod.html
    File listed twice: /usr/lib64/R/library/base/html/cumsum.html
    File listed twice: /usr/lib64/R/library/base/html/cut.POSIXt.html
    File listed twice: /usr/lib64/R/library/base/html/cut.html
    File listed twice: /usr/lib64/R/library/base/html/data.class.html
    File listed twice: /usr/lib64/R/library/base/html/data.frame.html
    File listed twice: /usr/lib64/R/library/base/html/data.matrix.html
    File listed twice: /usr/lib64/R/library/base/html/dataframeHelpers.html
    File listed twice: /usr/lib64/R/library/base/html/date.html
    File listed twice: /usr/lib64/R/library/base/html/dcf.html
    File listed twice: /usr/lib64/R/library/base/html/debug.html
    File listed twice: /usr/lib64/R/library/base/html/delayedAssign.html
    File listed twice: /usr/lib64/R/library/base/html/deparse.html
    File listed twice: /usr/lib64/R/library/base/html/deparseOpts.html
    File listed twice: /usr/lib64/R/library/base/html/det.html
    File listed twice: /usr/lib64/R/library/base/html/detach.html
    File listed twice: /usr/lib64/R/library/base/html/dev.html
    File listed twice: /usr/lib64/R/library/base/html/diag.html
    File listed twice: /usr/lib64/R/library/base/html/diff.html
    File listed twice: /usr/lib64/R/library/base/html/difftime.html
    File listed twice: /usr/lib64/R/library/base/html/dim.html
    File listed twice: /usr/lib64/R/library/base/html/dimnames.html
    File listed twice: /usr/lib64/R/library/base/html/do.call.html
    File listed twice: /usr/lib64/R/library/base/html/dontCheck.html
    File listed twice: /usr/lib64/R/library/base/html/double.html
    File listed twice: /usr/lib64/R/library/base/html/dput.html
    File listed twice: /usr/lib64/R/library/base/html/drop.html
    File listed twice: /usr/lib64/R/library/base/html/droplevels.html
    File listed twice: /usr/lib64/R/library/base/html/dump.html
    File listed twice: /usr/lib64/R/library/base/html/duplicated.html
    File listed twice: /usr/lib64/R/library/base/html/dynload.html
    File listed twice: /usr/lib64/R/library/base/html/eapply.html
    File listed twice: /usr/lib64/R/library/base/html/eigen.html
    File listed twice: /usr/lib64/R/library/base/html/encodeString.html
    File listed twice: /usr/lib64/R/library/base/html/environment.html
    File listed twice: /usr/lib64/R/library/base/html/eval.html
    File listed twice: /usr/lib64/R/library/base/html/exists.html
    File listed twice: /usr/lib64/R/library/base/html/expand.grid.html
    File listed twice: /usr/lib64/R/library/base/html/expression.html
    File listed twice: /usr/lib64/R/library/base/html/factor.html
    File listed twice: /usr/lib64/R/library/base/html/file.access.html
    File listed twice: /usr/lib64/R/library/base/html/file.choose.html
    File listed twice: /usr/lib64/R/library/base/html/file.info.html
    File listed twice: /usr/lib64/R/library/base/html/file.path.html
    File listed twice: /usr/lib64/R/library/base/html/file.show.html
    File listed twice: /usr/lib64/R/library/base/html/files.html
    File listed twice: /usr/lib64/R/library/base/html/files2.html
    File listed twice: /usr/lib64/R/library/base/html/find.package.html
    File listed twice: /usr/lib64/R/library/base/html/findInterval.html
    File listed twice: /usr/lib64/R/library/base/html/force.html
    File listed twice: /usr/lib64/R/library/base/html/formals.html
    File listed twice: /usr/lib64/R/library/base/html/format.html
    File listed twice: /usr/lib64/R/library/base/html/format.info.html
    File listed twice: /usr/lib64/R/library/base/html/format.pval.html
    File listed twice: /usr/lib64/R/library/base/html/formatDL.html
    File listed twice: /usr/lib64/R/library/base/html/formatc.html
    File listed twice: /usr/lib64/R/library/base/html/function.html
    File listed twice: /usr/lib64/R/library/base/html/funprog.html
    File listed twice: /usr/lib64/R/library/base/html/gc.html
    File listed twice: /usr/lib64/R/library/base/html/gc.time.html
    File listed twice: /usr/lib64/R/library/base/html/gctorture.html
    File listed twice: /usr/lib64/R/library/base/html/get.html
    File listed twice: /usr/lib64/R/library/base/html/getCallingDLL.html
    File listed twice: /usr/lib64/R/library/base/html/getDLLRegisteredRoutines.html
    File listed twice: /usr/lib64/R/library/base/html/getLoadedDLLs.html
    File listed twice: /usr/lib64/R/library/base/html/getNativeSymbolInfo.html
    File listed twice: /usr/lib64/R/library/base/html/gettext.html
    File listed twice: /usr/lib64/R/library/base/html/getwd.html
    File listed twice: /usr/lib64/R/library/base/html/gl.html
    File listed twice: /usr/lib64/R/library/base/html/grep.html
    File listed twice: /usr/lib64/R/library/base/html/grepRaw.html
    File listed twice: /usr/lib64/R/library/base/html/groupGeneric.html
    File listed twice: /usr/lib64/R/library/base/html/gzcon.html
    File listed twice: /usr/lib64/R/library/base/html/hexmode.html
    File listed twice: /usr/lib64/R/library/base/html/iconv.html
    File listed twice: /usr/lib64/R/library/base/html/icuSetCollate.html
    File listed twice: /usr/lib64/R/library/base/html/identical.html
    File listed twice: /usr/lib64/R/library/base/html/identity.html
    File listed twice: /usr/lib64/R/library/base/html/ifelse.html
    File listed twice: /usr/lib64/R/library/base/html/integer.html
    File listed twice: /usr/lib64/R/library/base/html/interaction.html
    File listed twice: /usr/lib64/R/library/base/html/interactive.html
    File listed twice: /usr/lib64/R/library/base/html/invisible.html
    File listed twice: /usr/lib64/R/library/base/html/is.finite.html
    File listed twice: /usr/lib64/R/library/base/html/is.function.html
    File listed twice: /usr/lib64/R/library/base/html/is.language.html
    File listed twice: /usr/lib64/R/library/base/html/is.object.html
    File listed twice: /usr/lib64/R/library/base/html/is.recursive.html
    File listed twice: /usr/lib64/R/library/base/html/is.single.html
    File listed twice: /usr/lib64/R/library/base/html/is.unsorted.html
    File listed twice: /usr/lib64/R/library/base/html/isR.html
    File listed twice: /usr/lib64/R/library/base/html/isS4.html
    File listed twice: /usr/lib64/R/library/base/html/isSymmetric.html
    File listed twice: /usr/lib64/R/library/base/html/jitter.html
    File listed twice: /usr/lib64/R/library/base/html/kappa.html
    File listed twice: /usr/lib64/R/library/base/html/kronecker.html
    File listed twice: /usr/lib64/R/library/base/html/l10n_info.html
    File listed twice: /usr/lib64/R/library/base/html/labels.html
    File listed twice: /usr/lib64/R/library/base/html/lapply.html
    File listed twice: /usr/lib64/R/library/base/html/lazyload.html
    File listed twice: /usr/lib64/R/library/base/html/length.html
    File listed twice: /usr/lib64/R/library/base/html/levels.html
    File listed twice: /usr/lib64/R/library/base/html/libPaths.html
    File listed twice: /usr/lib64/R/library/base/html/library.dynam.html
    File listed twice: /usr/lib64/R/library/base/html/library.html
    File listed twice: /usr/lib64/R/library/base/html/license.html
    File listed twice: /usr/lib64/R/library/base/html/list.files.html
    File listed twice: /usr/lib64/R/library/base/html/list.html
    File listed twice: /usr/lib64/R/library/base/html/list2env.html
    File listed twice: /usr/lib64/R/library/base/html/load.html
    File listed twice: /usr/lib64/R/library/base/html/locales.html
    File listed twice: /usr/lib64/R/library/base/html/logical.html
    File listed twice: /usr/lib64/R/library/base/html/lower.tri.html
    File listed twice: /usr/lib64/R/library/base/html/ls.html
    File listed twice: /usr/lib64/R/library/base/html/make.names.html
    File listed twice: /usr/lib64/R/library/base/html/make.unique.html
    File listed twice: /usr/lib64/R/library/base/html/mapply.html
    File listed twice: /usr/lib64/R/library/base/html/margin.table.html
    File listed twice: /usr/lib64/R/library/base/html/mat.or.vec.html
    File listed twice: /usr/lib64/R/library/base/html/match.arg.html
    File listed twice: /usr/lib64/R/library/base/html/match.call.html
    File listed twice: /usr/lib64/R/library/base/html/match.fun.html
    File listed twice: /usr/lib64/R/library/base/html/match.html
    File listed twice: /usr/lib64/R/library/base/html/matmult.html
    File listed twice: /usr/lib64/R/library/base/html/matrix.html
    File listed twice: /usr/lib64/R/library/base/html/maxCol.html
    File listed twice: /usr/lib64/R/library/base/html/mean.html
    File listed twice: /usr/lib64/R/library/base/html/memCompress.html
    File listed twice: /usr/lib64/R/library/base/html/memory.profile.html
    File listed twice: /usr/lib64/R/library/base/html/merge.html
    File listed twice: /usr/lib64/R/library/base/html/message.html
    File listed twice: /usr/lib64/R/library/base/html/missing.html
    File listed twice: /usr/lib64/R/library/base/html/mode.html
    File listed twice: /usr/lib64/R/library/base/html/name.html
    File listed twice: /usr/lib64/R/library/base/html/names.html
    File listed twice: /usr/lib64/R/library/base/html/nargs.html
    File listed twice: /usr/lib64/R/library/base/html/nchar.html
    File listed twice: /usr/lib64/R/library/base/html/nlevels.html
    File listed twice: /usr/lib64/R/library/base/html/noquote.html
    File listed twice: /usr/lib64/R/library/base/html/norm.html
    File listed twice: /usr/lib64/R/library/base/html/normalizePath.html
    File listed twice: /usr/lib64/R/library/base/html/notyet.html
    File listed twice: /usr/lib64/R/library/base/html/nrow.html
    File listed twice: /usr/lib64/R/library/base/html/ns-dblcolon.html
    File listed twice: /usr/lib64/R/library/base/html/ns-hooks.html
    File listed twice: /usr/lib64/R/library/base/html/ns-internal.html
    File listed twice: /usr/lib64/R/library/base/html/ns-load.html
    File listed twice: /usr/lib64/R/library/base/html/ns-reflect.html
    File listed twice: /usr/lib64/R/library/base/html/ns-topenv.html
    File listed twice: /usr/lib64/R/library/base/html/numeric.html
    File listed twice: /usr/lib64/R/library/base/html/numeric_version.html
    File listed twice: /usr/lib64/R/library/base/html/octmode.html
    File listed twice: /usr/lib64/R/library/base/html/on.exit.html
    File listed twice: /usr/lib64/R/library/base/html/options.html
    File listed twice: /usr/lib64/R/library/base/html/order.html
    File listed twice: /usr/lib64/R/library/base/html/outer.html
    File listed twice: /usr/lib64/R/library/base/html/parse.html
    File listed twice: /usr/lib64/R/library/base/html/paste.html
    File listed twice: /usr/lib64/R/library/base/html/path.expand.html
    File listed twice: /usr/lib64/R/library/base/html/pmatch.html
    File listed twice: /usr/lib64/R/library/base/html/polyroot.html
    File listed twice: /usr/lib64/R/library/base/html/pos.to.env.html
    File listed twice: /usr/lib64/R/library/base/html/pretty.html
    File listed twice: /usr/lib64/R/library/base/html/print.dataframe.html
    File listed twice: /usr/lib64/R/library/base/html/print.default.html
    File listed twice: /usr/lib64/R/library/base/html/print.html
    File listed twice: /usr/lib64/R/library/base/html/prmatrix.html
    File listed twice: /usr/lib64/R/library/base/html/proc.time.html
    File listed twice: /usr/lib64/R/library/base/html/prod.html
    File listed twice: /usr/lib64/R/library/base/html/prop.table.html
    File listed twice: /usr/lib64/R/library/base/html/pushBack.html
    File listed twice: /usr/lib64/R/library/base/html/qr.html
    File listed twice: /usr/lib64/R/library/base/html/qraux.html
    File listed twice: /usr/lib64/R/library/base/html/quit.html
    File listed twice: /usr/lib64/R/library/base/html/range.html
    File listed twice: /usr/lib64/R/library/base/html/rank.html
    File listed twice: /usr/lib64/R/library/base/html/rapply.html
    File listed twice: /usr/lib64/R/library/base/html/raw.html
    File listed twice: /usr/lib64/R/library/base/html/rawConnection.html
    File listed twice: /usr/lib64/R/library/base/html/rawConversion.html
    File listed twice: /usr/lib64/R/library/base/html/readBin.html
    File listed twice: /usr/lib64/R/library/base/html/readChar.html
    File listed twice: /usr/lib64/R/library/base/html/readLines.html
    File listed twice: /usr/lib64/R/library/base/html/readRDS.html
    File listed twice: /usr/lib64/R/library/base/html/readRenviron.html
    File listed twice: /usr/lib64/R/library/base/html/readline.html
    File listed twice: /usr/lib64/R/library/base/html/reg.finalizer.html
    File listed twice: /usr/lib64/R/library/base/html/regex.html
    File listed twice: /usr/lib64/R/library/base/html/regmatches.html
    File listed twice: /usr/lib64/R/library/base/html/rep.html
    File listed twice: /usr/lib64/R/library/base/html/replace.html
    File listed twice: /usr/lib64/R/library/base/html/rev.html
    File listed twice: /usr/lib64/R/library/base/html/rle.html
    File listed twice: /usr/lib64/R/library/base/html/rm.html
    File listed twice: /usr/lib64/R/library/base/html/round.POSIXt.html
    File listed twice: /usr/lib64/R/library/base/html/row.html
    File listed twice: /usr/lib64/R/library/base/html/row.names.html
    File listed twice: /usr/lib64/R/library/base/html/rowsum.html
    File listed twice: /usr/lib64/R/library/base/html/sQuote.html
    File listed twice: /usr/lib64/R/library/base/html/sample.html
    File listed twice: /usr/lib64/R/library/base/html/save.html
    File listed twice: /usr/lib64/R/library/base/html/scale.html
    File listed twice: /usr/lib64/R/library/base/html/scan.html
    File listed twice: /usr/lib64/R/library/base/html/search.html
    File listed twice: /usr/lib64/R/library/base/html/seek.html
    File listed twice: /usr/lib64/R/library/base/html/seq.Date.html
    File listed twice: /usr/lib64/R/library/base/html/seq.POSIXt.html
    File listed twice: /usr/lib64/R/library/base/html/seq.html
    File listed twice: /usr/lib64/R/library/base/html/sequence.html
    File listed twice: /usr/lib64/R/library/base/html/serialize.html
    File listed twice: /usr/lib64/R/library/base/html/setTimeLimit.html
    File listed twice: /usr/lib64/R/library/base/html/sets.html
    File listed twice: /usr/lib64/R/library/base/html/shQuote.html
    File listed twice: /usr/lib64/R/library/base/html/showConnections.html
    File listed twice: /usr/lib64/R/library/base/html/sign.html
    File listed twice: /usr/lib64/R/library/base/html/sink.html
    File listed twice: /usr/lib64/R/library/base/html/slice.index.html
    File listed twice: /usr/lib64/R/library/base/html/slotOp.html
    File listed twice: /usr/lib64/R/library/base/html/socketSelect.html
    File listed twice: /usr/lib64/R/library/base/html/solve.html
    File listed twice: /usr/lib64/R/library/base/html/sort.html
    File listed twice: /usr/lib64/R/library/base/html/source.html
    File listed twice: /usr/lib64/R/library/base/html/split.html
    File listed twice: /usr/lib64/R/library/base/html/sprintf.html
    File listed twice: /usr/lib64/R/library/base/html/srcfile.html
    File listed twice: /usr/lib64/R/library/base/html/standardGeneric.html
    File listed twice: /usr/lib64/R/library/base/html/stop.html
    File listed twice: /usr/lib64/R/library/base/html/stopifnot.html
    File listed twice: /usr/lib64/R/library/base/html/strptime.html
    File listed twice: /usr/lib64/R/library/base/html/strsplit.html
    File listed twice: /usr/lib64/R/library/base/html/strtoi.html
    File listed twice: /usr/lib64/R/library/base/html/strtrim.html
    File listed twice: /usr/lib64/R/library/base/html/structure.html
    File listed twice: /usr/lib64/R/library/base/html/strwrap.html
    File listed twice: /usr/lib64/R/library/base/html/subset.html
    File listed twice: /usr/lib64/R/library/base/html/substitute.html
    File listed twice: /usr/lib64/R/library/base/html/substr.html
    File listed twice: /usr/lib64/R/library/base/html/sum.html
    File listed twice: /usr/lib64/R/library/base/html/summary.html
    File listed twice: /usr/lib64/R/library/base/html/svd.html
    File listed twice: /usr/lib64/R/library/base/html/sweep.html
    File listed twice: /usr/lib64/R/library/base/html/switch.html
    File listed twice: /usr/lib64/R/library/base/html/sys.parent.html
    File listed twice: /usr/lib64/R/library/base/html/sys.source.html
    File listed twice: /usr/lib64/R/library/base/html/system.file.html
    File listed twice: /usr/lib64/R/library/base/html/system.html
    File listed twice: /usr/lib64/R/library/base/html/system.time.html
    File listed twice: /usr/lib64/R/library/base/html/system2.html
    File listed twice: /usr/lib64/R/library/base/html/t.html
    File listed twice: /usr/lib64/R/library/base/html/table.html
    File listed twice: /usr/lib64/R/library/base/html/tabulate.html
    File listed twice: /usr/lib64/R/library/base/html/tapply.html
    File listed twice: /usr/lib64/R/library/base/html/taskCallback.html
    File listed twice: /usr/lib64/R/library/base/html/taskCallbackManager.html
    File listed twice: /usr/lib64/R/library/base/html/taskCallbackNames.html
    File listed twice: /usr/lib64/R/library/base/html/tempfile.html
    File listed twice: /usr/lib64/R/library/base/html/textconnections.html
    File listed twice: /usr/lib64/R/library/base/html/tilde.html
    File listed twice: /usr/lib64/R/library/base/html/timezones.html
    File listed twice: /usr/lib64/R/library/base/html/toString.html
    File listed twice: /usr/lib64/R/library/base/html/trace.html
    File listed twice: /usr/lib64/R/library/base/html/traceback.html
    File listed twice: /usr/lib64/R/library/base/html/tracemem.html
    File listed twice: /usr/lib64/R/library/base/html/transform.html
    File listed twice: /usr/lib64/R/library/base/html/try.html
    File listed twice: /usr/lib64/R/library/base/html/typeof.html
    File listed twice: /usr/lib64/R/library/base/html/unique.html
    File listed twice: /usr/lib64/R/library/base/html/unlink.html
    File listed twice: /usr/lib64/R/library/base/html/unlist.html
    File listed twice: /usr/lib64/R/library/base/html/unname.html
    File listed twice: /usr/lib64/R/library/base/html/userhooks.html
    File listed twice: /usr/lib64/R/library/base/html/utf8Conversion.html
    File listed twice: /usr/lib64/R/library/base/html/vector.html
    File listed twice: /usr/lib64/R/library/base/html/warning.html
    File listed twice: /usr/lib64/R/library/base/html/warnings.html
    File listed twice: /usr/lib64/R/library/base/html/weekday.POSIXt.html
    File listed twice: /usr/lib64/R/library/base/html/which.html
    File listed twice: /usr/lib64/R/library/base/html/which.min.html
    File listed twice: /usr/lib64/R/library/base/html/with.html
    File listed twice: /usr/lib64/R/library/base/html/withVisible.html
    File listed twice: /usr/lib64/R/library/base/html/write.html
    File listed twice: /usr/lib64/R/library/base/html/writeLines.html
    File listed twice: /usr/lib64/R/library/base/html/xtfrm.html
    File listed twice: /usr/lib64/R/library/base/html/zMachine.html
    File listed twice: /usr/lib64/R/library/base/html/zScript.html
    File listed twice: /usr/lib64/R/library/base/html/zapsmall.html
    File listed twice: /usr/lib64/R/library/base/html/zpackages.html
    File listed twice: /usr/lib64/R/library/base/html/zutils.html
    File listed twice: /usr/lib64/R/library/boot/html
    File listed twice: /usr/lib64/R/library/boot/html/00Index.html
    File listed twice: /usr/lib64/R/library/boot/html/EEF.profile.html
    File listed twice: /usr/lib64/R/library/boot/html/Imp.Estimates.html
    File listed twice: /usr/lib64/R/library/boot/html/R.css
    File listed twice: /usr/lib64/R/library/boot/html/abc.ci.html
    File listed twice: /usr/lib64/R/library/boot/html/acme.html
    File listed twice: /usr/lib64/R/library/boot/html/aids.html
    File listed twice: /usr/lib64/R/library/boot/html/aircondit.html
    File listed twice: /usr/lib64/R/library/boot/html/amis.html
    File listed twice: /usr/lib64/R/library/boot/html/aml.html
    File listed twice: /usr/lib64/R/library/boot/html/beaver.html
    File listed twice: /usr/lib64/R/library/boot/html/bigcity.html
    File listed twice: /usr/lib64/R/library/boot/html/boot-practicals.html
    File listed twice: /usr/lib64/R/library/boot/html/boot.array.html
    File listed twice: /usr/lib64/R/library/boot/html/boot.ci.html
    File listed twice: /usr/lib64/R/library/boot/html/boot.html
    File listed twice: /usr/lib64/R/library/boot/html/brambles.html
    File listed twice: /usr/lib64/R/library/boot/html/breslow.html
    File listed twice: /usr/lib64/R/library/boot/html/calcium.html
    File listed twice: /usr/lib64/R/library/boot/html/cane.html
    File listed twice: /usr/lib64/R/library/boot/html/capability.html
    File listed twice: /usr/lib64/R/library/boot/html/catsM.html
    File listed twice: /usr/lib64/R/library/boot/html/cav.html
    File listed twice: /usr/lib64/R/library/boot/html/cd4.html
    File listed twice: /usr/lib64/R/library/boot/html/cd4.nested.html
    File listed twice: /usr/lib64/R/library/boot/html/censboot.html
    File listed twice: /usr/lib64/R/library/boot/html/channing.html
    File listed twice: /usr/lib64/R/library/boot/html/claridge.html
    File listed twice: /usr/lib64/R/library/boot/html/cloth.html
    File listed twice: /usr/lib64/R/library/boot/html/co.transfer.html
    File listed twice: /usr/lib64/R/library/boot/html/coal.html
    File listed twice: /usr/lib64/R/library/boot/html/control.html
    File listed twice: /usr/lib64/R/library/boot/html/corr.html
    File listed twice: /usr/lib64/R/library/boot/html/cum3.html
    File listed twice: /usr/lib64/R/library/boot/html/cv.glm.html
    File listed twice: /usr/lib64/R/library/boot/html/darwin.html
    File listed twice: /usr/lib64/R/library/boot/html/dogs.html
    File listed twice: /usr/lib64/R/library/boot/html/downs.bc.html
    File listed twice: /usr/lib64/R/library/boot/html/ducks.html
    File listed twice: /usr/lib64/R/library/boot/html/empinf.html
    File listed twice: /usr/lib64/R/library/boot/html/envelope.html
    File listed twice: /usr/lib64/R/library/boot/html/exp.tilt.html
    File listed twice: /usr/lib64/R/library/boot/html/fir.html
    File listed twice: /usr/lib64/R/library/boot/html/freq.array.html
    File listed twice: /usr/lib64/R/library/boot/html/frets.html
    File listed twice: /usr/lib64/R/library/boot/html/glm.diag.html
    File listed twice: /usr/lib64/R/library/boot/html/glm.diag.plots.html
    File listed twice: /usr/lib64/R/library/boot/html/gravity.html
    File listed twice: /usr/lib64/R/library/boot/html/hirose.html
    File listed twice: /usr/lib64/R/library/boot/html/imp.weights.html
    File listed twice: /usr/lib64/R/library/boot/html/inv.logit.html
    File listed twice: /usr/lib64/R/library/boot/html/islay.html
    File listed twice: /usr/lib64/R/library/boot/html/jack.after.boot.html
    File listed twice: /usr/lib64/R/library/boot/html/k3.linear.html
    File listed twice: /usr/lib64/R/library/boot/html/linear.approx.html
    File listed twice: /usr/lib64/R/library/boot/html/lines.saddle.distn.html
    File listed twice: /usr/lib64/R/library/boot/html/logit.html
    File listed twice: /usr/lib64/R/library/boot/html/manaus.html
    File listed twice: /usr/lib64/R/library/boot/html/melanoma.html
    File listed twice: /usr/lib64/R/library/boot/html/motor.html
    File listed twice: /usr/lib64/R/library/boot/html/neuro.html
    File listed twice: /usr/lib64/R/library/boot/html/nitrofen.html
    File listed twice: /usr/lib64/R/library/boot/html/nodal.html
    File listed twice: /usr/lib64/R/library/boot/html/norm.ci.html
