RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '9104a2a6755e804c098d2bd63e011ff2840520ce', '/home/buildd/filecache-default/4b5c49e7847975aad50de8925d7d18ee889b3105'] Uncompressing the tarball... Synching the system clock with the buildd NTP service... 15 Jan 13:11:30 ntpdate[3407]: step time server 10.211.37.1 offset -121427.087166 sec Unpacking chroot for build 9104a2a6755e804c098d2bd63e011ff2840520ce RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '9104a2a6755e804c098d2bd63e011ff2840520ce'] Mounting chroot for build 9104a2a6755e804c098d2bd63e011ff2840520ce RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '9104a2a6755e804c098d2bd63e011ff2840520ce', 'deb http://ppa.launchpad.net/maverick-bleed/ppa/ubuntu maverick main', 'deb http://ftpmaster.internal/ubuntu maverick main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu maverick-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu maverick-updates main restricted universe multiverse'] Overriding sources.list in build-9104a2a6755e804c098d2bd63e011ff2840520ce RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '9104a2a6755e804c098d2bd63e011ff2840520ce', 'amd64'] Updating debian chroot for build 9104a2a6755e804c098d2bd63e011ff2840520ce Get:1 http://ftpmaster.internal maverick Release.gpg [198B] Get:2 http://ppa.launchpad.net maverick Release.gpg [316B] Ign http://ppa.launchpad.net/maverick-bleed/ppa/ubuntu/ maverick/main Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick/main Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick/multiverse Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick/restricted Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick/universe Translation-en Get:3 http://ftpmaster.internal maverick-security Release.gpg [198B] Ign http://ftpmaster.internal/ubuntu/ maverick-security/main Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick-security/multiverse Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick-security/restricted Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick-security/universe Translation-en Get:4 http://ppa.launchpad.net maverick Release [9746B] Get:5 http://ftpmaster.internal maverick-updates Release.gpg [198B] Ign http://ftpmaster.internal/ubuntu/ maverick-updates/main Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick-updates/multiverse Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick-updates/restricted Translation-en Ign http://ftpmaster.internal/ubuntu/ maverick-updates/universe Translation-en Get:6 http://ftpmaster.internal maverick Release [39.8kB] Get:7 http://ftpmaster.internal maverick-security Release [27.2kB] Get:8 http://ftpmaster.internal maverick-updates Release [31.4kB] Ign http://ppa.launchpad.net maverick Release Get:9 http://ppa.launchpad.net maverick/main amd64 Packages [37.7kB] Get:10 http://ftpmaster.internal maverick/main amd64 Packages [1491kB] Get:11 http://ftpmaster.internal maverick/restricted amd64 Packages [6002B] Get:12 http://ftpmaster.internal maverick/universe amd64 Packages [5771kB] Get:13 http://ftpmaster.internal maverick/multiverse amd64 Packages [180kB] Get:14 http://ftpmaster.internal maverick-security/main amd64 Packages [65.9kB] Get:15 http://ftpmaster.internal maverick-security/restricted amd64 Packages [14B] Get:16 http://ftpmaster.internal maverick-security/universe amd64 Packages [33.3kB] Get:17 http://ftpmaster.internal maverick-security/multiverse amd64 Packages [1531B] Get:18 http://ftpmaster.internal maverick-updates/main amd64 Packages [195kB] Get:19 http://ftpmaster.internal maverick-updates/restricted amd64 