~/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 --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 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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 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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 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(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 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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) ⅈ ^ 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' 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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 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'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 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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]] ) [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) 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 )] 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) [15 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) This is `epsf.tex' v2.7.4 <14 February 2011> )) (./R-FAQ.aux 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] ) [8] (./epsf.tex] ) localization,> formatting, 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 . 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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)] [58]] [60 [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) 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 . 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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 . 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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)] indexing, toc, 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 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/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def) (/usr/share/texmf-texlive/tex/latex/base/t1enc.def] (/etc/texmf/tex/latex/config/color.cfg) (/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). 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(/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. 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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) ]< [155/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr10.pfb] [250]> [251] [254] [40 [41] ] [130] [132] Chapter 9] [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) [96] [189] [175 [22]) (/usr/share/texmf-texlive/fonts/source/jknappen/ec/exaccent.mf [2] [176 [5] 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 [37] [159]) [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) [209] [210< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb>]< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmss10.pfb [213> ] 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 <- "(?[[:upper:]][[:lower:]]+) (?[[: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/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb]> [305] [23 ] Chapter 5] [27]]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]]] 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)]] [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]]] [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) defuns,] macros,] insertions, This is `epsf.tex' v2.7.4 <14 February 2011> )< localization,/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb]> ) [131 [469] [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/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb [27 [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 [30]]< Chapter 8/usr/share/texmf- texlive/fonts/type1/bluesky/cm/cmtt12.pfb [32]> 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) 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/bluesky/cm/cmbx7.pfb>] [583] ]]<]/usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmtt9.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) 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/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> ] [835 (./R-exts.vrs ] Underfull \hbox (badness 10000) in paragraph at lines 4918--4920 Underfull \vbox (badness 10000) has occurred while \output is active [836] [837 [159 ]] [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/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb> [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 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 Overfull \hbox (31.57222pt too wide) in paragraph at lines 6515--6516 [][] [860 ] 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. 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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 \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 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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 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[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/share/texmf-texlive/fonts/type1/bluesky/cm/cmbx7.pfb> 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/cmsl9.pfb> [68 1 vers ions visible:[] [1041]> [1042] [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 \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 \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 \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 \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 \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 \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) 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/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> ] \T1/ptm/ m/n/10 and William N. Ven-ables [1155>]] [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 \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) [1424< /usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi10.pfb> ]] Underfull \vbox (badness 10000) has occurred while \output is active [1427 [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 \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 \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 \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 \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 \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 \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 \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 \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() 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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 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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 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. 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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 <- "(?[[:upper:]][[:lower:]]+) (?[[: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 [835 ] Underfull \hbox (badness 10000) in paragraph at lines 4918--4920 Underfull \vbox (badness 10000) has occurred while \output is active [836] [837 ] [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 Overfull \hbox (31.57222pt too wide) in paragraph at lines 6515--6516 [][] [860 ] 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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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() 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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 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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 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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 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. 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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 <- "(?[[:upper:]][[:lower:]]+) (?[[: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 [835 ] Underfull \hbox (badness 10000) in paragraph at lines 4918--4920 Underfull \vbox (badness 10000) has occurred while \output is active [836] [837 ] [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 Overfull \hbox (31.57222pt too wide) in paragraph at lines 6515--6516 [][] [860 ] 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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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() 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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 \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 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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 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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] "" > [2] "" > [3] "" > [4] "The Comprehensive R Archive Network" > [5] "" > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > [11] "" > [12] "" > [13] "" > [14] "" > [15] "" > [16] "" > [17] "" > [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] "" > [23] "" > > 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: 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/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:ndjZA3vbl6nFSTkjHpHJtqV9UXveF6PVWlVmoSYpedG8BII3xQkDGvL8S8DohnwGGDxXMnWqVAhlshZ1Ru9YXr6GDlZGWRVy13RBaZ4RUlZ8wqKGCD2dfi1ZmZifE9EEJLou8NxJxMzClAiWoCsnCZdKWvtYT1QlihEWskY33F6iFja4jx4MJVBQpPsm6dkPH6Zem4yfPPMZmABl0e9ihnMtD7hnZbzbrvvKbriRPUtgKcXVB3p45Af7pCpGwrnbey9YB9mEOHqPBpVgXULu0ysTvvamZJpGddDZaJO0mdHjEvIbfGOuUOEPNLPKza1LNKiaEpFoXOH257YFcd6dmVSw3ZHJAHZysWi1xxXDsICAAONntFClpn5BaaEr3lFuHDBO6SuWr95sg4RZt5pYfKsrzZJzt1HjkiGUH44Iu3dZ49356HQa23XEmEwRdQNeBbFaF4vc2tXNQizt5t43qqMjDGVcft6YGrJZHorrnG8NQyqVdbicxz3sUO0DWZ1GFT0jzHhFcfYSwdpQMzOtRZEXiCbenJZ5AJHmSOyS0y3Nc5FihOZnmSkyNuEfm6q7hwuVcOTDqiFc5P7NInR0GUwZ8mpg3z4qVYWbRYturObszugAZixg8iZ0lfBlPnBAuasZv2TyArg0QBQa8nYIZqRfXzcqq1G3PUbWOUnCFPvnGmx3nihsxPPxGjlq2Gjfd2jLs3zAopa2bXqn2VED25C4AjUfExuLkPkrpCnaZFltQoshmTlymmiXaUuMCZCfInPNtH0xME5qMdp4Ai6noIBi1rFcUDZ1hOo3nnRSVIZGWxKgnr6aL1VwSko81juDWhr8V5xfwSntp3BKKZtnkNP4pUuKrFMBhd2zPUw37EP4DyZzaQ52dvuDBGVvQQtBLUqxW1mMPRFOOfuquuuOUR8hpAICwDCxZ6h2IIYKsoWKnOmJFNA3F98E6roUC4EZrfu3hPfRKQySwcrgFfBiGf5lC5tycBiKszhoqdNeuBrZDHI81Qf2vHZo9h3zNwqAsQCgaNksC7xMgdrfLgK81z0leEZmcMjbwaLR7sJenJLA8lDwzrKOz6rLYeV2ePVgC2EzBxPbGXRchkLktLNucg3xZrf7t2V1C1AOIIyiOeQ83jPe9xNPYReLZfT8pBRH4wrwT02TTZASLcI74O0VQwQcHxgFQLggiOZxjlQejkaBdH2nIwwQhB8UMaLUM6JIZ5zvj2EZILJ8l46gfAhjYIuvNSIhFHNiNZo7sHv9cDiW7EbOEEHB1Et4bpoUv55eLxCYmHDST0xM3HOmTsPUQY1MZzvpZEGKBeXCwW2LfKrydZHiv5Z9qTxSUfcNpU9ImtvykuTw5L2146sT2sZzgqwJ6x4P4dxuhOxKxkf3EuUeJceermZdjaQhZJQ6XJHwgi5qVrTCbm69HXZeatfKujP7JFgkMtwaEohqA30NKqAUmp83BcZIQ2K6r3ZAa5hOfviOYGldIIsvkRuk4vwK6THUMZeFZ5l9GUAtH3ZBLtWiZCRpqDjtqwwCtXqcVJcpv4nDGlRdyEzAF5fKBF9eeQeXfKesleYz4y5fwPVRqvRPrMR3XQcE8GJsgg6yGjpaj8jSaCeZo4gZpwxTMHUlrRZ34fPSfv6pTEJoAdyTCpfsajMip5iN272wriFoo8xBu31yEow4TI8ijqzNf2WHZ5JV793PO35lYZ55bNFhAcCa3dAuNO93cyOskwiTDKwZl9jt4A2bl7ZANPwBP1qigvuZok0j62eiA9r8rIfuNAJsIp1YVQVu3TRVMZvuzo5Z1PX8dGostLT8H9tyZ0ydzPxXRFeVB5WuW7PO2Psf4Shj4a6uTVFc9CoaaAXKlTpEkeaSnPAZkVdddj4ZEKCBICAB0rt3cN25JiyLqNC5ncjwdoxQQK8leUKox0YWkp4pmOQ5ZhCmjH7ohx2qWrLfCrglpRdgNor1 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: 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(0avgtext+0avgdata 163556maxresident)k 0inputs+0outputs (0major+21736500minor)pagefaults 0swaps hsh-rebuild: rebuild of `pkg.tar' failed. ERROR: build failed for R-base