    File listed twice: /usr/lib64/R/library/boot/html/nuclear.html
    File listed twice: /usr/lib64/R/library/boot/html/paulsen.html
    File listed twice: /usr/lib64/R/library/boot/html/plot.boot.html
    File listed twice: /usr/lib64/R/library/boot/html/poisons.html
    File listed twice: /usr/lib64/R/library/boot/html/polar.html
    File listed twice: /usr/lib64/R/library/boot/html/print.boot.html
    File listed twice: /usr/lib64/R/library/boot/html/print.bootci.html
    File listed twice: /usr/lib64/R/library/boot/html/print.saddle.distn.html
    File listed twice: /usr/lib64/R/library/boot/html/print.simplex.html
    File listed twice: /usr/lib64/R/library/boot/html/remission.html
    File listed twice: /usr/lib64/R/library/boot/html/saddle.distn.html
    File listed twice: /usr/lib64/R/library/boot/html/saddle.distn.object.html
    File listed twice: /usr/lib64/R/library/boot/html/saddle.html
    File listed twice: /usr/lib64/R/library/boot/html/salinity.html
    File listed twice: /usr/lib64/R/library/boot/html/simplex.html
    File listed twice: /usr/lib64/R/library/boot/html/simplex.object.html
    File listed twice: /usr/lib64/R/library/boot/html/smooth.f.html
    File listed twice: /usr/lib64/R/library/boot/html/sunspot.html
    File listed twice: /usr/lib64/R/library/boot/html/survival.html
    File listed twice: /usr/lib64/R/library/boot/html/tau.html
    File listed twice: /usr/lib64/R/library/boot/html/tilt.boot.html
    File listed twice: /usr/lib64/R/library/boot/html/tsboot.html
    File listed twice: /usr/lib64/R/library/boot/html/tuna.html
    File listed twice: /usr/lib64/R/library/boot/html/urine.html
    File listed twice: /usr/lib64/R/library/boot/html/var.linear.html
    File listed twice: /usr/lib64/R/library/boot/html/wool.html
    File listed twice: /usr/lib64/R/library/class/html
    File listed twice: /usr/lib64/R/library/class/html/00Index.html
    File listed twice: /usr/lib64/R/library/class/html/R.css
    File listed twice: /usr/lib64/R/library/class/html/SOM.html
    File listed twice: /usr/lib64/R/library/class/html/batchSOM.html
    File listed twice: /usr/lib64/R/library/class/html/condense.html
    File listed twice: /usr/lib64/R/library/class/html/knn.cv.html
    File listed twice: /usr/lib64/R/library/class/html/knn.html
    File listed twice: /usr/lib64/R/library/class/html/knn1.html
    File listed twice: /usr/lib64/R/library/class/html/lvq1.html
    File listed twice: /usr/lib64/R/library/class/html/lvq2.html
    File listed twice: /usr/lib64/R/library/class/html/lvq3.html
    File listed twice: /usr/lib64/R/library/class/html/lvqinit.html
    File listed twice: /usr/lib64/R/library/class/html/lvqtest.html
    File listed twice: /usr/lib64/R/library/class/html/multiedit.html
    File listed twice: /usr/lib64/R/library/class/html/olvq1.html
    File listed twice: /usr/lib64/R/library/class/html/reduce.nn.html
    File listed twice: /usr/lib64/R/library/class/html/somgrid.html
    File listed twice: /usr/lib64/R/library/cluster/html
    File listed twice: /usr/lib64/R/library/cluster/html/00Index.html
    File listed twice: /usr/lib64/R/library/cluster/html/R.css
    File listed twice: /usr/lib64/R/library/cluster/html/agnes.html
    File listed twice: /usr/lib64/R/library/cluster/html/agnes.object.html
    File listed twice: /usr/lib64/R/library/cluster/html/agriculture.html
    File listed twice: /usr/lib64/R/library/cluster/html/animals.html
    File listed twice: /usr/lib64/R/library/cluster/html/bannerplot.html
    File listed twice: /usr/lib64/R/library/cluster/html/chorSub.html
    File listed twice: /usr/lib64/R/library/cluster/html/clara.html
    File listed twice: /usr/lib64/R/library/cluster/html/clara.object.html
    File listed twice: /usr/lib64/R/library/cluster/html/clusGap.html
    File listed twice: /usr/lib64/R/library/cluster/html/clusplot.default.html
    File listed twice: /usr/lib64/R/library/cluster/html/clusplot.partition.html
    File listed twice: /usr/lib64/R/library/cluster/html/cluster-internal.html
    File listed twice: /usr/lib64/R/library/cluster/html/coef.hclust.html
    File listed twice: /usr/lib64/R/library/cluster/html/daisy.html
    File listed twice: /usr/lib64/R/library/cluster/html/diana.html
    File listed twice: /usr/lib64/R/library/cluster/html/dissimilarity.object.html
    File listed twice: /usr/lib64/R/library/cluster/html/ellipsoidhull.html
    File listed twice: /usr/lib64/R/library/cluster/html/fanny.html
    File listed twice: /usr/lib64/R/library/cluster/html/fanny.object.html
    File listed twice: /usr/lib64/R/library/cluster/html/flower.html
    File listed twice: /usr/lib64/R/library/cluster/html/lower.to.upper.tri.inds.html
    File listed twice: /usr/lib64/R/library/cluster/html/mona.html
    File listed twice: /usr/lib64/R/library/cluster/html/mona.object.html
    File listed twice: /usr/lib64/R/library/cluster/html/pam.html
    File listed twice: /usr/lib64/R/library/cluster/html/pam.object.html
    File listed twice: /usr/lib64/R/library/cluster/html/partition.object.html
    File listed twice: /usr/lib64/R/library/cluster/html/plantTraits.html
    File listed twice: /usr/lib64/R/library/cluster/html/plot.agnes.html
    File listed twice: /usr/lib64/R/library/cluster/html/plot.diana.html
    File listed twice: /usr/lib64/R/library/cluster/html/plot.mona.html
    File listed twice: /usr/lib64/R/library/cluster/html/plot.partition.html
    File listed twice: /usr/lib64/R/library/cluster/html/pltree.html
    File listed twice: /usr/lib64/R/library/cluster/html/pltree.twins.html
    File listed twice: /usr/lib64/R/library/cluster/html/pluton.html
    File listed twice: /usr/lib64/R/library/cluster/html/predict.ellipsoid.html
    File listed twice: /usr/lib64/R/library/cluster/html/print.agnes.html
    File listed twice: /usr/lib64/R/library/cluster/html/print.clara.html
    File listed twice: /usr/lib64/R/library/cluster/html/print.diana.html
    File listed twice: /usr/lib64/R/library/cluster/html/print.dissimilarity.html
    File listed twice: /usr/lib64/R/library/cluster/html/print.fanny.html
    File listed twice: /usr/lib64/R/library/cluster/html/print.mona.html
    File listed twice: /usr/lib64/R/library/cluster/html/print.pam.html
    File listed twice: /usr/lib64/R/library/cluster/html/ruspini.html
    File listed twice: /usr/lib64/R/library/cluster/html/silhouette.html
    File listed twice: /usr/lib64/R/library/cluster/html/sizeDiss.html
    File listed twice: /usr/lib64/R/library/cluster/html/summary.agnes.html
    File listed twice: /usr/lib64/R/library/cluster/html/summary.clara.html
    File listed twice: /usr/lib64/R/library/cluster/html/summary.diana.html
    File listed twice: /usr/lib64/R/library/cluster/html/summary.mona.html
    File listed twice: /usr/lib64/R/library/cluster/html/summary.pam.html
    File listed twice: /usr/lib64/R/library/cluster/html/twins.object.html
    File listed twice: /usr/lib64/R/library/cluster/html/volume.ellipsoid.html
    File listed twice: /usr/lib64/R/library/cluster/html/votes.repub.html
    File listed twice: /usr/lib64/R/library/cluster/html/xclara.html
    File listed twice: /usr/lib64/R/library/codetools/html
    File listed twice: /usr/lib64/R/library/codetools/html/00Index.html
    File listed twice: /usr/lib64/R/library/codetools/html/R.css
    File listed twice: /usr/lib64/R/library/codetools/html/checkUsage.html
    File listed twice: /usr/lib64/R/library/codetools/html/codetools.html
    File listed twice: /usr/lib64/R/library/codetools/html/findGlobals.html
    File listed twice: /usr/lib64/R/library/codetools/html/showTree.html
    File listed twice: /usr/lib64/R/library/compiler/html
    File listed twice: /usr/lib64/R/library/compiler/html/00Index.html
    File listed twice: /usr/lib64/R/library/compiler/html/R.css
    File listed twice: /usr/lib64/R/library/compiler/html/compile.html
    File listed twice: /usr/lib64/R/library/datasets/html
    File listed twice: /usr/lib64/R/library/datasets/html/00Index.html
    File listed twice: /usr/lib64/R/library/datasets/html/AirPassengers.html
    File listed twice: /usr/lib64/R/library/datasets/html/BJsales.html
    File listed twice: /usr/lib64/R/library/datasets/html/BOD.html
    File listed twice: /usr/lib64/R/library/datasets/html/ChickWeight.html
    File listed twice: /usr/lib64/R/library/datasets/html/DNase.html
    File listed twice: /usr/lib64/R/library/datasets/html/EuStockMarkets.html
    File listed twice: /usr/lib64/R/library/datasets/html/Formaldehyde.html
    File listed twice: /usr/lib64/R/library/datasets/html/HairEyeColor.html
    File listed twice: /usr/lib64/R/library/datasets/html/Harman23.cor.html
    File listed twice: /usr/lib64/R/library/datasets/html/Harman74.cor.html
    File listed twice: /usr/lib64/R/library/datasets/html/Indometh.html
    File listed twice: /usr/lib64/R/library/datasets/html/InsectSprays.html
    File listed twice: /usr/lib64/R/library/datasets/html/JohnsonJohnson.html
    File listed twice: /usr/lib64/R/library/datasets/html/LakeHuron.html
    File listed twice: /usr/lib64/R/library/datasets/html/LifeCycleSavings.html
    File listed twice: /usr/lib64/R/library/datasets/html/Loblolly.html
    File listed twice: /usr/lib64/R/library/datasets/html/Nile.html
    File listed twice: /usr/lib64/R/library/datasets/html/Orange.html
    File listed twice: /usr/lib64/R/library/datasets/html/OrchardSprays.html
    File listed twice: /usr/lib64/R/library/datasets/html/PlantGrowth.html
    File listed twice: /usr/lib64/R/library/datasets/html/Puromycin.html
    File listed twice: /usr/lib64/R/library/datasets/html/R.css
    File listed twice: /usr/lib64/R/library/datasets/html/Theoph.html
    File listed twice: /usr/lib64/R/library/datasets/html/Titanic.html
    File listed twice: /usr/lib64/R/library/datasets/html/ToothGrowth.html
    File listed twice: /usr/lib64/R/library/datasets/html/UCBAdmissions.html
    File listed twice: /usr/lib64/R/library/datasets/html/UKDriverDeaths.html
    File listed twice: /usr/lib64/R/library/datasets/html/UKLungDeaths.html
    File listed twice: /usr/lib64/R/library/datasets/html/UKgas.html
    File listed twice: /usr/lib64/R/library/datasets/html/USAccDeaths.html
    File listed twice: /usr/lib64/R/library/datasets/html/USArrests.html
    File listed twice: /usr/lib64/R/library/datasets/html/USJudgeRatings.html
    File listed twice: /usr/lib64/R/library/datasets/html/USPersonalExpenditure.html
    File listed twice: /usr/lib64/R/library/datasets/html/VADeaths.html
    File listed twice: /usr/lib64/R/library/datasets/html/WWWusage.html
    File listed twice: /usr/lib64/R/library/datasets/html/WorldPhones.html
    File listed twice: /usr/lib64/R/library/datasets/html/ability.cov.html
    File listed twice: /usr/lib64/R/library/datasets/html/airmiles.html
    File listed twice: /usr/lib64/R/library/datasets/html/airquality.html
    File listed twice: /usr/lib64/R/library/datasets/html/anscombe.html
    File listed twice: /usr/lib64/R/library/datasets/html/attenu.html
    File listed twice: /usr/lib64/R/library/datasets/html/attitude.html
    File listed twice: /usr/lib64/R/library/datasets/html/austres.html
    File listed twice: /usr/lib64/R/library/datasets/html/beavers.html
    File listed twice: /usr/lib64/R/library/datasets/html/cars.html
    File listed twice: /usr/lib64/R/library/datasets/html/chickwts.html
    File listed twice: /usr/lib64/R/library/datasets/html/co2.html
    File listed twice: /usr/lib64/R/library/datasets/html/crimtab.html
    File listed twice: /usr/lib64/R/library/datasets/html/datasets-package.html
    File listed twice: /usr/lib64/R/library/datasets/html/discoveries.html
    File listed twice: /usr/lib64/R/library/datasets/html/esoph.html
    File listed twice: /usr/lib64/R/library/datasets/html/euro.html
    File listed twice: /usr/lib64/R/library/datasets/html/eurodist.html
    File listed twice: /usr/lib64/R/library/datasets/html/faithful.html
    File listed twice: /usr/lib64/R/library/datasets/html/freeny.html
    File listed twice: /usr/lib64/R/library/datasets/html/infert.html
    File listed twice: /usr/lib64/R/library/datasets/html/iris.html
    File listed twice: /usr/lib64/R/library/datasets/html/islands.html
    File listed twice: /usr/lib64/R/library/datasets/html/lh.html
    File listed twice: /usr/lib64/R/library/datasets/html/longley.html
    File listed twice: /usr/lib64/R/library/datasets/html/lynx.html
    File listed twice: /usr/lib64/R/library/datasets/html/morley.html
    File listed twice: /usr/lib64/R/library/datasets/html/mtcars.html
    File listed twice: /usr/lib64/R/library/datasets/html/nhtemp.html
    File listed twice: /usr/lib64/R/library/datasets/html/nottem.html
    File listed twice: /usr/lib64/R/library/datasets/html/npk.html
    File listed twice: /usr/lib64/R/library/datasets/html/occupationalStatus.html
    File listed twice: /usr/lib64/R/library/datasets/html/precip.html
    File listed twice: /usr/lib64/R/library/datasets/html/presidents.html
    File listed twice: /usr/lib64/R/library/datasets/html/pressure.html
    File listed twice: /usr/lib64/R/library/datasets/html/quakes.html
    File listed twice: /usr/lib64/R/library/datasets/html/randu.html
    File listed twice: /usr/lib64/R/library/datasets/html/rivers.html
    File listed twice: /usr/lib64/R/library/datasets/html/rock.html
    File listed twice: /usr/lib64/R/library/datasets/html/sleep.html
    File listed twice: /usr/lib64/R/library/datasets/html/stackloss.html
    File listed twice: /usr/lib64/R/library/datasets/html/state.html
    File listed twice: /usr/lib64/R/library/datasets/html/sunspot.month.html
    File listed twice: /usr/lib64/R/library/datasets/html/sunspot.year.html
    File listed twice: /usr/lib64/R/library/datasets/html/sunspots.html
    File listed twice: /usr/lib64/R/library/datasets/html/swiss.html
    File listed twice: /usr/lib64/R/library/datasets/html/treering.html
    File listed twice: /usr/lib64/R/library/datasets/html/trees.html
    File listed twice: /usr/lib64/R/library/datasets/html/uspop.html
    File listed twice: /usr/lib64/R/library/datasets/html/volcano.html
    File listed twice: /usr/lib64/R/library/datasets/html/warpbreaks.html
    File listed twice: /usr/lib64/R/library/datasets/html/women.html
    File listed twice: /usr/lib64/R/library/datasets/html/zCO2.html
    File listed twice: /usr/lib64/R/library/foreign/html
    File listed twice: /usr/lib64/R/library/foreign/html/00Index.html
    File listed twice: /usr/lib64/R/library/foreign/html/R.css
    File listed twice: /usr/lib64/R/library/foreign/html/lookup.xport.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.S.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.arff.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.dbf.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.dta.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.epiinfo.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.mtp.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.octave.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.spss.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.ssd.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.systat.html
    File listed twice: /usr/lib64/R/library/foreign/html/read.xport.html
    File listed twice: /usr/lib64/R/library/foreign/html/write.arff.html
    File listed twice: /usr/lib64/R/library/foreign/html/write.dbf.html
    File listed twice: /usr/lib64/R/library/foreign/html/write.dta.html
    File listed twice: /usr/lib64/R/library/foreign/html/write.foreign.html
    File listed twice: /usr/lib64/R/library/grDevices/html
    File listed twice: /usr/lib64/R/library/grDevices/html/00Index.html
    File listed twice: /usr/lib64/R/library/grDevices/html/Devices.html
    File listed twice: /usr/lib64/R/library/grDevices/html/Hershey.html
    File listed twice: /usr/lib64/R/library/grDevices/html/Japanese.html
    File listed twice: /usr/lib64/R/library/grDevices/html/R.css
    File listed twice: /usr/lib64/R/library/grDevices/html/Type1Font.html
    File listed twice: /usr/lib64/R/library/grDevices/html/adjustcolor.html
    File listed twice: /usr/lib64/R/library/grDevices/html/as.graphicsAnnot.html
    File listed twice: /usr/lib64/R/library/grDevices/html/as.raster.html
    File listed twice: /usr/lib64/R/library/grDevices/html/axisTicks.html
    File listed twice: /usr/lib64/R/library/grDevices/html/boxplot.stats.html
    File listed twice: /usr/lib64/R/library/grDevices/html/cairo.html
    File listed twice: /usr/lib64/R/library/grDevices/html/check.options.html
    File listed twice: /usr/lib64/R/library/grDevices/html/chull.html
    File listed twice: /usr/lib64/R/library/grDevices/html/cm.html
    File listed twice: /usr/lib64/R/library/grDevices/html/col2rgb.html
    File listed twice: /usr/lib64/R/library/grDevices/html/colorRamp.html
    File listed twice: /usr/lib64/R/library/grDevices/html/colors.html
    File listed twice: /usr/lib64/R/library/grDevices/html/contourLines.html
    File listed twice: /usr/lib64/R/library/grDevices/html/convertColor.html
    File listed twice: /usr/lib64/R/library/grDevices/html/densCols.html
    File listed twice: /usr/lib64/R/library/grDevices/html/dev.capabilities.html
    File listed twice: /usr/lib64/R/library/grDevices/html/dev.capture.html
    File listed twice: /usr/lib64/R/library/grDevices/html/dev.flush.html
    File listed twice: /usr/lib64/R/library/grDevices/html/dev.html
    File listed twice: /usr/lib64/R/library/grDevices/html/dev.interactive.html
    File listed twice: /usr/lib64/R/library/grDevices/html/dev.size.html
    File listed twice: /usr/lib64/R/library/grDevices/html/dev2.html
    File listed twice: /usr/lib64/R/library/grDevices/html/dev2bitmap.html
    File listed twice: /usr/lib64/R/library/grDevices/html/devAskNewPage.html
    File listed twice: /usr/lib64/R/library/grDevices/html/embedFonts.html
    File listed twice: /usr/lib64/R/library/grDevices/html/extendrange.html
    File listed twice: /usr/lib64/R/library/grDevices/html/getGraphicsEvent.html
    File listed twice: /usr/lib64/R/library/grDevices/html/grDevices-package.html
    File listed twice: /usr/lib64/R/library/grDevices/html/gray.colors.html
    File listed twice: /usr/lib64/R/library/grDevices/html/gray.html
    File listed twice: /usr/lib64/R/library/grDevices/html/hcl.html
    File listed twice: /usr/lib64/R/library/grDevices/html/hsv.html
    File listed twice: /usr/lib64/R/library/grDevices/html/make.rgb.html
    File listed twice: /usr/lib64/R/library/grDevices/html/n2mfrow.html
    File listed twice: /usr/lib64/R/library/grDevices/html/nclass.html
    File listed twice: /usr/lib64/R/library/grDevices/html/palette.html
    File listed twice: /usr/lib64/R/library/grDevices/html/palettes.html
    File listed twice: /usr/lib64/R/library/grDevices/html/pdf.html
    File listed twice: /usr/lib64/R/library/grDevices/html/pdf.options.html
    File listed twice: /usr/lib64/R/library/grDevices/html/pictex.html
    File listed twice: /usr/lib64/R/library/grDevices/html/plotmath.html
    File listed twice: /usr/lib64/R/library/grDevices/html/png.html
    File listed twice: /usr/lib64/R/library/grDevices/html/postscript.html
    File listed twice: /usr/lib64/R/library/grDevices/html/postscriptFonts.html
    File listed twice: /usr/lib64/R/library/grDevices/html/pretty.Date.html
    File listed twice: /usr/lib64/R/library/grDevices/html/ps.options.html
    File listed twice: /usr/lib64/R/library/grDevices/html/quartz.html
    File listed twice: /usr/lib64/R/library/grDevices/html/quartzFonts.html
    File listed twice: /usr/lib64/R/library/grDevices/html/recordGraphics.html
    File listed twice: /usr/lib64/R/library/grDevices/html/recordplot.html
    File listed twice: /usr/lib64/R/library/grDevices/html/rgb.html
    File listed twice: /usr/lib64/R/library/grDevices/html/rgb2hsv.html
    File listed twice: /usr/lib64/R/library/grDevices/html/savePlot.html
    File listed twice: /usr/lib64/R/library/grDevices/html/trans3d.html
    File listed twice: /usr/lib64/R/library/grDevices/html/x11.html
    File listed twice: /usr/lib64/R/library/grDevices/html/x11Fonts.html
    File listed twice: /usr/lib64/R/library/grDevices/html/xfig.html
    File listed twice: /usr/lib64/R/library/grDevices/html/xy.coords.html
    File listed twice: /usr/lib64/R/library/grDevices/html/xyTable.html
    File listed twice: /usr/lib64/R/library/grDevices/html/xyz.coords.html
    File listed twice: /usr/lib64/R/library/graphics/html
    File listed twice: /usr/lib64/R/library/graphics/html/00Index.html
    File listed twice: /usr/lib64/R/library/graphics/html/R.css
    File listed twice: /usr/lib64/R/library/graphics/html/abline.html
    File listed twice: /usr/lib64/R/library/graphics/html/arrows.html
    File listed twice: /usr/lib64/R/library/graphics/html/assocplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/axTicks.html
    File listed twice: /usr/lib64/R/library/graphics/html/axis.POSIXct.html
    File listed twice: /usr/lib64/R/library/graphics/html/axis.html
    File listed twice: /usr/lib64/R/library/graphics/html/barplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/box.html
    File listed twice: /usr/lib64/R/library/graphics/html/boxplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/boxplot.matrix.html
    File listed twice: /usr/lib64/R/library/graphics/html/bxp.html
    File listed twice: /usr/lib64/R/library/graphics/html/cdplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/clip.html
    File listed twice: /usr/lib64/R/library/graphics/html/contour.html
    File listed twice: /usr/lib64/R/library/graphics/html/convertXY.html
    File listed twice: /usr/lib64/R/library/graphics/html/coplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/curve.html
    File listed twice: /usr/lib64/R/library/graphics/html/dotchart.html
    File listed twice: /usr/lib64/R/library/graphics/html/filled.contour.html
    File listed twice: /usr/lib64/R/library/graphics/html/fourfoldplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/frame.html
    File listed twice: /usr/lib64/R/library/graphics/html/graphics-defunct.html
    File listed twice: /usr/lib64/R/library/graphics/html/graphics-package.html
    File listed twice: /usr/lib64/R/library/graphics/html/grid.html
    File listed twice: /usr/lib64/R/library/graphics/html/hist.POSIXt.html
    File listed twice: /usr/lib64/R/library/graphics/html/hist.html
    File listed twice: /usr/lib64/R/library/graphics/html/identify.html
    File listed twice: /usr/lib64/R/library/graphics/html/image.html
    File listed twice: /usr/lib64/R/library/graphics/html/layout.html
    File listed twice: /usr/lib64/R/library/graphics/html/legend.html
    File listed twice: /usr/lib64/R/library/graphics/html/lines.html
    File listed twice: /usr/lib64/R/library/graphics/html/locator.html
    File listed twice: /usr/lib64/R/library/graphics/html/matplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/mosaicplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/mtext.html
    File listed twice: /usr/lib64/R/library/graphics/html/pairs.html
    File listed twice: /usr/lib64/R/library/graphics/html/panel.smooth.html
    File listed twice: /usr/lib64/R/library/graphics/html/par.html
    File listed twice: /usr/lib64/R/library/graphics/html/persp.html
    File listed twice: /usr/lib64/R/library/graphics/html/pie.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.dataframe.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.default.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.design.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.factor.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.formula.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.table.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.window.html