Packages [14B] Get:20 http://ftpmaster.internal maverick-updates/universe amd64 Packages [77.0kB] Get:21 http://ftpmaster.internal maverick-updates/multiverse amd64 Packages [2382B] Fetched 7972kB in 4s (1927kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net maverick Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 48C18E890A02563F Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: dpkg dpkg-dev ifupdown initscripts libc-bin libc-dev-bin libc6 libc6-dev libdpkg-perl libdrm-intel1 libdrm-nouveau1 libdrm-radeon1 libdrm2 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libpam-modules libpam-runtime libpam0g libplymouth2 libssl0.9.8 libudev0 linux-libc-dev openssl plymouth python-minimal sysv-rc sysvinit-utils tzdata udev 32 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 17.0MB of archives. After this operation, 45.1kB disk space will be freed. WARNING: The following packages cannot be authenticated! dpkg python-minimal libpam-modules libc-dev-bin libc6-dev libc-bin libc6 linux-libc-dev tzdata libssl0.9.8 libpam-runtime libpam0g ifupdown sysvinit-utils sysv-rc initscripts libdrm2 libdrm-intel1 libdrm-nouveau1 libdrm-radeon1 udev plymouth libplymouth2 libudev0 libk5crypto3 libgssapi-krb5-2 libkrb5-3 libkrb5support0 libldap-2.4-2 dpkg-dev libdpkg-perl openssl Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ maverick-security/main dpkg amd64 1.15.8.4ubuntu3.1 [2133kB] Get:2 http://ftpmaster.internal/ubuntu/ maverick-updates/main python-minimal all 2.6.6-2ubuntu2 [35.7kB] Get:3 http://ftpmaster.internal/ubuntu/ maverick-security/main libpam-modules amd64 1.1.1-4ubuntu2 [347kB] Get:4 http://ftpmaster.internal/ubuntu/ maverick-security/main libc-dev-bin amd64 2.12.1-0ubuntu10.1 [228kB] Get:5 http://ftpmaster.internal/ubuntu/ maverick-security/main libc6-dev amd64 2.12.1-0ubuntu10.1 [2726kB] Get:6 http://ftpmaster.internal/ubuntu/ maverick-security/main libc-bin amd64 2.12.1-0ubuntu10.1 [818kB] Get:7 http://ftpmaster.internal/ubuntu/ maverick-security/main libc6 amd64 2.12.1-0ubuntu10.1 [4259kB] Get:8 http://ftpmaster.internal/ubuntu/ maverick-security/main linux-libc-dev amd64 2.6.35-1024.42 [804kB] Get:9 http://ftpmaster.internal/ubuntu/ maverick-updates/main tzdata all 2010o-0ubuntu0.10.10 [680kB] Get:10 http://ftpmaster.internal/ubuntu/ maverick-security/main libssl0.9.8 amd64 0.9.8o-1ubuntu4.3 [923kB] Get:11 http://ftpmaster.internal/ubuntu/ maverick-security/main libpam-runtime all 1.1.1-4ubuntu2 [85.3kB] Get:12 http://ftpmaster.internal/ubuntu/ maverick-security/main libpam0g amd64 1.1.1-4ubuntu2 [94.7kB] Get:13 http://ftpmaster.internal/ubuntu/ maverick-security/main ifupdown amd64 0.6.10ubuntu3.1 [59.2kB] Get:14 http://ftpmaster.internal/ubuntu/ maverick-updates/main sysvinit-utils amd64 2.87dsf-4ubuntu19 [118kB] Get:15 http://ftpmaster.internal/ubuntu/ maverick-updates/main sysv-rc all 2.87dsf-4ubuntu19 [79.5kB] Get:16 http://ftpmaster.internal/ubuntu/ maverick-updates/main initscripts amd64 2.87dsf-4ubuntu19 [73.5kB] Get:17 http://ftpmaster.internal/ubuntu/ maverick-updates/main libdrm2 amd64 2.4.21-1ubuntu2.1 [32.6kB] Get:18 http://ftpmaster.internal/ubuntu/ maverick-updates/main libdrm-intel1 amd64 2.4.21-1ubuntu2.1 [33.4kB] Get:19 http://ftpmaster.internal/ubuntu/ maverick-updates/main libdrm-nouveau1 amd64 2.4.21-1ubuntu2.1 [22.5kB] Get:20 http://ftpmaster.internal/ubuntu/ maverick-updates/main libdrm-radeon1 amd64 2.4.21-1ubuntu2.1 [23.4kB] Get:21 http://ftpmaster.internal/ubuntu/ maverick-updates/main udev amd64 162-2.2 [496kB] Get:22 http://ftpmaster.internal/ubuntu/ maverick-updates/main