    File listed twice: /usr/lib64/R/library/graphics/html/plot.xy.html
    File listed twice: /usr/lib64/R/library/graphics/html/plothistogram.html
    File listed twice: /usr/lib64/R/library/graphics/html/points.html
    File listed twice: /usr/lib64/R/library/graphics/html/polygon.html
    File listed twice: /usr/lib64/R/library/graphics/html/polypath.html
    File listed twice: /usr/lib64/R/library/graphics/html/rasterImage.html
    File listed twice: /usr/lib64/R/library/graphics/html/rect.html
    File listed twice: /usr/lib64/R/library/graphics/html/rug.html
    File listed twice: /usr/lib64/R/library/graphics/html/screen.html
    File listed twice: /usr/lib64/R/library/graphics/html/segments.html
    File listed twice: /usr/lib64/R/library/graphics/html/smoothScatter.html
    File listed twice: /usr/lib64/R/library/graphics/html/spineplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/stars.html
    File listed twice: /usr/lib64/R/library/graphics/html/stem.html
    File listed twice: /usr/lib64/R/library/graphics/html/stripchart.html
    File listed twice: /usr/lib64/R/library/graphics/html/strwidth.html
    File listed twice: /usr/lib64/R/library/graphics/html/sunflowerplot.html
    File listed twice: /usr/lib64/R/library/graphics/html/symbols.html
    File listed twice: /usr/lib64/R/library/graphics/html/text.html
    File listed twice: /usr/lib64/R/library/graphics/html/title.html
    File listed twice: /usr/lib64/R/library/graphics/html/units.html
    File listed twice: /usr/lib64/R/library/graphics/html/xspline.html
    File listed twice: /usr/lib64/R/library/graphics/html/zAxis.html
    File listed twice: /usr/lib64/R/library/grid/html
    File listed twice: /usr/lib64/R/library/grid/html/00Index.html
    File listed twice: /usr/lib64/R/library/grid/html/Grid.html
    File listed twice: /usr/lib64/R/library/grid/html/R.css
    File listed twice: /usr/lib64/R/library/grid/html/absolute.size.html
    File listed twice: /usr/lib64/R/library/grid/html/arrow.html
    File listed twice: /usr/lib64/R/library/grid/html/calcStringMetric.html
    File listed twice: /usr/lib64/R/library/grid/html/current.viewport.html
    File listed twice: /usr/lib64/R/library/grid/html/dataViewport.html
    File listed twice: /usr/lib64/R/library/grid/html/depth.html
    File listed twice: /usr/lib64/R/library/grid/html/drawDetails.html
    File listed twice: /usr/lib64/R/library/grid/html/editDetails.html
    File listed twice: /usr/lib64/R/library/grid/html/explode.html
    File listed twice: /usr/lib64/R/library/grid/html/gEdit.html
    File listed twice: /usr/lib64/R/library/grid/html/gPath.html
    File listed twice: /usr/lib64/R/library/grid/html/getNames.html
    File listed twice: /usr/lib64/R/library/grid/html/gpar.html
    File listed twice: /usr/lib64/R/library/grid/html/grid-defunct.html
    File listed twice: /usr/lib64/R/library/grid/html/grid-internal.html
    File listed twice: /usr/lib64/R/library/grid/html/grid-package.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.DLapply.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.add.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.bezier.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.cap.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.circle.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.clip.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.convert.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.copy.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.curve.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.delay.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.display.list.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.draw.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.edit.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.force.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.frame.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.function.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.get.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.grab.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.grep.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.grill.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.grob.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.layout.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.lines.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.locator.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.ls.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.move.to.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.newpage.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.null.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.pack.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.path.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.place.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.plot.and.legend.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.points.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.polygon.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.pretty.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.raster.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.record.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.rect.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.refresh.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.remove.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.reorder.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.roundrect.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.segments.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.set.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.show.layout.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.show.viewport.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.text.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.xaxis.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.xspline.html
    File listed twice: /usr/lib64/R/library/grid/html/grid.yaxis.html
    File listed twice: /usr/lib64/R/library/grid/html/grobName.html
    File listed twice: /usr/lib64/R/library/grid/html/grobWidth.html
    File listed twice: /usr/lib64/R/library/grid/html/grobX.html
    File listed twice: /usr/lib64/R/library/grid/html/legendGrob.html
    File listed twice: /usr/lib64/R/library/grid/html/makeContent.html
    File listed twice: /usr/lib64/R/library/grid/html/plotViewport.html
    File listed twice: /usr/lib64/R/library/grid/html/resolveRasterSize.html
    File listed twice: /usr/lib64/R/library/grid/html/showGrob.html
    File listed twice: /usr/lib64/R/library/grid/html/showViewport.html
    File listed twice: /usr/lib64/R/library/grid/html/stringWidth.html
    File listed twice: /usr/lib64/R/library/grid/html/unit.c.html
    File listed twice: /usr/lib64/R/library/grid/html/unit.html
    File listed twice: /usr/lib64/R/library/grid/html/unit.length.html
    File listed twice: /usr/lib64/R/library/grid/html/unit.pmin.html
    File listed twice: /usr/lib64/R/library/grid/html/unit.rep.html
    File listed twice: /usr/lib64/R/library/grid/html/valid.just.html
    File listed twice: /usr/lib64/R/library/grid/html/validDetails.html
    File listed twice: /usr/lib64/R/library/grid/html/viewport.html
    File listed twice: /usr/lib64/R/library/grid/html/viewports.html
    File listed twice: /usr/lib64/R/library/grid/html/vpPath.html
    File listed twice: /usr/lib64/R/library/grid/html/widthDetails.html
    File listed twice: /usr/lib64/R/library/grid/html/xDetails.html
    File listed twice: /usr/lib64/R/library/grid/html/xsplinePoints.html
    File listed twice: /usr/lib64/R/library/lattice/html
    File listed twice: /usr/lib64/R/library/lattice/html/00Index.html
    File listed twice: /usr/lib64/R/library/lattice/html/Lattice.html
    File listed twice: /usr/lib64/R/library/lattice/html/R.css
    File listed twice: /usr/lib64/R/library/lattice/html/Rows.html
    File listed twice: /usr/lib64/R/library/lattice/html/axis.default.html
    File listed twice: /usr/lib64/R/library/lattice/html/banking.html
    File listed twice: /usr/lib64/R/library/lattice/html/barchart.table.html
    File listed twice: /usr/lib64/R/library/lattice/html/barley.html
    File listed twice: /usr/lib64/R/library/lattice/html/cloud.html
    File listed twice: /usr/lib64/R/library/lattice/html/draw.colorkey.html
    File listed twice: /usr/lib64/R/library/lattice/html/draw.key.html
    File listed twice: /usr/lib64/R/library/lattice/html/environmental.html
    File listed twice: /usr/lib64/R/library/lattice/html/ethanol.html
    File listed twice: /usr/lib64/R/library/lattice/html/histogram.html
    File listed twice: /usr/lib64/R/library/lattice/html/interaction.html
    File listed twice: /usr/lib64/R/library/lattice/html/lattice.options.html
    File listed twice: /usr/lib64/R/library/lattice/html/latticeParseFormula.html
    File listed twice: /usr/lib64/R/library/lattice/html/level.colors.html
    File listed twice: /usr/lib64/R/library/lattice/html/levelplot.html
    File listed twice: /usr/lib64/R/library/lattice/html/llines.html
    File listed twice: /usr/lib64/R/library/lattice/html/lset.html
    File listed twice: /usr/lib64/R/library/lattice/html/make.groups.html
    File listed twice: /usr/lib64/R/library/lattice/html/melanoma.html
    File listed twice: /usr/lib64/R/library/lattice/html/oneway.html
    File listed twice: /usr/lib64/R/library/lattice/html/packet.panel.default.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.axis.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.barchart.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.bwplot.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.cloud.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.densityplot.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.dotplot.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.functions.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.histogram.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.levelplot.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.loess.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.number.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.pairs.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.parallel.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.qqmath.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.qqmathline.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.smoothScatter.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.spline.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.stripplot.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.superpose.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.violin.html
    File listed twice: /usr/lib64/R/library/lattice/html/panel.xyplot.html
    File listed twice: /usr/lib64/R/library/lattice/html/prepanel.default.html
    File listed twice: /usr/lib64/R/library/lattice/html/prepanel.functions.html
    File listed twice: /usr/lib64/R/library/lattice/html/print.trellis.html
    File listed twice: /usr/lib64/R/library/lattice/html/qq.html
    File listed twice: /usr/lib64/R/library/lattice/html/qqmath.html
    File listed twice: /usr/lib64/R/library/lattice/html/rfs.html
    File listed twice: /usr/lib64/R/library/lattice/html/shingles.html
    File listed twice: /usr/lib64/R/library/lattice/html/simpleKey.html
    File listed twice: /usr/lib64/R/library/lattice/html/simpleTheme.html
    File listed twice: /usr/lib64/R/library/lattice/html/singer.html
    File listed twice: /usr/lib64/R/library/lattice/html/splom.html
    File listed twice: /usr/lib64/R/library/lattice/html/strip.default.html
    File listed twice: /usr/lib64/R/library/lattice/html/tmd.html
    File listed twice: /usr/lib64/R/library/lattice/html/trellis.device.html
    File listed twice: /usr/lib64/R/library/lattice/html/trellis.object.html
    File listed twice: /usr/lib64/R/library/lattice/html/trellis.par.get.html
    File listed twice: /usr/lib64/R/library/lattice/html/update.trellis.html
    File listed twice: /usr/lib64/R/library/lattice/html/utilities.3d.html
    File listed twice: /usr/lib64/R/library/lattice/html/xyplot.html
    File listed twice: /usr/lib64/R/library/lattice/html/xyplot.ts.html
    File listed twice: /usr/lib64/R/library/methods/html
    File listed twice: /usr/lib64/R/library/methods/html/00Index.html
    File listed twice: /usr/lib64/R/library/methods/html/BasicClasses.html
    File listed twice: /usr/lib64/R/library/methods/html/Classes.html
    File listed twice: /usr/lib64/R/library/methods/html/Documentation.html
    File listed twice: /usr/lib64/R/library/methods/html/EmptyMethodsList-class.html
    File listed twice: /usr/lib64/R/library/methods/html/EnvironmentClass.html
    File listed twice: /usr/lib64/R/library/methods/html/GenericFunctions.html
    File listed twice: /usr/lib64/R/library/methods/html/LanguageClasses.html
    File listed twice: /usr/lib64/R/library/methods/html/LinearMethodsList-class.html
    File listed twice: /usr/lib64/R/library/methods/html/MethodDefinition-class.html
    File listed twice: /usr/lib64/R/library/methods/html/MethodSupport.html
    File listed twice: /usr/lib64/R/library/methods/html/MethodWithNext-class.html
    File listed twice: /usr/lib64/R/library/methods/html/Methods.html
    File listed twice: /usr/lib64/R/library/methods/html/MethodsList-class.html
    File listed twice: /usr/lib64/R/library/methods/html/MethodsList.html
    File listed twice: /usr/lib64/R/library/methods/html/NextMethod.html
    File listed twice: /usr/lib64/R/library/methods/html/ObjectsWithPackage-class.html
    File listed twice: /usr/lib64/R/library/methods/html/R.css
    File listed twice: /usr/lib64/R/library/methods/html/RClassUtils.html
    File listed twice: /usr/lib64/R/library/methods/html/RMethodUtils.html
    File listed twice: /usr/lib64/R/library/methods/html/S3Part.html
    File listed twice: /usr/lib64/R/library/methods/html/S4groupGeneric.html
    File listed twice: /usr/lib64/R/library/methods/html/SClassExtension-class.html
    File listed twice: /usr/lib64/R/library/methods/html/StructureClasses.html
    File listed twice: /usr/lib64/R/library/methods/html/TraceClasses.html
    File listed twice: /usr/lib64/R/library/methods/html/as.html
    File listed twice: /usr/lib64/R/library/methods/html/callGeneric.html
    File listed twice: /usr/lib64/R/library/methods/html/canCoerce.html
    File listed twice: /usr/lib64/R/library/methods/html/cbind2.html
    File listed twice: /usr/lib64/R/library/methods/html/className.html
    File listed twice: /usr/lib64/R/library/methods/html/classRepresentation-class.html
    File listed twice: /usr/lib64/R/library/methods/html/classesToAM.html
    File listed twice: /usr/lib64/R/library/methods/html/dotsMethods.html
    File listed twice: /usr/lib64/R/library/methods/html/evalSource.html
    File listed twice: /usr/lib64/R/library/methods/html/findClass.html
    File listed twice: /usr/lib64/R/library/methods/html/findMethods.html
    File listed twice: /usr/lib64/R/library/methods/html/fixPrevious.html
    File listed twice: /usr/lib64/R/library/methods/html/genericFunction-class.html
    File listed twice: /usr/lib64/R/library/methods/html/getClass.html
    File listed twice: /usr/lib64/R/library/methods/html/getMethod.html
    File listed twice: /usr/lib64/R/library/methods/html/getPackageName.html
    File listed twice: /usr/lib64/R/library/methods/html/hasArg.html
    File listed twice: /usr/lib64/R/library/methods/html/implicitGeneric.html
    File listed twice: /usr/lib64/R/library/methods/html/inheritedSlotNames.html
    File listed twice: /usr/lib64/R/library/methods/html/initialize-methods.html
    File listed twice: /usr/lib64/R/library/methods/html/is.html
    File listed twice: /usr/lib64/R/library/methods/html/isSealedMethod.html
    File listed twice: /usr/lib64/R/library/methods/html/languageEl.html
    File listed twice: /usr/lib64/R/library/methods/html/localRefClass.html
    File listed twice: /usr/lib64/R/library/methods/html/method.skeleton.html
    File listed twice: /usr/lib64/R/library/methods/html/methodUtilities.html
    File listed twice: /usr/lib64/R/library/methods/html/methods-defunct.html
    File listed twice: /usr/lib64/R/library/methods/html/methods-deprecated.html
    File listed twice: /usr/lib64/R/library/methods/html/methods-package.html
    File listed twice: /usr/lib64/R/library/methods/html/new.html
    File listed twice: /usr/lib64/R/library/methods/html/nonStructure-class.html
    File listed twice: /usr/lib64/R/library/methods/html/promptClass.html
    File listed twice: /usr/lib64/R/library/methods/html/promptMethods.html
    File listed twice: /usr/lib64/R/library/methods/html/refClass.html
    File listed twice: /usr/lib64/R/library/methods/html/representation.html
    File listed twice: /usr/lib64/R/library/methods/html/selectSuperClasses.html
    File listed twice: /usr/lib64/R/library/methods/html/setClass.html
    File listed twice: /usr/lib64/R/library/methods/html/setClassUnion.html
    File listed twice: /usr/lib64/R/library/methods/html/setGeneric.html
    File listed twice: /usr/lib64/R/library/methods/html/setLoadActions.html
    File listed twice: /usr/lib64/R/library/methods/html/setMethod.html
    File listed twice: /usr/lib64/R/library/methods/html/setOldClass.html
    File listed twice: /usr/lib64/R/library/methods/html/setSClass.html
    File listed twice: /usr/lib64/R/library/methods/html/show.html
    File listed twice: /usr/lib64/R/library/methods/html/showMethods.html
    File listed twice: /usr/lib64/R/library/methods/html/signature-class.html
    File listed twice: /usr/lib64/R/library/methods/html/slot.html
    File listed twice: /usr/lib64/R/library/methods/html/stdRefClass.html
    File listed twice: /usr/lib64/R/library/methods/html/substituteDirect.html
    File listed twice: /usr/lib64/R/library/methods/html/testInheritedMethods.html
    File listed twice: /usr/lib64/R/library/methods/html/validObject.html
    File listed twice: /usr/lib64/R/library/methods/html/zBasicFunsList.html
    File listed twice: /usr/lib64/R/library/mgcv/html
    File listed twice: /usr/lib64/R/library/mgcv/html/00Index.html
    File listed twice: /usr/lib64/R/library/mgcv/html/Beta.html
    File listed twice: /usr/lib64/R/library/mgcv/html/Predict.matrix.cr.smooth.html
    File listed twice: /usr/lib64/R/library/mgcv/html/Predict.matrix.html
    File listed twice: /usr/lib64/R/library/mgcv/html/Predict.matrix.soap.film.html
    File listed twice: /usr/lib64/R/library/mgcv/html/R.css
    File listed twice: /usr/lib64/R/library/mgcv/html/Rrank.html
    File listed twice: /usr/lib64/R/library/mgcv/html/Tweedie.html
    File listed twice: /usr/lib64/R/library/mgcv/html/anova.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/bam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/bam.update.html
    File listed twice: /usr/lib64/R/library/mgcv/html/cSplineDes.html
    File listed twice: /usr/lib64/R/library/mgcv/html/choose.k.html
    File listed twice: /usr/lib64/R/library/mgcv/html/columb.html
    File listed twice: /usr/lib64/R/library/mgcv/html/concurvity.html
    File listed twice: /usr/lib64/R/library/mgcv/html/coxph.html
    File listed twice: /usr/lib64/R/library/mgcv/html/exclude.too.far.html
    File listed twice: /usr/lib64/R/library/mgcv/html/extract.lme.cov.html
    File listed twice: /usr/lib64/R/library/mgcv/html/family.mgcv.html
    File listed twice: /usr/lib64/R/library/mgcv/html/fix.family.link.html
    File listed twice: /usr/lib64/R/library/mgcv/html/fixDependence.html
    File listed twice: /usr/lib64/R/library/mgcv/html/formXtViX.html
    File listed twice: /usr/lib64/R/library/mgcv/html/formula.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/fs.test.html
    File listed twice: /usr/lib64/R/library/mgcv/html/full.score.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.check.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.control.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.convergence.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.fit.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.fit3.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.models.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.outer.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.scale.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.selection.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.side.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam.vcomp.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gam2objective.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gamObject.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gamSim.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gamm.html
    File listed twice: /usr/lib64/R/library/mgcv/html/gaulss.html
    File listed twice: /usr/lib64/R/library/mgcv/html/get.var.html
    File listed twice: /usr/lib64/R/library/mgcv/html/in.out.html
    File listed twice: /usr/lib64/R/library/mgcv/html/inSide.html
    File listed twice: /usr/lib64/R/library/mgcv/html/influence.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/initial.sp.html
    File listed twice: /usr/lib64/R/library/mgcv/html/interpret.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/ldTweedie.html
    File listed twice: /usr/lib64/R/library/mgcv/html/linear.functional.terms.html
    File listed twice: /usr/lib64/R/library/mgcv/html/logLik.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/ls.size.html
    File listed twice: /usr/lib64/R/library/mgcv/html/magic.html
    File listed twice: /usr/lib64/R/library/mgcv/html/magic.post.proc.html
    File listed twice: /usr/lib64/R/library/mgcv/html/mgcv-FAQ.html
    File listed twice: /usr/lib64/R/library/mgcv/html/mgcv-package.html
    File listed twice: /usr/lib64/R/library/mgcv/html/mgcv-parallel.html
    File listed twice: /usr/lib64/R/library/mgcv/html/model.matrix.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/mono.con.html
    File listed twice: /usr/lib64/R/library/mgcv/html/mroot.html
    File listed twice: /usr/lib64/R/library/mgcv/html/mvn.html
    File listed twice: /usr/lib64/R/library/mgcv/html/negbin.html
    File listed twice: /usr/lib64/R/library/mgcv/html/new.name.html
    File listed twice: /usr/lib64/R/library/mgcv/html/notExp.html
    File listed twice: /usr/lib64/R/library/mgcv/html/notExp2.html
    File listed twice: /usr/lib64/R/library/mgcv/html/null.space.dimension.html
    File listed twice: /usr/lib64/R/library/mgcv/html/ocat.html
    File listed twice: /usr/lib64/R/library/mgcv/html/pcls.html
    File listed twice: /usr/lib64/R/library/mgcv/html/pdIdnot.html
    File listed twice: /usr/lib64/R/library/mgcv/html/pdTens.html
    File listed twice: /usr/lib64/R/library/mgcv/html/pen.edf.html
    File listed twice: /usr/lib64/R/library/mgcv/html/place.knots.html
    File listed twice: /usr/lib64/R/library/mgcv/html/plot.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/polys.plot.html
    File listed twice: /usr/lib64/R/library/mgcv/html/predict.bam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/predict.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/print.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/qq.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/rTweedie.html
    File listed twice: /usr/lib64/R/library/mgcv/html/random.effects.html
    File listed twice: /usr/lib64/R/library/mgcv/html/residuals.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/rig.html
    File listed twice: /usr/lib64/R/library/mgcv/html/s.html
    File listed twice: /usr/lib64/R/library/mgcv/html/scat.html
    File listed twice: /usr/lib64/R/library/mgcv/html/slanczos.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.ad.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.cr.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.ds.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.fs.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.mrf.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.ps.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.re.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.so.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.sos.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.t2.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.tensor.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.construct.tp.smooth.spec.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smooth.terms.html
    File listed twice: /usr/lib64/R/library/mgcv/html/smoothCon.html
    File listed twice: /usr/lib64/R/library/mgcv/html/sp.vcov.html
    File listed twice: /usr/lib64/R/library/mgcv/html/spasm.construct.html
    File listed twice: /usr/lib64/R/library/mgcv/html/step.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/summary.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/t2.html
    File listed twice: /usr/lib64/R/library/mgcv/html/te.html
    File listed twice: /usr/lib64/R/library/mgcv/html/tensor.prod.model.matrix.html
    File listed twice: /usr/lib64/R/library/mgcv/html/uniquecombs.html
    File listed twice: /usr/lib64/R/library/mgcv/html/vcov.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/vis.gam.html
    File listed twice: /usr/lib64/R/library/mgcv/html/ziP.html
    File listed twice: /usr/lib64/R/library/mgcv/html/ziplss.html
    File listed twice: /usr/lib64/R/library/nlme/html
    File listed twice: /usr/lib64/R/library/nlme/html/00Index.html
    File listed twice: /usr/lib64/R/library/nlme/html/ACF.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/ACF.html
    File listed twice: /usr/lib64/R/library/nlme/html/ACF.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/Alfalfa.html
    File listed twice: /usr/lib64/R/library/nlme/html/Assay.html
    File listed twice: /usr/lib64/R/library/nlme/html/BodyWeight.html
    File listed twice: /usr/lib64/R/library/nlme/html/Cefamandole.html
    File listed twice: /usr/lib64/R/library/nlme/html/Coef.html
    File listed twice: /usr/lib64/R/library/nlme/html/Covariate.html
    File listed twice: /usr/lib64/R/library/nlme/html/Covariate.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/Dialyzer.html
    File listed twice: /usr/lib64/R/library/nlme/html/Dim.corSpatial.html
    File listed twice: /usr/lib64/R/library/nlme/html/Dim.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/Dim.html
    File listed twice: /usr/lib64/R/library/nlme/html/Dim.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/Earthquake.html
    File listed twice: /usr/lib64/R/library/nlme/html/Extract.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/Fatigue.html
    File listed twice: /usr/lib64/R/library/nlme/html/Gasoline.html
    File listed twice: /usr/lib64/R/library/nlme/html/Glucose.html
    File listed twice: /usr/lib64/R/library/nlme/html/Glucose2.html
    File listed twice: /usr/lib64/R/library/nlme/html/Gun.html
    File listed twice: /usr/lib64/R/library/nlme/html/IGF.html
    File listed twice: /usr/lib64/R/library/nlme/html/Initialize.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/Initialize.glsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/Initialize.html
    File listed twice: /usr/lib64/R/library/nlme/html/Initialize.lmeStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/Initialize.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/Initialize.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/LDEsysMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/Machines.html
    File listed twice: /usr/lib64/R/library/nlme/html/MathAchSchool.html
    File listed twice: /usr/lib64/R/library/nlme/html/MathAchieve.html
    File listed twice: /usr/lib64/R/library/nlme/html/Matrix.html
    File listed twice: /usr/lib64/R/library/nlme/html/Matrix.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/Matrix.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/Meat.html
    File listed twice: /usr/lib64/R/library/nlme/html/Milk.html
    File listed twice: /usr/lib64/R/library/nlme/html/Muscle.html
    File listed twice: /usr/lib64/R/library/nlme/html/Names.formula.html
    File listed twice: /usr/lib64/R/library/nlme/html/Names.html
    File listed twice: /usr/lib64/R/library/nlme/html/Names.pdBlocked.html
    File listed twice: /usr/lib64/R/library/nlme/html/Names.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/Names.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/Nitrendipene.html
    File listed twice: /usr/lib64/R/library/nlme/html/Oats.html
    File listed twice: /usr/lib64/R/library/nlme/html/Orthodont.html
    File listed twice: /usr/lib64/R/library/nlme/html/Ovary.html
    File listed twice: /usr/lib64/R/library/nlme/html/Oxboys.html
    File listed twice: /usr/lib64/R/library/nlme/html/Oxide.html
    File listed twice: /usr/lib64/R/library/nlme/html/PBG.html
    File listed twice: /usr/lib64/R/library/nlme/html/Phenobarb.html
    File listed twice: /usr/lib64/R/library/nlme/html/Pixel.html
    File listed twice: /usr/lib64/R/library/nlme/html/Quinidine.html
    File listed twice: /usr/lib64/R/library/nlme/html/R.css
    File listed twice: /usr/lib64/R/library/nlme/html/Rail.html
    File listed twice: /usr/lib64/R/library/nlme/html/RatPupWeight.html
    File listed twice: /usr/lib64/R/library/nlme/html/Relaxin.html
    File listed twice: /usr/lib64/R/library/nlme/html/Remifentanil.html
    File listed twice: /usr/lib64/R/library/nlme/html/Soybean.html
    File listed twice: /usr/lib64/R/library/nlme/html/Spruce.html
    File listed twice: /usr/lib64/R/library/nlme/html/Tetracycline1.html
    File listed twice: /usr/lib64/R/library/nlme/html/Tetracycline2.html
    File listed twice: /usr/lib64/R/library/nlme/html/VarCorr.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corExp.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corGaus.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corLin.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corRatio.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corSpatial.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.corSpher.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.default.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.html
    File listed twice: /usr/lib64/R/library/nlme/html/Variogram.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/Wafer.html
    File listed twice: /usr/lib64/R/library/nlme/html/Wheat.html
    File listed twice: /usr/lib64/R/library/nlme/html/Wheat2.html
    File listed twice: /usr/lib64/R/library/nlme/html/allCoef.html
    File listed twice: /usr/lib64/R/library/nlme/html/anova.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/anova.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/as.matrix.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/as.matrix.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/as.matrix.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/asOneFormula.html
    File listed twice: /usr/lib64/R/library/nlme/html/asTable.html
    File listed twice: /usr/lib64/R/library/nlme/html/augPred.html
    File listed twice: /usr/lib64/R/library/nlme/html/balancedGrouped.html
    File listed twice: /usr/lib64/R/library/nlme/html/bdf.html
    File listed twice: /usr/lib64/R/library/nlme/html/coef.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/coef.gnls.html
    File listed twice: /usr/lib64/R/library/nlme/html/coef.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/coef.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/coef.modelStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/coef.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/coef.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/coef.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/collapse.groupedData.html
    File listed twice: /usr/lib64/R/library/nlme/html/collapse.html
    File listed twice: /usr/lib64/R/library/nlme/html/compareFits.html
    File listed twice: /usr/lib64/R/library/nlme/html/comparePred.html
    File listed twice: /usr/lib64/R/library/nlme/html/corAR1.html
    File listed twice: /usr/lib64/R/library/nlme/html/corARMA.html
    File listed twice: /usr/lib64/R/library/nlme/html/corCAR1.html
    File listed twice: /usr/lib64/R/library/nlme/html/corClasses.html
    File listed twice: /usr/lib64/R/library/nlme/html/corCompSymm.html
    File listed twice: /usr/lib64/R/library/nlme/html/corExp.html
    File listed twice: /usr/lib64/R/library/nlme/html/corFactor.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/corFactor.html
    File listed twice: /usr/lib64/R/library/nlme/html/corGaus.html
    File listed twice: /usr/lib64/R/library/nlme/html/corLin.html
    File listed twice: /usr/lib64/R/library/nlme/html/corMatrix.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/corMatrix.html
    File listed twice: /usr/lib64/R/library/nlme/html/corMatrix.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/corMatrix.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/corNatural.html
    File listed twice: /usr/lib64/R/library/nlme/html/corRatio.html
    File listed twice: /usr/lib64/R/library/nlme/html/corSpatial.html
    File listed twice: /usr/lib64/R/library/nlme/html/corSpher.html
    File listed twice: /usr/lib64/R/library/nlme/html/corSymm.html
    File listed twice: /usr/lib64/R/library/nlme/html/ergoStool.html
    File listed twice: /usr/lib64/R/library/nlme/html/fdHess.html
    File listed twice: /usr/lib64/R/library/nlme/html/fitted.glsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/fitted.gnlsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/fitted.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/fitted.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/fitted.lmeStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/fitted.nlmeStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/fixed.effects.html
    File listed twice: /usr/lib64/R/library/nlme/html/fixef.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/formula.pdBlocked.html
    File listed twice: /usr/lib64/R/library/nlme/html/formula.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/formula.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/gapply.html
    File listed twice: /usr/lib64/R/library/nlme/html/getCovariate.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/getCovariate.data.frame.html
    File listed twice: /usr/lib64/R/library/nlme/html/getCovariate.html
    File listed twice: /usr/lib64/R/library/nlme/html/getCovariate.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/getCovariateFormula.html
    File listed twice: /usr/lib64/R/library/nlme/html/getData.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/getData.html
    File listed twice: /usr/lib64/R/library/nlme/html/getData.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/getData.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/getGroups.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/getGroups.data.frame.html
    File listed twice: /usr/lib64/R/library/nlme/html/getGroups.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/getGroups.html
    File listed twice: /usr/lib64/R/library/nlme/html/getGroups.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/getGroups.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/getGroups.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/getGroupsFormula.html
    File listed twice: /usr/lib64/R/library/nlme/html/getResponse.html
    File listed twice: /usr/lib64/R/library/nlme/html/getResponseFormula.html
    File listed twice: /usr/lib64/R/library/nlme/html/getVarCov.html
    File listed twice: /usr/lib64/R/library/nlme/html/gls-internal.html
    File listed twice: /usr/lib64/R/library/nlme/html/gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/glsControl.html
    File listed twice: /usr/lib64/R/library/nlme/html/glsObject.html
    File listed twice: /usr/lib64/R/library/nlme/html/glsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/gnls.html
    File listed twice: /usr/lib64/R/library/nlme/html/gnlsControl.html
    File listed twice: /usr/lib64/R/library/nlme/html/gnlsObject.html
    File listed twice: /usr/lib64/R/library/nlme/html/gnlsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/groupedData.html
    File listed twice: /usr/lib64/R/library/nlme/html/gsummary.html
    File listed twice: /usr/lib64/R/library/nlme/html/intervals.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/intervals.html
    File listed twice: /usr/lib64/R/library/nlme/html/intervals.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/intervals.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/isBalanced.html
    File listed twice: /usr/lib64/R/library/nlme/html/isInitialized.html
    File listed twice: /usr/lib64/R/library/nlme/html/lmList.groupedData.html
    File listed twice: /usr/lib64/R/library/nlme/html/lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/lme.groupedData.html
    File listed twice: /usr/lib64/R/library/nlme/html/lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/lme.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/lmeControl.html
    File listed twice: /usr/lib64/R/library/nlme/html/lmeObject.html
    File listed twice: /usr/lib64/R/library/nlme/html/lmeStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/logDet.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/logDet.html
    File listed twice: /usr/lib64/R/library/nlme/html/logDet.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/logDet.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.glsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.gnls.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.gnlsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.lmeStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/logLik.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/model.matrix.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/needUpdate.html
    File listed twice: /usr/lib64/R/library/nlme/html/needUpdate.modelStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/nlme.html
    File listed twice: /usr/lib64/R/library/nlme/html/nlme.nlsList.html
    File listed twice: /usr/lib64/R/library/nlme/html/nlmeControl.html
    File listed twice: /usr/lib64/R/library/nlme/html/nlmeObject.html
    File listed twice: /usr/lib64/R/library/nlme/html/nlmeStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/nlsList.html
    File listed twice: /usr/lib64/R/library/nlme/html/nlsList.selfStart.html
    File listed twice: /usr/lib64/R/library/nlme/html/pairs.compareFits.html
    File listed twice: /usr/lib64/R/library/nlme/html/pairs.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/pairs.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdBlocked.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdClasses.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdCompSymm.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdConstruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdConstruct.pdBlocked.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdDiag.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdFactor.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdFactor.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdIdent.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdLogChol.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdMatrix.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdMatrix.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdNatural.html
    File listed twice: /usr/lib64/R/library/nlme/html/pdSymm.html
    File listed twice: /usr/lib64/R/library/nlme/html/phenoModel.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.ACF.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.Variogram.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.augPred.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.compareFits.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.intervals.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.nffGroupedData.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.nfnGroupedData.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.nmGroupedData.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.ranef.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/plot.ranef.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/pooledSD.html
    File listed twice: /usr/lib64/R/library/nlme/html/predict.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/predict.gnls.html
    File listed twice: /usr/lib64/R/library/nlme/html/predict.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/predict.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/predict.nlme.html
    File listed twice: /usr/lib64/R/library/nlme/html/print.summary.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/print.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/qqnorm.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/qqnorm.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/quinModel.html
    File listed twice: /usr/lib64/R/library/nlme/html/random.effects.html
    File listed twice: /usr/lib64/R/library/nlme/html/ranef.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/ranef.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/recalc.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/recalc.html
    File listed twice: /usr/lib64/R/library/nlme/html/recalc.modelStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/recalc.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/recalc.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/residuals.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/residuals.glsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/residuals.gnlsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/residuals.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/residuals.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/residuals.lmeStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/residuals.nlmeStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/simulate.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/solve.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/solve.reStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/splitFormula.html
    File listed twice: /usr/lib64/R/library/nlme/html/summary.corStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/summary.gls.html
    File listed twice: /usr/lib64/R/library/nlme/html/summary.lmList.html
    File listed twice: /usr/lib64/R/library/nlme/html/summary.lme.html
    File listed twice: /usr/lib64/R/library/nlme/html/summary.modelStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/summary.nlsList.html
    File listed twice: /usr/lib64/R/library/nlme/html/summary.pdMat.html
    File listed twice: /usr/lib64/R/library/nlme/html/summary.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/update.modelStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/update.varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/varClasses.html
    File listed twice: /usr/lib64/R/library/nlme/html/varComb.html
    File listed twice: /usr/lib64/R/library/nlme/html/varConstPower.html
    File listed twice: /usr/lib64/R/library/nlme/html/varExp.html
    File listed twice: /usr/lib64/R/library/nlme/html/varFixed.html
    File listed twice: /usr/lib64/R/library/nlme/html/varFunc.html
    File listed twice: /usr/lib64/R/library/nlme/html/varIdent.html
    File listed twice: /usr/lib64/R/library/nlme/html/varPower.html
    File listed twice: /usr/lib64/R/library/nlme/html/varWeights.glsStruct.html
    File listed twice: /usr/lib64/R/library/nlme/html/varWeights.html
    File listed twice: /usr/lib64/R/library/nlme/html/varWeights.lmeStruct.html
    File listed twice: /usr/lib64/R/library/nnet/html
    File listed twice: /usr/lib64/R/library/nnet/html/00Index.html
    File listed twice: /usr/lib64/R/library/nnet/html/R.css
    File listed twice: /usr/lib64/R/library/nnet/html/class.ind.html
    File listed twice: /usr/lib64/R/library/nnet/html/multinom.html
    File listed twice: /usr/lib64/R/library/nnet/html/nnet.Hess.html
    File listed twice: /usr/lib64/R/library/nnet/html/nnet.html
    File listed twice: /usr/lib64/R/library/nnet/html/predict.nnet.html
    File listed twice: /usr/lib64/R/library/nnet/html/which.is.max.html
    File listed twice: /usr/lib64/R/library/parallel/html
    File listed twice: /usr/lib64/R/library/parallel/html/00Index.html
    File listed twice: /usr/lib64/R/library/parallel/html/R.css
    File listed twice: /usr/lib64/R/library/parallel/html/RngStream.html
    File listed twice: /usr/lib64/R/library/parallel/html/children.html
    File listed twice: /usr/lib64/R/library/parallel/html/clusterApply.html
    File listed twice: /usr/lib64/R/library/parallel/html/detectCores.html
    File listed twice: /usr/lib64/R/library/parallel/html/makeCluster.html
    File listed twice: /usr/lib64/R/library/parallel/html/mcaffinity.html
    File listed twice: /usr/lib64/R/library/parallel/html/mcfork.html
    File listed twice: /usr/lib64/R/library/parallel/html/mclapply.html
    File listed twice: /usr/lib64/R/library/parallel/html/mcparallel.html
    File listed twice: /usr/lib64/R/library/parallel/html/parallel-package.html
    File listed twice: /usr/lib64/R/library/parallel/html/pvec.html
    File listed twice: /usr/lib64/R/library/parallel/html/splitIndices.html
    File listed twice: /usr/lib64/R/library/rpart/html
    File listed twice: /usr/lib64/R/library/rpart/html/00Index.html
    File listed twice: /usr/lib64/R/library/rpart/html/R.css
    File listed twice: /usr/lib64/R/library/rpart/html/car.test.frame.html
    File listed twice: /usr/lib64/R/library/rpart/html/car90.html
    File listed twice: /usr/lib64/R/library/rpart/html/cu.summary.html
    File listed twice: /usr/lib64/R/library/rpart/html/kyphosis.html
    File listed twice: /usr/lib64/R/library/rpart/html/labels.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/meanvar.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/na.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/path.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/plot.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/plotcp.html
    File listed twice: /usr/lib64/R/library/rpart/html/post.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/predict.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/print.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/printcp.html
    File listed twice: /usr/lib64/R/library/rpart/html/prune.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/residuals.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/rpart-internal.html
    File listed twice: /usr/lib64/R/library/rpart/html/rpart.control.html
    File listed twice: /usr/lib64/R/library/rpart/html/rpart.exp.html
    File listed twice: /usr/lib64/R/library/rpart/html/rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/rpart.object.html
    File listed twice: /usr/lib64/R/library/rpart/html/rsq.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/snip.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/solder.html
    File listed twice: /usr/lib64/R/library/rpart/html/stagec.html
    File listed twice: /usr/lib64/R/library/rpart/html/summary.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/text.rpart.html