plymouth amd64 0.8.2-2ubuntu5.1 [122kB] Get:23 http://ftpmaster.internal/ubuntu/ maverick-updates/main libplymouth2 amd64 0.8.2-2ubuntu5.1 [99.5kB] Get:24 http://ftpmaster.internal/ubuntu/ maverick-updates/main libudev0 amd64 162-2.2 [128kB] Get:25 http://ftpmaster.internal/ubuntu/ maverick-security/main libk5crypto3 amd64 1.8.1+dfsg-5ubuntu0.2 [104kB] Get:26 http://ftpmaster.internal/ubuntu/ maverick-security/main libgssapi-krb5-2 amd64 1.8.1+dfsg-5ubuntu0.2 [128kB] Get:27 http://ftpmaster.internal/ubuntu/ maverick-security/main libkrb5-3 amd64 1.8.1+dfsg-5ubuntu0.2 [367kB] Get:28 http://ftpmaster.internal/ubuntu/ maverick-security/main libkrb5support0 amd64 1.8.1+dfsg-5ubuntu0.2 [45.0kB] Get:29 http://ftpmaster.internal/ubuntu/ maverick-updates/main libldap-2.4-2 amd64 2.4.23-0ubuntu3.4 [215kB] Get:30 http://ftpmaster.internal/ubuntu/ maverick-security/main dpkg-dev all 1.15.8.4ubuntu3.1 [772kB] Get:31 http://ftpmaster.internal/ubuntu/ maverick-security/main libdpkg-perl all 1.15.8.4ubuntu3.1 [505kB] Get:32 http://ftpmaster.internal/ubuntu/ maverick-security/main openssl amd64 0.9.8o-1ubuntu4.3 [407kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.0MB in 0s (25.6MB/s) (Reading database ... 13456 files and directories currently installed.) Preparing to replace dpkg 1.15.8.4ubuntu3 (using .../dpkg_1.15.8.4ubuntu3.1_amd64.deb) ... Unpacking replacement dpkg ... Setting up dpkg (1.15.8.4ubuntu3.1) ... (Reading database ... 13456 files and directories currently installed.) Preparing to replace python-minimal 2.6.6-2ubuntu1 (using .../python-minimal_2.6.6-2ubuntu2_all.deb) ... Unpacking replacement python-minimal ... Setting up python-minimal (2.6.6-2ubuntu2) ... (Reading database ... 13456 files and directories currently installed.) Preparing to replace libpam-modules 1.1.1-4ubuntu1 (using .../libpam-modules_1.1.1-4ubuntu2_amd64.deb) ... Unpacking replacement libpam-modules ... Setting up libpam-modules (1.1.1-4ubuntu2) ... (Reading database ... 13456 files and directories currently installed.) Preparing to replace libc-dev-bin 2.12.1-0ubuntu6 (using .../libc-dev-bin_2.12.1-0ubuntu10.1_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6-dev 2.12.1-0ubuntu6 (using .../libc6-dev_2.12.1-0ubuntu10.1_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-bin 2.12.1-0ubuntu6 (using .../libc-bin_2.12.1-0ubuntu10.1_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.12.1-0ubuntu10.1) ... (Reading database ... 13456 files and directories currently installed.) Preparing to replace libc6 2.12.1-0ubuntu6 (using .../libc6_2.12.1-0ubuntu10.1_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.12.1-0ubuntu10.1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13456 files and directories currently installed.) Preparing to replace linux-libc-dev 2.6.35-1022.33 (using .../linux-libc-dev_2.6.35-1024.42_amd64.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace tzdata 2010l-1 (using .../tzdata_2010o-0ubuntu0.10.10_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2010o-0ubuntu0.10.10) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 14 03:28:28 UTC 2011. Universal Time is now: Fri Jan 14 03:28:28 UTC 2011. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 13456 files and directories currently installed.) Preparing to replace libssl0.9.8 0.9.8o-1ubuntu4 (using .../libssl0.9.8_0.9.8o-1ubuntu4.3_amd64.deb) ... Unpacking replacement libssl0.9.8 ... Setting up libssl0.9.8 (0.9.8o-1ubuntu4.3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13456 files and directories currently installed.) Preparing to replace libpam-runtime 1.1.1-4ubuntu1 (using .../libpam-runtime_1.1.1-4ubuntu2_all.deb) ... Unpacking replacement libpam-runtime ... Setting up libpam-runtime (1.1.1-4ubuntu2) ... (Reading database ... 