    File listed twice: /usr/lib64/R/library/rpart/html/xpred.rpart.html
    File listed twice: /usr/lib64/R/library/spatial/html
    File listed twice: /usr/lib64/R/library/spatial/html/00Index.html
    File listed twice: /usr/lib64/R/library/spatial/html/Kaver.html
    File listed twice: /usr/lib64/R/library/spatial/html/Kenvl.html
    File listed twice: /usr/lib64/R/library/spatial/html/Kfn.html
    File listed twice: /usr/lib64/R/library/spatial/html/Psim.html
    File listed twice: /usr/lib64/R/library/spatial/html/R.css
    File listed twice: /usr/lib64/R/library/spatial/html/SSI.html
    File listed twice: /usr/lib64/R/library/spatial/html/Strauss.html
    File listed twice: /usr/lib64/R/library/spatial/html/anova.trls.html
    File listed twice: /usr/lib64/R/library/spatial/html/correlogram.html
    File listed twice: /usr/lib64/R/library/spatial/html/expcov.html
    File listed twice: /usr/lib64/R/library/spatial/html/ppgetregion.html
    File listed twice: /usr/lib64/R/library/spatial/html/ppinit.html
    File listed twice: /usr/lib64/R/library/spatial/html/pplik.html
    File listed twice: /usr/lib64/R/library/spatial/html/ppregion.html
    File listed twice: /usr/lib64/R/library/spatial/html/predict.trls.html
    File listed twice: /usr/lib64/R/library/spatial/html/prmat.html
    File listed twice: /usr/lib64/R/library/spatial/html/semat.html
    File listed twice: /usr/lib64/R/library/spatial/html/surf.gls.html
    File listed twice: /usr/lib64/R/library/spatial/html/surf.ls.html
    File listed twice: /usr/lib64/R/library/spatial/html/trls.influence.html
    File listed twice: /usr/lib64/R/library/spatial/html/trmat.html
    File listed twice: /usr/lib64/R/library/spatial/html/variogram.html
    File listed twice: /usr/lib64/R/library/splines/html
    File listed twice: /usr/lib64/R/library/splines/html/00Index.html
    File listed twice: /usr/lib64/R/library/splines/html/R.css
    File listed twice: /usr/lib64/R/library/splines/html/asVector.html
    File listed twice: /usr/lib64/R/library/splines/html/backSpline.html
    File listed twice: /usr/lib64/R/library/splines/html/bs.html
    File listed twice: /usr/lib64/R/library/splines/html/interpSpline.html
    File listed twice: /usr/lib64/R/library/splines/html/ns.html
    File listed twice: /usr/lib64/R/library/splines/html/periodicSpline.html
    File listed twice: /usr/lib64/R/library/splines/html/polySpline.html
    File listed twice: /usr/lib64/R/library/splines/html/predict.bSpline.html
    File listed twice: /usr/lib64/R/library/splines/html/predict.bs.html
    File listed twice: /usr/lib64/R/library/splines/html/splineDesign.html
    File listed twice: /usr/lib64/R/library/splines/html/splineKnots.html
    File listed twice: /usr/lib64/R/library/splines/html/splineOrder.html
    File listed twice: /usr/lib64/R/library/splines/html/splines-package.html
    File listed twice: /usr/lib64/R/library/splines/html/xyVector.html
    File listed twice: /usr/lib64/R/library/stats/html
    File listed twice: /usr/lib64/R/library/stats/html/00Index.html
    File listed twice: /usr/lib64/R/library/stats/html/AIC.html
    File listed twice: /usr/lib64/R/library/stats/html/ARMAacf.html
    File listed twice: /usr/lib64/R/library/stats/html/ARMAtoMA.html
    File listed twice: /usr/lib64/R/library/stats/html/Beta.html
    File listed twice: /usr/lib64/R/library/stats/html/Binomial.html
    File listed twice: /usr/lib64/R/library/stats/html/Cauchy.html
    File listed twice: /usr/lib64/R/library/stats/html/Chisquare.html
    File listed twice: /usr/lib64/R/library/stats/html/Distributions.html
    File listed twice: /usr/lib64/R/library/stats/html/Exponential.html
    File listed twice: /usr/lib64/R/library/stats/html/Fdist.html
    File listed twice: /usr/lib64/R/library/stats/html/GammaDist.html
    File listed twice: /usr/lib64/R/library/stats/html/Geometric.html
    File listed twice: /usr/lib64/R/library/stats/html/HoltWinters.html
    File listed twice: /usr/lib64/R/library/stats/html/Hypergeometric.html
    File listed twice: /usr/lib64/R/library/stats/html/IQR.html
    File listed twice: /usr/lib64/R/library/stats/html/KalmanLike.html
    File listed twice: /usr/lib64/R/library/stats/html/Logistic.html
    File listed twice: /usr/lib64/R/library/stats/html/Lognormal.html
    File listed twice: /usr/lib64/R/library/stats/html/Multinom.html
    File listed twice: /usr/lib64/R/library/stats/html/NLSstAsymptotic.html
    File listed twice: /usr/lib64/R/library/stats/html/NLSstClosestX.html
    File listed twice: /usr/lib64/R/library/stats/html/NLSstLfAsymptote.html
    File listed twice: /usr/lib64/R/library/stats/html/NLSstRtAsymptote.html
    File listed twice: /usr/lib64/R/library/stats/html/NegBinomial.html
    File listed twice: /usr/lib64/R/library/stats/html/Normal.html
    File listed twice: /usr/lib64/R/library/stats/html/Poisson.html
    File listed twice: /usr/lib64/R/library/stats/html/R.css
    File listed twice: /usr/lib64/R/library/stats/html/SSD.html
    File listed twice: /usr/lib64/R/library/stats/html/SSasymp.html
    File listed twice: /usr/lib64/R/library/stats/html/SSasympOff.html
    File listed twice: /usr/lib64/R/library/stats/html/SSasympOrig.html
    File listed twice: /usr/lib64/R/library/stats/html/SSbiexp.html
    File listed twice: /usr/lib64/R/library/stats/html/SSfol.html
    File listed twice: /usr/lib64/R/library/stats/html/SSfpl.html
    File listed twice: /usr/lib64/R/library/stats/html/SSgompertz.html
    File listed twice: /usr/lib64/R/library/stats/html/SSlogis.html
    File listed twice: /usr/lib64/R/library/stats/html/SSmicmen.html
    File listed twice: /usr/lib64/R/library/stats/html/SSweibull.html
    File listed twice: /usr/lib64/R/library/stats/html/SignRank.html
    File listed twice: /usr/lib64/R/library/stats/html/StructTS.html
    File listed twice: /usr/lib64/R/library/stats/html/TDist.html
    File listed twice: /usr/lib64/R/library/stats/html/Tukey.html
    File listed twice: /usr/lib64/R/library/stats/html/TukeyHSD.html
    File listed twice: /usr/lib64/R/library/stats/html/Uniform.html
    File listed twice: /usr/lib64/R/library/stats/html/Weibull.html
    File listed twice: /usr/lib64/R/library/stats/html/Wilcoxon.html
    File listed twice: /usr/lib64/R/library/stats/html/acf.html
    File listed twice: /usr/lib64/R/library/stats/html/acf2AR.html
    File listed twice: /usr/lib64/R/library/stats/html/add1.html
    File listed twice: /usr/lib64/R/library/stats/html/addmargins.html
    File listed twice: /usr/lib64/R/library/stats/html/aggregate.html
    File listed twice: /usr/lib64/R/library/stats/html/alias.html
    File listed twice: /usr/lib64/R/library/stats/html/anova.glm.html
    File listed twice: /usr/lib64/R/library/stats/html/anova.html
    File listed twice: /usr/lib64/R/library/stats/html/anova.lm.html
    File listed twice: /usr/lib64/R/library/stats/html/anova.mlm.html
    File listed twice: /usr/lib64/R/library/stats/html/ansari.test.html
    File listed twice: /usr/lib64/R/library/stats/html/aov.html
    File listed twice: /usr/lib64/R/library/stats/html/approxfun.html
    File listed twice: /usr/lib64/R/library/stats/html/ar.html
    File listed twice: /usr/lib64/R/library/stats/html/ar.ols.html
    File listed twice: /usr/lib64/R/library/stats/html/arima.html
    File listed twice: /usr/lib64/R/library/stats/html/arima.sim.html
    File listed twice: /usr/lib64/R/library/stats/html/arima0.html
    File listed twice: /usr/lib64/R/library/stats/html/as.hclust.html
    File listed twice: /usr/lib64/R/library/stats/html/asOneSidedFormula.html
    File listed twice: /usr/lib64/R/library/stats/html/ave.html
    File listed twice: /usr/lib64/R/library/stats/html/bandwidth.html
    File listed twice: /usr/lib64/R/library/stats/html/bartlett.test.html
    File listed twice: /usr/lib64/R/library/stats/html/binom.test.html
    File listed twice: /usr/lib64/R/library/stats/html/biplot.html
    File listed twice: /usr/lib64/R/library/stats/html/biplot.princomp.html
    File listed twice: /usr/lib64/R/library/stats/html/birthday.html
    File listed twice: /usr/lib64/R/library/stats/html/box.test.html
    File listed twice: /usr/lib64/R/library/stats/html/cancor.html
    File listed twice: /usr/lib64/R/library/stats/html/case.names.html
    File listed twice: /usr/lib64/R/library/stats/html/checkMFClasses.html
    File listed twice: /usr/lib64/R/library/stats/html/chisq.test.html
    File listed twice: /usr/lib64/R/library/stats/html/cmdscale.html
    File listed twice: /usr/lib64/R/library/stats/html/coef.html
    File listed twice: /usr/lib64/R/library/stats/html/complete.cases.html
    File listed twice: /usr/lib64/R/library/stats/html/confint.html
    File listed twice: /usr/lib64/R/library/stats/html/constrOptim.html
    File listed twice: /usr/lib64/R/library/stats/html/contrast.html
    File listed twice: /usr/lib64/R/library/stats/html/contrasts.html
    File listed twice: /usr/lib64/R/library/stats/html/convolve.html
    File listed twice: /usr/lib64/R/library/stats/html/cophenetic.html
    File listed twice: /usr/lib64/R/library/stats/html/cor.html
    File listed twice: /usr/lib64/R/library/stats/html/cor.test.html
    File listed twice: /usr/lib64/R/library/stats/html/cov.wt.html
    File listed twice: /usr/lib64/R/library/stats/html/cpgram.html
    File listed twice: /usr/lib64/R/library/stats/html/cutree.html
    File listed twice: /usr/lib64/R/library/stats/html/decompose.html
    File listed twice: /usr/lib64/R/library/stats/html/delete.response.html
    File listed twice: /usr/lib64/R/library/stats/html/dendrapply.html
    File listed twice: /usr/lib64/R/library/stats/html/dendrogram.html
    File listed twice: /usr/lib64/R/library/stats/html/density.html
    File listed twice: /usr/lib64/R/library/stats/html/deriv.html
    File listed twice: /usr/lib64/R/library/stats/html/deviance.html
    File listed twice: /usr/lib64/R/library/stats/html/df.residual.html
    File listed twice: /usr/lib64/R/library/stats/html/diffinv.html
    File listed twice: /usr/lib64/R/library/stats/html/dist.html
    File listed twice: /usr/lib64/R/library/stats/html/dummy.coef.html
    File listed twice: /usr/lib64/R/library/stats/html/ecdf.html
    File listed twice: /usr/lib64/R/library/stats/html/eff.aovlist.html
    File listed twice: /usr/lib64/R/library/stats/html/effects.html
    File listed twice: /usr/lib64/R/library/stats/html/embed.html
    File listed twice: /usr/lib64/R/library/stats/html/expand.model.frame.html
    File listed twice: /usr/lib64/R/library/stats/html/extractAIC.html
    File listed twice: /usr/lib64/R/library/stats/html/factanal.html
    File listed twice: /usr/lib64/R/library/stats/html/factor.scope.html
    File listed twice: /usr/lib64/R/library/stats/html/family.html
    File listed twice: /usr/lib64/R/library/stats/html/fft.html
    File listed twice: /usr/lib64/R/library/stats/html/filter.html
    File listed twice: /usr/lib64/R/library/stats/html/fisher.test.html
    File listed twice: /usr/lib64/R/library/stats/html/fitted.values.html
    File listed twice: /usr/lib64/R/library/stats/html/fivenum.html
    File listed twice: /usr/lib64/R/library/stats/html/fligner.test.html
    File listed twice: /usr/lib64/R/library/stats/html/formula.html
    File listed twice: /usr/lib64/R/library/stats/html/formula.nls.html
    File listed twice: /usr/lib64/R/library/stats/html/friedman.test.html
    File listed twice: /usr/lib64/R/library/stats/html/ftable.formula.html
    File listed twice: /usr/lib64/R/library/stats/html/ftable.html
    File listed twice: /usr/lib64/R/library/stats/html/getInitial.html
    File listed twice: /usr/lib64/R/library/stats/html/glm.control.html
    File listed twice: /usr/lib64/R/library/stats/html/glm.html
    File listed twice: /usr/lib64/R/library/stats/html/glm.summaries.html
    File listed twice: /usr/lib64/R/library/stats/html/hclust.html
    File listed twice: /usr/lib64/R/library/stats/html/heatmap.html
    File listed twice: /usr/lib64/R/library/stats/html/identify.hclust.html
    File listed twice: /usr/lib64/R/library/stats/html/influence.measures.html
    File listed twice: /usr/lib64/R/library/stats/html/integrate.html
    File listed twice: /usr/lib64/R/library/stats/html/interaction.plot.html
    File listed twice: /usr/lib64/R/library/stats/html/is.empty.html
    File listed twice: /usr/lib64/R/library/stats/html/isoreg.html
    File listed twice: /usr/lib64/R/library/stats/html/kernapply.html
    File listed twice: /usr/lib64/R/library/stats/html/kernel.html
    File listed twice: /usr/lib64/R/library/stats/html/kmeans.html
    File listed twice: /usr/lib64/R/library/stats/html/kruskal.test.html
    File listed twice: /usr/lib64/R/library/stats/html/ks.test.html
    File listed twice: /usr/lib64/R/library/stats/html/ksmooth.html
    File listed twice: /usr/lib64/R/library/stats/html/lag.html
    File listed twice: /usr/lib64/R/library/stats/html/lag.plot.html
    File listed twice: /usr/lib64/R/library/stats/html/line.html
    File listed twice: /usr/lib64/R/library/stats/html/listof.html
    File listed twice: /usr/lib64/R/library/stats/html/lm.html
    File listed twice: /usr/lib64/R/library/stats/html/lm.influence.html
    File listed twice: /usr/lib64/R/library/stats/html/lm.summaries.html
    File listed twice: /usr/lib64/R/library/stats/html/lmfit.html
    File listed twice: /usr/lib64/R/library/stats/html/loadings.html
    File listed twice: /usr/lib64/R/library/stats/html/loess.control.html
    File listed twice: /usr/lib64/R/library/stats/html/loess.html
    File listed twice: /usr/lib64/R/library/stats/html/logLik.html
    File listed twice: /usr/lib64/R/library/stats/html/loglin.html
    File listed twice: /usr/lib64/R/library/stats/html/lowess.html
    File listed twice: /usr/lib64/R/library/stats/html/ls.diag.html
    File listed twice: /usr/lib64/R/library/stats/html/ls.print.html
    File listed twice: /usr/lib64/R/library/stats/html/lsfit.html
    File listed twice: /usr/lib64/R/library/stats/html/mad.html
    File listed twice: /usr/lib64/R/library/stats/html/mahalanobis.html
    File listed twice: /usr/lib64/R/library/stats/html/make.link.html
    File listed twice: /usr/lib64/R/library/stats/html/makepredictcall.html
    File listed twice: /usr/lib64/R/library/stats/html/manova.html
    File listed twice: /usr/lib64/R/library/stats/html/mantelhaen.test.html
    File listed twice: /usr/lib64/R/library/stats/html/mauchly.test.html
    File listed twice: /usr/lib64/R/library/stats/html/mcnemar.test.html
    File listed twice: /usr/lib64/R/library/stats/html/median.html
    File listed twice: /usr/lib64/R/library/stats/html/medpolish.html
    File listed twice: /usr/lib64/R/library/stats/html/model.extract.html
    File listed twice: /usr/lib64/R/library/stats/html/model.frame.html
    File listed twice: /usr/lib64/R/library/stats/html/model.matrix.html
    File listed twice: /usr/lib64/R/library/stats/html/model.tables.html
    File listed twice: /usr/lib64/R/library/stats/html/monthplot.html
    File listed twice: /usr/lib64/R/library/stats/html/mood.test.html
    File listed twice: /usr/lib64/R/library/stats/html/na.action.html
    File listed twice: /usr/lib64/R/library/stats/html/na.contiguous.html
    File listed twice: /usr/lib64/R/library/stats/html/na.fail.html
    File listed twice: /usr/lib64/R/library/stats/html/nafns.html
    File listed twice: /usr/lib64/R/library/stats/html/naprint.html
    File listed twice: /usr/lib64/R/library/stats/html/nextn.html
    File listed twice: /usr/lib64/R/library/stats/html/nlm.html
    File listed twice: /usr/lib64/R/library/stats/html/nlminb.html
    File listed twice: /usr/lib64/R/library/stats/html/nls.control.html
    File listed twice: /usr/lib64/R/library/stats/html/nls.html
    File listed twice: /usr/lib64/R/library/stats/html/nobs.html
    File listed twice: /usr/lib64/R/library/stats/html/numericDeriv.html
    File listed twice: /usr/lib64/R/library/stats/html/offset.html
    File listed twice: /usr/lib64/R/library/stats/html/oneway.test.html
    File listed twice: /usr/lib64/R/library/stats/html/optim.html
    File listed twice: /usr/lib64/R/library/stats/html/optimize.html
    File listed twice: /usr/lib64/R/library/stats/html/order.dendrogram.html
    File listed twice: /usr/lib64/R/library/stats/html/p.adjust.html
    File listed twice: /usr/lib64/R/library/stats/html/pairwise.prop.test.html
    File listed twice: /usr/lib64/R/library/stats/html/pairwise.t.test.html
    File listed twice: /usr/lib64/R/library/stats/html/pairwise.table.html
    File listed twice: /usr/lib64/R/library/stats/html/pairwise.wilcox.test.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.HoltWinters.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.acf.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.density.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.isoreg.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.lm.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.ppr.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.profile.nls.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.spec.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.stepfun.html
    File listed twice: /usr/lib64/R/library/stats/html/plot.ts.html
    File listed twice: /usr/lib64/R/library/stats/html/poisson.test.html
    File listed twice: /usr/lib64/R/library/stats/html/poly.html
    File listed twice: /usr/lib64/R/library/stats/html/power.anova.test.html
    File listed twice: /usr/lib64/R/library/stats/html/power.html
    File listed twice: /usr/lib64/R/library/stats/html/power.prop.test.html
    File listed twice: /usr/lib64/R/library/stats/html/power.t.test.html
    File listed twice: /usr/lib64/R/library/stats/html/pp.test.html
    File listed twice: /usr/lib64/R/library/stats/html/ppoints.html
    File listed twice: /usr/lib64/R/library/stats/html/ppr.html
    File listed twice: /usr/lib64/R/library/stats/html/prcomp.html
    File listed twice: /usr/lib64/R/library/stats/html/predict.HoltWinters.html
    File listed twice: /usr/lib64/R/library/stats/html/predict.arima.html
    File listed twice: /usr/lib64/R/library/stats/html/predict.glm.html
    File listed twice: /usr/lib64/R/library/stats/html/predict.html
    File listed twice: /usr/lib64/R/library/stats/html/predict.lm.html
    File listed twice: /usr/lib64/R/library/stats/html/predict.loess.html
    File listed twice: /usr/lib64/R/library/stats/html/predict.nls.html
    File listed twice: /usr/lib64/R/library/stats/html/predict.smooth.spline.html
    File listed twice: /usr/lib64/R/library/stats/html/preplot.html
    File listed twice: /usr/lib64/R/library/stats/html/princomp.html
    File listed twice: /usr/lib64/R/library/stats/html/print.power.htest.html
    File listed twice: /usr/lib64/R/library/stats/html/print.ts.html
    File listed twice: /usr/lib64/R/library/stats/html/printCoefmat.html
    File listed twice: /usr/lib64/R/library/stats/html/profile.html
    File listed twice: /usr/lib64/R/library/stats/html/profile.nls.html
    File listed twice: /usr/lib64/R/library/stats/html/proj.html
    File listed twice: /usr/lib64/R/library/stats/html/prop.test.html
    File listed twice: /usr/lib64/R/library/stats/html/prop.trend.test.html
    File listed twice: /usr/lib64/R/library/stats/html/qqnorm.html
    File listed twice: /usr/lib64/R/library/stats/html/quade.test.html
    File listed twice: /usr/lib64/R/library/stats/html/quantile.html
    File listed twice: /usr/lib64/R/library/stats/html/r2dtable.html
    File listed twice: /usr/lib64/R/library/stats/html/rWishart.html
    File listed twice: /usr/lib64/R/library/stats/html/read.ftable.html
    File listed twice: /usr/lib64/R/library/stats/html/rect.hclust.html
    File listed twice: /usr/lib64/R/library/stats/html/relevel.html
    File listed twice: /usr/lib64/R/library/stats/html/reorder.dendrogram.html
    File listed twice: /usr/lib64/R/library/stats/html/reorder.factor.html
    File listed twice: /usr/lib64/R/library/stats/html/replications.html
    File listed twice: /usr/lib64/R/library/stats/html/reshape.html
    File listed twice: /usr/lib64/R/library/stats/html/residuals.html
    File listed twice: /usr/lib64/R/library/stats/html/runmed.html
    File listed twice: /usr/lib64/R/library/stats/html/scatter.smooth.html
    File listed twice: /usr/lib64/R/library/stats/html/screeplot.html
    File listed twice: /usr/lib64/R/library/stats/html/sd.html
    File listed twice: /usr/lib64/R/library/stats/html/se.contrast.html
    File listed twice: /usr/lib64/R/library/stats/html/selfStart.html
    File listed twice: /usr/lib64/R/library/stats/html/setNames.html
    File listed twice: /usr/lib64/R/library/stats/html/shapiro.test.html
    File listed twice: /usr/lib64/R/library/stats/html/simulate.html
    File listed twice: /usr/lib64/R/library/stats/html/smooth.html
    File listed twice: /usr/lib64/R/library/stats/html/smooth.spline.html
    File listed twice: /usr/lib64/R/library/stats/html/smoothEnds.html
    File listed twice: /usr/lib64/R/library/stats/html/sortedXyData.html
    File listed twice: /usr/lib64/R/library/stats/html/spec.ar.html
    File listed twice: /usr/lib64/R/library/stats/html/spec.pgram.html
    File listed twice: /usr/lib64/R/library/stats/html/spec.taper.html
    File listed twice: /usr/lib64/R/library/stats/html/spectrum.html
    File listed twice: /usr/lib64/R/library/stats/html/splinefun.html
    File listed twice: /usr/lib64/R/library/stats/html/start.html
    File listed twice: /usr/lib64/R/library/stats/html/stat.anova.html
    File listed twice: /usr/lib64/R/library/stats/html/stats-defunct.html
    File listed twice: /usr/lib64/R/library/stats/html/stats-deprecated.html
    File listed twice: /usr/lib64/R/library/stats/html/stats-package.html
    File listed twice: /usr/lib64/R/library/stats/html/step.html
    File listed twice: /usr/lib64/R/library/stats/html/stepfun.html
    File listed twice: /usr/lib64/R/library/stats/html/stl.html
    File listed twice: /usr/lib64/R/library/stats/html/stlmethods.html
    File listed twice: /usr/lib64/R/library/stats/html/summary.aov.html
    File listed twice: /usr/lib64/R/library/stats/html/summary.glm.html
    File listed twice: /usr/lib64/R/library/stats/html/summary.lm.html
    File listed twice: /usr/lib64/R/library/stats/html/summary.manova.html
    File listed twice: /usr/lib64/R/library/stats/html/summary.nls.html
    File listed twice: /usr/lib64/R/library/stats/html/summary.princomp.html
    File listed twice: /usr/lib64/R/library/stats/html/supsmu.html
    File listed twice: /usr/lib64/R/library/stats/html/symnum.html
    File listed twice: /usr/lib64/R/library/stats/html/t.test.html
    File listed twice: /usr/lib64/R/library/stats/html/termplot.html
    File listed twice: /usr/lib64/R/library/stats/html/terms.formula.html
    File listed twice: /usr/lib64/R/library/stats/html/terms.html
    File listed twice: /usr/lib64/R/library/stats/html/terms.object.html
    File listed twice: /usr/lib64/R/library/stats/html/time.html
    File listed twice: /usr/lib64/R/library/stats/html/toeplitz.html
    File listed twice: /usr/lib64/R/library/stats/html/ts-methods.html
    File listed twice: /usr/lib64/R/library/stats/html/ts.html
    File listed twice: /usr/lib64/R/library/stats/html/ts.plot.html
    File listed twice: /usr/lib64/R/library/stats/html/ts.union.html
    File listed twice: /usr/lib64/R/library/stats/html/tsSmooth.html
    File listed twice: /usr/lib64/R/library/stats/html/tsdiag.html
    File listed twice: /usr/lib64/R/library/stats/html/tsp.html
    File listed twice: /usr/lib64/R/library/stats/html/uniroot.html
    File listed twice: /usr/lib64/R/library/stats/html/update.formula.html
    File listed twice: /usr/lib64/R/library/stats/html/update.html
    File listed twice: /usr/lib64/R/library/stats/html/var.test.html
    File listed twice: /usr/lib64/R/library/stats/html/varimax.html
    File listed twice: /usr/lib64/R/library/stats/html/vcov.html
    File listed twice: /usr/lib64/R/library/stats/html/weighted.mean.html
    File listed twice: /usr/lib64/R/library/stats/html/weighted.residuals.html
    File listed twice: /usr/lib64/R/library/stats/html/weights.html
    File listed twice: /usr/lib64/R/library/stats/html/wilcox.test.html
    File listed twice: /usr/lib64/R/library/stats/html/window.html
    File listed twice: /usr/lib64/R/library/stats/html/xtabs.html
    File listed twice: /usr/lib64/R/library/stats/html/zC.html
    File listed twice: /usr/lib64/R/library/stats4/html
    File listed twice: /usr/lib64/R/library/stats4/html/00Index.html
    File listed twice: /usr/lib64/R/library/stats4/html/R.css
    File listed twice: /usr/lib64/R/library/stats4/html/coef-methods.html
    File listed twice: /usr/lib64/R/library/stats4/html/confint-methods.html
    File listed twice: /usr/lib64/R/library/stats4/html/logLik-methods.html
    File listed twice: /usr/lib64/R/library/stats4/html/mle-class.html
    File listed twice: /usr/lib64/R/library/stats4/html/mle.html
    File listed twice: /usr/lib64/R/library/stats4/html/plot-methods.html
    File listed twice: /usr/lib64/R/library/stats4/html/profile-methods.html
    File listed twice: /usr/lib64/R/library/stats4/html/profile.mle-class.html
    File listed twice: /usr/lib64/R/library/stats4/html/show-methods.html
    File listed twice: /usr/lib64/R/library/stats4/html/stats4-package.html
    File listed twice: /usr/lib64/R/library/stats4/html/summary-methods.html
    File listed twice: /usr/lib64/R/library/stats4/html/summary.mle-class.html
    File listed twice: /usr/lib64/R/library/stats4/html/update-methods.html
    File listed twice: /usr/lib64/R/library/stats4/html/vcov-methods.html
    File listed twice: /usr/lib64/R/library/survival/html
    File listed twice: /usr/lib64/R/library/survival/html/00Index.html
    File listed twice: /usr/lib64/R/library/survival/html/R.css
    File listed twice: /usr/lib64/R/library/survival/html/Surv.html
    File listed twice: /usr/lib64/R/library/survival/html/aareg.html
    File listed twice: /usr/lib64/R/library/survival/html/agreg.fit.html
    File listed twice: /usr/lib64/R/library/survival/html/aml.html
    File listed twice: /usr/lib64/R/library/survival/html/anova.coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/attrassign.html
    File listed twice: /usr/lib64/R/library/survival/html/basehaz.html
    File listed twice: /usr/lib64/R/library/survival/html/bladder.html
    File listed twice: /usr/lib64/R/library/survival/html/cch.html
    File listed twice: /usr/lib64/R/library/survival/html/cgd.html
    File listed twice: /usr/lib64/R/library/survival/html/clogit.html
    File listed twice: /usr/lib64/R/library/survival/html/cluster.html
    File listed twice: /usr/lib64/R/library/survival/html/colon.html
    File listed twice: /usr/lib64/R/library/survival/html/cox.zph.html
    File listed twice: /usr/lib64/R/library/survival/html/coxph.control.html
    File listed twice: /usr/lib64/R/library/survival/html/coxph.detail.html
    File listed twice: /usr/lib64/R/library/survival/html/coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/coxph.object.html
    File listed twice: /usr/lib64/R/library/survival/html/coxph.wtest.html
    File listed twice: /usr/lib64/R/library/survival/html/dsurvreg.html
    File listed twice: /usr/lib64/R/library/survival/html/flchain.html
    File listed twice: /usr/lib64/R/library/survival/html/frailty.html
    File listed twice: /usr/lib64/R/library/survival/html/heart.html
    File listed twice: /usr/lib64/R/library/survival/html/is.ratetable.html
    File listed twice: /usr/lib64/R/library/survival/html/kidney.html
    File listed twice: /usr/lib64/R/library/survival/html/lines.survfit.html
    File listed twice: /usr/lib64/R/library/survival/html/logan.html
    File listed twice: /usr/lib64/R/library/survival/html/lung.html
    File listed twice: /usr/lib64/R/library/survival/html/mgus.html
    File listed twice: /usr/lib64/R/library/survival/html/model.frame.coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/model.matrix.coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/nwtco.html
    File listed twice: /usr/lib64/R/library/survival/html/ovarian.html
    File listed twice: /usr/lib64/R/library/survival/html/pbc.html
    File listed twice: /usr/lib64/R/library/survival/html/pbcseq.html
    File listed twice: /usr/lib64/R/library/survival/html/plot.aareg.html
    File listed twice: /usr/lib64/R/library/survival/html/plot.cox.zph.html
    File listed twice: /usr/lib64/R/library/survival/html/plot.survfit.html
    File listed twice: /usr/lib64/R/library/survival/html/predict.coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/predict.survreg.html
    File listed twice: /usr/lib64/R/library/survival/html/print.aareg.html
    File listed twice: /usr/lib64/R/library/survival/html/print.summary.coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/print.summary.survexp.html
    File listed twice: /usr/lib64/R/library/survival/html/print.summary.survfit.html
    File listed twice: /usr/lib64/R/library/survival/html/print.survfit.html
    File listed twice: /usr/lib64/R/library/survival/html/pspline.html
    File listed twice: /usr/lib64/R/library/survival/html/pyears.html
    File listed twice: /usr/lib64/R/library/survival/html/quantile.survfit.html
    File listed twice: /usr/lib64/R/library/survival/html/ratetable.html
    File listed twice: /usr/lib64/R/library/survival/html/ratetableDate.html
    File listed twice: /usr/lib64/R/library/survival/html/rats.html
    File listed twice: /usr/lib64/R/library/survival/html/rats2.html
    File listed twice: /usr/lib64/R/library/survival/html/residuals.coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/residuals.survreg.html
    File listed twice: /usr/lib64/R/library/survival/html/ridge.html
    File listed twice: /usr/lib64/R/library/survival/html/stanford2.html
    File listed twice: /usr/lib64/R/library/survival/html/strata.html
    File listed twice: /usr/lib64/R/library/survival/html/summary.aareg.html
    File listed twice: /usr/lib64/R/library/survival/html/summary.coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/summary.survexp.html
    File listed twice: /usr/lib64/R/library/survival/html/summary.survfit.html
    File listed twice: /usr/lib64/R/library/survival/html/survConcordance.html
    File listed twice: /usr/lib64/R/library/survival/html/survSplit.html
    File listed twice: /usr/lib64/R/library/survival/html/survdiff.html
    File listed twice: /usr/lib64/R/library/survival/html/survexp.fit.html
    File listed twice: /usr/lib64/R/library/survival/html/survexp.html
    File listed twice: /usr/lib64/R/library/survival/html/survexp.us.html
    File listed twice: /usr/lib64/R/library/survival/html/survfit.coxph.html
    File listed twice: /usr/lib64/R/library/survival/html/survfit.formula.html
    File listed twice: /usr/lib64/R/library/survival/html/survfit.html
    File listed twice: /usr/lib64/R/library/survival/html/survfit.object.html
    File listed twice: /usr/lib64/R/library/survival/html/survfitcoxph.fit.html
    File listed twice: /usr/lib64/R/library/survival/html/survival-internal.html
    File listed twice: /usr/lib64/R/library/survival/html/survobrien.html
    File listed twice: /usr/lib64/R/library/survival/html/survreg.control.html
    File listed twice: /usr/lib64/R/library/survival/html/survreg.distributions.html
    File listed twice: /usr/lib64/R/library/survival/html/survreg.html
    File listed twice: /usr/lib64/R/library/survival/html/survreg.object.html
    File listed twice: /usr/lib64/R/library/survival/html/survregDtest.html
    File listed twice: /usr/lib64/R/library/survival/html/tcut.html
    File listed twice: /usr/lib64/R/library/survival/html/tobin.html
    File listed twice: /usr/lib64/R/library/survival/html/untangle.specials.html
    File listed twice: /usr/lib64/R/library/survival/html/uspop2.html
    File listed twice: /usr/lib64/R/library/survival/html/veteran.html
    File listed twice: /usr/lib64/R/library/tools/html
    File listed twice: /usr/lib64/R/library/tools/html/00Index.html
    File listed twice: /usr/lib64/R/library/tools/html/HTMLheader.html
    File listed twice: /usr/lib64/R/library/tools/html/HTMLlinks.html
    File listed twice: /usr/lib64/R/library/tools/html/QC.html
    File listed twice: /usr/lib64/R/library/tools/html/R.css
    File listed twice: /usr/lib64/R/library/tools/html/Rd2HTML.html
    File listed twice: /usr/lib64/R/library/tools/html/Rd2txt_options.html
    File listed twice: /usr/lib64/R/library/tools/html/RdTextFilter.html
    File listed twice: /usr/lib64/R/library/tools/html/Rdiff.html
    File listed twice: /usr/lib64/R/library/tools/html/Rdindex.html
    File listed twice: /usr/lib64/R/library/tools/html/Rdutils.html
    File listed twice: /usr/lib64/R/library/tools/html/SweaveTeXFilter.html
    File listed twice: /usr/lib64/R/library/tools/html/add_datalist.html
    File listed twice: /usr/lib64/R/library/tools/html/assertCondition.html
    File listed twice: /usr/lib64/R/library/tools/html/bibstyle.html
    File listed twice: /usr/lib64/R/library/tools/html/buildVignette.html
    File listed twice: /usr/lib64/R/library/tools/html/buildVignettes.html
    File listed twice: /usr/lib64/R/library/tools/html/charsets.html
    File listed twice: /usr/lib64/R/library/tools/html/checkFF.html
    File listed twice: /usr/lib64/R/library/tools/html/checkMD5sums.html
    File listed twice: /usr/lib64/R/library/tools/html/checkPoFiles.html
    File listed twice: /usr/lib64/R/library/tools/html/checkRd.html
    File listed twice: /usr/lib64/R/library/tools/html/checkRdaFiles.html
    File listed twice: /usr/lib64/R/library/tools/html/checkTnF.html
    File listed twice: /usr/lib64/R/library/tools/html/checkVignettes.html
    File listed twice: /usr/lib64/R/library/tools/html/check_packages_in_dir.html
    File listed twice: /usr/lib64/R/library/tools/html/codoc.html
    File listed twice: /usr/lib64/R/library/tools/html/compactPDF.html
    File listed twice: /usr/lib64/R/library/tools/html/delimMatch.html
    File listed twice: /usr/lib64/R/library/tools/html/dependsOnPkgs.html
    File listed twice: /usr/lib64/R/library/tools/html/encoded.html
    File listed twice: /usr/lib64/R/library/tools/html/fileutils.html
    File listed twice: /usr/lib64/R/library/tools/html/find_gs_cmd.html
    File listed twice: /usr/lib64/R/library/tools/html/getDepList.html
    File listed twice: /usr/lib64/R/library/tools/html/getVignetteInfo.html
    File listed twice: /usr/lib64/R/library/tools/html/installFoundDepends.html
    File listed twice: /usr/lib64/R/library/tools/html/makeLazyLoading.html
    File listed twice: /usr/lib64/R/library/tools/html/make_translations_pkg.html
    File listed twice: /usr/lib64/R/library/tools/html/md5sum.html
    File listed twice: /usr/lib64/R/library/tools/html/package.dependencies.html
    File listed twice: /usr/lib64/R/library/tools/html/package_dependencies.html
    File listed twice: /usr/lib64/R/library/tools/html/parseLatex.html
    File listed twice: /usr/lib64/R/library/tools/html/parse_Rd.html
    File listed twice: /usr/lib64/R/library/tools/html/print.via.format.html
    File listed twice: /usr/lib64/R/library/tools/html/pskill.html
    File listed twice: /usr/lib64/R/library/tools/html/psnice.html
    File listed twice: /usr/lib64/R/library/tools/html/read.00Index.html
    File listed twice: /usr/lib64/R/library/tools/html/showNonASCII.html
    File listed twice: /usr/lib64/R/library/tools/html/startDynamicHelp.html
    File listed twice: /usr/lib64/R/library/tools/html/testInstalledPackage.html
    File listed twice: /usr/lib64/R/library/tools/html/texi2dvi.html
    File listed twice: /usr/lib64/R/library/tools/html/toHTML.html
    File listed twice: /usr/lib64/R/library/tools/html/toRd.html
    File listed twice: /usr/lib64/R/library/tools/html/tools-defunct.html
    File listed twice: /usr/lib64/R/library/tools/html/tools-deprecated.html
    File listed twice: /usr/lib64/R/library/tools/html/tools-package.html
    File listed twice: /usr/lib64/R/library/tools/html/undoc.html
    File listed twice: /usr/lib64/R/library/tools/html/update_pkg_po.html
    File listed twice: /usr/lib64/R/library/tools/html/vignetteDepends.html
    File listed twice: /usr/lib64/R/library/tools/html/vignetteEngine.html
    File listed twice: /usr/lib64/R/library/tools/html/writePACKAGES.html
    File listed twice: /usr/lib64/R/library/tools/html/xgettext.html
    File listed twice: /usr/lib64/R/library/utils/html
    File listed twice: /usr/lib64/R/library/utils/html/00Index.html
    File listed twice: /usr/lib64/R/library/utils/html/BATCH.html
    File listed twice: /usr/lib64/R/library/utils/html/COMPILE.html
    File listed twice: /usr/lib64/R/library/utils/html/INSTALL.html
    File listed twice: /usr/lib64/R/library/utils/html/LINK.html
    File listed twice: /usr/lib64/R/library/utils/html/PkgUtils.html
    File listed twice: /usr/lib64/R/library/utils/html/Question.html
    File listed twice: /usr/lib64/R/library/utils/html/R.css
    File listed twice: /usr/lib64/R/library/utils/html/REMOVE.html
    File listed twice: /usr/lib64/R/library/utils/html/RHOME.html
    File listed twice: /usr/lib64/R/library/utils/html/RShowDoc.html
    File listed twice: /usr/lib64/R/library/utils/html/RSiteSearch.html
    File listed twice: /usr/lib64/R/library/utils/html/Rprof.html
    File listed twice: /usr/lib64/R/library/utils/html/Rprofmem.html
    File listed twice: /usr/lib64/R/library/utils/html/Rscript.html
    File listed twice: /usr/lib64/R/library/utils/html/Rtangle.html
    File listed twice: /usr/lib64/R/library/utils/html/RweaveLatex.html
    File listed twice: /usr/lib64/R/library/utils/html/SHLIB.html
    File listed twice: /usr/lib64/R/library/utils/html/Sweave.html
    File listed twice: /usr/lib64/R/library/utils/html/SweaveSyntConv.html
    File listed twice: /usr/lib64/R/library/utils/html/SweaveUtils.html
    File listed twice: /usr/lib64/R/library/utils/html/URLencode.html
    File listed twice: /usr/lib64/R/library/utils/html/View.html
    File listed twice: /usr/lib64/R/library/utils/html/adist.html
    File listed twice: /usr/lib64/R/library/utils/html/alarm.html
    File listed twice: /usr/lib64/R/library/utils/html/apropos.html
    File listed twice: /usr/lib64/R/library/utils/html/aregexec.html
    File listed twice: /usr/lib64/R/library/utils/html/aspell-utils.html
    File listed twice: /usr/lib64/R/library/utils/html/aspell.html
    File listed twice: /usr/lib64/R/library/utils/html/available.packages.html
    File listed twice: /usr/lib64/R/library/utils/html/bibentry.html
    File listed twice: /usr/lib64/R/library/utils/html/browseEnv.html
    File listed twice: /usr/lib64/R/library/utils/html/browseURL.html
    File listed twice: /usr/lib64/R/library/utils/html/browseVignettes.html
    File listed twice: /usr/lib64/R/library/utils/html/bug.report.html
    File listed twice: /usr/lib64/R/library/utils/html/capture.output.html
    File listed twice: /usr/lib64/R/library/utils/html/changedFiles.html
    File listed twice: /usr/lib64/R/library/utils/html/chooseBioCmirror.html
    File listed twice: /usr/lib64/R/library/utils/html/chooseCRANmirror.html
    File listed twice: /usr/lib64/R/library/utils/html/citEntry.html
    File listed twice: /usr/lib64/R/library/utils/html/citation.html
    File listed twice: /usr/lib64/R/library/utils/html/cite.html
    File listed twice: /usr/lib64/R/library/utils/html/close.socket.html
    File listed twice: /usr/lib64/R/library/utils/html/combn.html
    File listed twice: /usr/lib64/R/library/utils/html/compareVersion.html
    File listed twice: /usr/lib64/R/library/utils/html/contrib.url.html
    File listed twice: /usr/lib64/R/library/utils/html/count.fields.html
    File listed twice: /usr/lib64/R/library/utils/html/create.post.html
    File listed twice: /usr/lib64/R/library/utils/html/data.html
    File listed twice: /usr/lib64/R/library/utils/html/dataentry.html
    File listed twice: /usr/lib64/R/library/utils/html/debugger.html
    File listed twice: /usr/lib64/R/library/utils/html/demo.html
    File listed twice: /usr/lib64/R/library/utils/html/download.file.html
    File listed twice: /usr/lib64/R/library/utils/html/download.packages.html
    File listed twice: /usr/lib64/R/library/utils/html/edit.data.frame.html
    File listed twice: /usr/lib64/R/library/utils/html/edit.html
    File listed twice: /usr/lib64/R/library/utils/html/example.html
    File listed twice: /usr/lib64/R/library/utils/html/file.edit.html
    File listed twice: /usr/lib64/R/library/utils/html/filetest.html
    File listed twice: /usr/lib64/R/library/utils/html/findLineNum.html
    File listed twice: /usr/lib64/R/library/utils/html/fix.html
    File listed twice: /usr/lib64/R/library/utils/html/flush.console.html
    File listed twice: /usr/lib64/R/library/utils/html/format.html
    File listed twice: /usr/lib64/R/library/utils/html/getAnywhere.html
    File listed twice: /usr/lib64/R/library/utils/html/getFromNamespace.html
    File listed twice: /usr/lib64/R/library/utils/html/getParseData.html
    File listed twice: /usr/lib64/R/library/utils/html/getS3method.html
    File listed twice: /usr/lib64/R/library/utils/html/glob2rx.html
    File listed twice: /usr/lib64/R/library/utils/html/globalVariables.html
    File listed twice: /usr/lib64/R/library/utils/html/head.html
    File listed twice: /usr/lib64/R/library/utils/html/help.html
    File listed twice: /usr/lib64/R/library/utils/html/help.request.html
    File listed twice: /usr/lib64/R/library/utils/html/help.search.html
    File listed twice: /usr/lib64/R/library/utils/html/help.start.html
    File listed twice: /usr/lib64/R/library/utils/html/install.packages.html
    File listed twice: /usr/lib64/R/library/utils/html/installed.packages.html
    File listed twice: /usr/lib64/R/library/utils/html/localeToCharset.html
    File listed twice: /usr/lib64/R/library/utils/html/ls_str.html
    File listed twice: /usr/lib64/R/library/utils/html/maintainer.html
    File listed twice: /usr/lib64/R/library/utils/html/make.packages.html.html
    File listed twice: /usr/lib64/R/library/utils/html/make.socket.html
    File listed twice: /usr/lib64/R/library/utils/html/memory.size.html
    File listed twice: /usr/lib64/R/library/utils/html/menu.html
    File listed twice: /usr/lib64/R/library/utils/html/methods.html
    File listed twice: /usr/lib64/R/library/utils/html/mirrorAdmin.html
    File listed twice: /usr/lib64/R/library/utils/html/modifyList.html
    File listed twice: /usr/lib64/R/library/utils/html/news.html
    File listed twice: /usr/lib64/R/library/utils/html/nsl.html
    File listed twice: /usr/lib64/R/library/utils/html/object.size.html
    File listed twice: /usr/lib64/R/library/utils/html/package.skeleton.html
    File listed twice: /usr/lib64/R/library/utils/html/packageDescription.html
    File listed twice: /usr/lib64/R/library/utils/html/packageName.html
    File listed twice: /usr/lib64/R/library/utils/html/packageStatus.html
    File listed twice: /usr/lib64/R/library/utils/html/page.html
    File listed twice: /usr/lib64/R/library/utils/html/person.html
    File listed twice: /usr/lib64/R/library/utils/html/process.events.html
    File listed twice: /usr/lib64/R/library/utils/html/prompt.html
    File listed twice: /usr/lib64/R/library/utils/html/promptData.html
    File listed twice: /usr/lib64/R/library/utils/html/promptPackage.html
    File listed twice: /usr/lib64/R/library/utils/html/rcompgen.html
    File listed twice: /usr/lib64/R/library/utils/html/read.DIF.html
    File listed twice: /usr/lib64/R/library/utils/html/read.fortran.html
    File listed twice: /usr/lib64/R/library/utils/html/read.fwf.html
    File listed twice: /usr/lib64/R/library/utils/html/read.socket.html
    File listed twice: /usr/lib64/R/library/utils/html/read.table.html
    File listed twice: /usr/lib64/R/library/utils/html/recover.html
    File listed twice: /usr/lib64/R/library/utils/html/relist.html
    File listed twice: /usr/lib64/R/library/utils/html/remove.packages.html
    File listed twice: /usr/lib64/R/library/utils/html/removeSource.html
    File listed twice: /usr/lib64/R/library/utils/html/roman.html
    File listed twice: /usr/lib64/R/library/utils/html/rtags.html
    File listed twice: /usr/lib64/R/library/utils/html/savehistory.html
    File listed twice: /usr/lib64/R/library/utils/html/select.list.html
    File listed twice: /usr/lib64/R/library/utils/html/sessionInfo.html
    File listed twice: /usr/lib64/R/library/utils/html/setRepositories.html
    File listed twice: /usr/lib64/R/library/utils/html/sourceutils.html
    File listed twice: /usr/lib64/R/library/utils/html/stack.html
    File listed twice: /usr/lib64/R/library/utils/html/str.html
    File listed twice: /usr/lib64/R/library/utils/html/summaryRprof.html
    File listed twice: /usr/lib64/R/library/utils/html/tar.html
    File listed twice: /usr/lib64/R/library/utils/html/toLatex.html
    File listed twice: /usr/lib64/R/library/utils/html/txtProgressBar.html
    File listed twice: /usr/lib64/R/library/utils/html/type.convert.html
    File listed twice: /usr/lib64/R/library/utils/html/untar.html
    File listed twice: /usr/lib64/R/library/utils/html/unzip.html
    File listed twice: /usr/lib64/R/library/utils/html/update.packages.html
    File listed twice: /usr/lib64/R/library/utils/html/url.show.html
    File listed twice: /usr/lib64/R/library/utils/html/utils-defunct.html
    File listed twice: /usr/lib64/R/library/utils/html/utils-deprecated.html
    File listed twice: /usr/lib64/R/library/utils/html/utils-package.html
    File listed twice: /usr/lib64/R/library/utils/html/vignette.html
    File listed twice: /usr/lib64/R/library/utils/html/write.table.html
    File listed twice: /usr/lib64/R/library/utils/html/zip.html
    File listed twice: /usr/lib64/R/library/tcltk/html
    File listed twice: /usr/lib64/R/library/tcltk/html/00Index.html
    File listed twice: /usr/lib64/R/library/tcltk/html/R.css
    File listed twice: /usr/lib64/R/library/tcltk/html/TclInterface.html
    File listed twice: /usr/lib64/R/library/tcltk/html/TkCommands.html
    File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgetcmds.html
    File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgets.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tclServiceMode.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-defunct.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-package.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tkProgressBar.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tkStartGUI.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.dir.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.files.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tk_messageBox.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tk_select.list.html
    File listed twice: /usr/lib64/R/library/tcltk/html/tkpager.html
    File not found by glob: /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/*.html
Command exited with non-zero status 1
784.99user 51.56system 18:39.43elapsed 74%CPU (0avgtext+0avgdata 163556maxresident)k
0inputs+0outputs (0major+21736500minor)pagefaults 0swaps
hsh-rebuild: rebuild of `pkg.tar' failed.
ERROR: build failed for R-base

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Gleb Fotengauer-Malinovskiy]

[-- Attachment #1: Type: text/plain, Size: 2114 bytes --]

On Fri, Dec 11, 2015 at 03:54:46PM +0300, Dmitry V. Levin wrote:
> On Fri, Dec 11, 2015 at 03:33:56PM +0300, Gleb Fotengauer-Malinovskiy wrote:
> > On Fri, Dec 11, 2015 at 02:45:09PM +0300, Kirill Maslinsky wrote:
> > > On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:
> > > > Уважаемые коллеги,
> > > > по итогам транзакции по добавлению BR: texinfo
> > > > 1) из 64 пакетов которым нужно было добавить BR: texinfo
> > > > и на которые у меня не было acl, осталось 49 пакетов.
> > > 
> > > [...]
> > > 
> > > > далее, 31 пакет, которые тоже нуждаются в NMU
> > > > но сломаны и я их сходу не смог починить:
> > > > 
> > > > R-base	kirill ldv @everybody
> > > 
> > > А что именно в нем сломано? Я могу его обновить и попробовать починить,
> > > но пока не понимаю суть проблемы.
> > 
> > /beehive/logs/Sisyphus-x86_64/latest/error/R-base-3.1.2-alt1:
> > > 'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
> > > file R-lang.html will be missing
> > 
> > Добавить зависимость на makeinfo.
> 
> Добавить зависимость на makeinfo И texi2dvi И починить сборку
> документации.  После добавления makeinfo и texi2dvi в сборочную среду
> возникают ошибки вида
> 
> ERROR: 'makeinfo' v4.7 or later needed but missing on your system.
> make[2]: *** [R-FAQ.info] Error 1
> File not found by glob: /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/*.html

checking whether makeinfo version is at least 4.7... no
Оно не может определить версию makeinfo потому что:

$ makeinfo --version | head -1
texi2any (GNU texinfo) 6.0

Ожидается что будет написано makeinfo, а не texi2any.

-- 
glebfm

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 181 bytes --]

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Michael Shigorin]

On Fri, Dec 11, 2015 at 02:45:09PM +0300, Kirill Maslinsky wrote:
> > по итогам транзакции по добавлению BR: texinfo
> > R-base	kirill ldv @everybody
> А что именно в нем сломано? Я могу его обновить и попробовать
> починить, но пока не понимаю суть проблемы.

http://altlinux.org/Changes/devel
https://lists.altlinux.org/pipermail/devel/2015-November/200445.html
https://lists.altlinux.org/pipermail/devel/2015-December/200461.html

PS: привет :)

-- 
 ---- WBR, Michael Shigorin / http://altlinux.org
  ------ http://opennet.ru / http://anna-news.info

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Dmitry V. Levin]

[-- Attachment #1: Type: text/plain, Size: 1963 bytes --]

On Fri, Dec 11, 2015 at 03:59:00PM +0300, Gleb Fotengauer-Malinovskiy wrote:
> On Fri, Dec 11, 2015 at 03:54:46PM +0300, Dmitry V. Levin wrote:
> > On Fri, Dec 11, 2015 at 03:33:56PM +0300, Gleb Fotengauer-Malinovskiy wrote:
> > > On Fri, Dec 11, 2015 at 02:45:09PM +0300, Kirill Maslinsky wrote:
> > > > On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:
> > > > > Уважаемые коллеги,
> > > > > по итогам транзакции по добавлению BR: texinfo
> > > > > 1) из 64 пакетов которым нужно было добавить BR: texinfo
> > > > > и на которые у меня не было acl, осталось 49 пакетов.
> > > > 
> > > > [...]
> > > > 
> > > > > далее, 31 пакет, которые тоже нуждаются в NMU
> > > > > но сломаны и я их сходу не смог починить:
> > > > > 
> > > > > R-base	kirill ldv @everybody
> > > > 
> > > > А что именно в нем сломано? Я могу его обновить и попробовать починить,
> > > > но пока не понимаю суть проблемы.
> > > 
> > > /beehive/logs/Sisyphus-x86_64/latest/error/R-base-3.1.2-alt1:
> > > > 'makeinfo' v4.7 or later needed to make HTML docs but missing on your system.
> > > > file R-lang.html will be missing
> > > 
> > > Добавить зависимость на makeinfo.
> > 
> > Добавить зависимость на makeinfo И texi2dvi И починить сборку
> > документации.  После добавления makeinfo и texi2dvi в сборочную среду
> > возникают ошибки вида
> > 
> > ERROR: 'makeinfo' v4.7 or later needed but missing on your system.
> > make[2]: *** [R-FAQ.info] Error 1
> > File not found by glob: /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/*.html
> 
> checking whether makeinfo version is at least 4.7... no
> Оно не может определить версию makeinfo потому что:
> 
> 
> $ makeinfo --version | head -1
> texi2any (GNU texinfo) 6.0
> 
> Ожидается что будет написано makeinfo, а не texi2any.

В результате мы поправили makeinfo --version, чтобы оно представлялось
как традиционное makeinfo вместо самоназванного texi2any.


-- 
ldv

[-- Attachment #2: Type: application/pgp-signature, Size: 819 bytes --]

Re: [devel] I: итоги NMU по добавлению BR: texinfo

[Kirill Maslinsky]

On Sat, Dec 12, 2015 at 03:58:45AM +0300, Dmitry V. Levin wrote:
> On Fri, Dec 11, 2015 at 03:59:00PM +0300, Gleb Fotengauer-Malinovskiy wrote:
> > On Fri, Dec 11, 2015 at 03:54:46PM +0300, Dmitry V. Levin wrote:
> > > On Fri, Dec 11, 2015 at 03:33:56PM +0300, Gleb Fotengauer-Malinovskiy wrote:
> > > > On Fri, Dec 11, 2015 at 02:45:09PM +0300, Kirill Maslinsky wrote:
> > > > > On Wed, Dec 09, 2015 at 07:43:25PM +0200, Igor Vlasenko wrote:

[...]

> > > ERROR: 'makeinfo' v4.7 or later needed but missing on your system.
> > > make[2]: *** [R-FAQ.info] Error 1
> > > File not found by glob: /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.1/manual/*.html

[...]

> В результате мы поправили makeinfo --version, чтобы оно представлялось
> как традиционное makeinfo вместо самоназванного texi2any.

Пока я собирался и разбирался починили без меня :) 
Ну я хотя бы обновил R-base до версии 3.2.3, которую апстрим
называет «рождественской». Всех с наступающим!

-- 
КМ