13456 files and directories currently installed.) Preparing to replace libpam0g 1.1.1-4ubuntu1 (using .../libpam0g_1.1.1-4ubuntu2_amd64.deb) ... Unpacking replacement libpam0g ... Setting up libpam0g (1.1.1-4ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13456 files and directories currently installed.) Preparing to replace ifupdown 0.6.10ubuntu3 (using .../ifupdown_0.6.10ubuntu3.1_amd64.deb) ... Unpacking replacement ifupdown ... Preparing to replace sysvinit-utils 2.87dsf-4ubuntu18 (using .../sysvinit-utils_2.87dsf-4ubuntu19_amd64.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace sysv-rc 2.87dsf-4ubuntu18 (using .../sysv-rc_2.87dsf-4ubuntu19_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace initscripts 2.87dsf-4ubuntu18 (using .../initscripts_2.87dsf-4ubuntu19_amd64.deb) ... Unpacking replacement initscripts ... Preparing to replace libdrm2 2.4.21-1ubuntu2 (using .../libdrm2_2.4.21-1ubuntu2.1_amd64.deb) ... Unpacking replacement libdrm2 ... Preparing to replace libdrm-intel1 2.4.21-1ubuntu2 (using .../libdrm-intel1_2.4.21-1ubuntu2.1_amd64.deb) ... Unpacking replacement libdrm-intel1 ... Preparing to replace libdrm-nouveau1 2.4.21-1ubuntu2 (using .../libdrm-nouveau1_2.4.21-1ubuntu2.1_amd64.deb) ... Unpacking replacement libdrm-nouveau1 ... Preparing to replace libdrm-radeon1 2.4.21-1ubuntu2 (using .../libdrm-radeon1_2.4.21-1ubuntu2.1_amd64.deb) ... Unpacking replacement libdrm-radeon1 ... Preparing to replace udev 162-2 (using .../udev_162-2.2_amd64.deb) ... Adding 'local diversion of /sbin/udevadm to /sbin/udevadm.upgrade' Unpacking replacement udev ... Preparing to replace plymouth 0.8.2-2ubuntu5 (using .../plymouth_0.8.2-2ubuntu5.1_amd64.deb) ... Unpacking replacement plymouth ... Preparing to replace libplymouth2 0.8.2-2ubuntu5 (using .../libplymouth2_0.8.2-2ubuntu5.1_amd64.deb) ... Unpacking replacement libplymouth2 ... Preparing to replace libudev0 162-2 (using .../libudev0_162-2.2_amd64.deb) ... Unpacking replacement libudev0 ... Preparing to replace libk5crypto3 1.8.1+dfsg-5 (using .../libk5crypto3_1.8.1+dfsg-5ubuntu0.2_amd64.deb) ... Unpacking replacement libk5crypto3 ... Preparing to replace libgssapi-krb5-2 1.8.1+dfsg-5 (using .../libgssapi-krb5-2_1.8.1+dfsg-5ubuntu0.2_amd64.deb) ... Unpacking replacement libgssapi-krb5-2 ... Preparing to replace libkrb5-3 1.8.1+dfsg-5 (using .../libkrb5-3_1.8.1+dfsg-5ubuntu0.2_amd64.deb) ... Unpacking replacement libkrb5-3 ... Preparing to replace libkrb5support0 1.8.1+dfsg-5 (using .../libkrb5support0_1.8.1+dfsg-5ubuntu0.2_amd64.deb) ... Unpacking replacement libkrb5support0 ... Preparing to replace libldap-2.4-2 2.4.23-0ubuntu3 (using .../libldap-2.4-2_2.4.23-0ubuntu3.4_amd64.deb) ... Unpacking replacement libldap-2.4-2 ... Preparing to replace dpkg-dev 1.15.8.4ubuntu3 (using .../dpkg-dev_1.15.8.4ubuntu3.1_all.deb) ... Unpacking replacement dpkg-dev ... Preparing to replace libdpkg-perl 1.15.8.4ubuntu3 (using .../libdpkg-perl_1.15.8.4ubuntu3.1_all.deb) ... Unpacking replacement libdpkg-perl ... Preparing to replace openssl 0.9.8o-1ubuntu4 (using .../openssl_0.9.8o-1ubuntu4.3_amd64.deb) ... Unpacking replacement openssl ... Setting up libc-dev-bin (2.12.1-0ubuntu10.1) ... Setting up linux-libc-dev (2.6.35-1024.42) ... Setting up libc6-dev (2.12.1-0ubuntu10.1) ... Setting up ifupdown (0.6.10ubuntu3.1) ... Installing new version of config file /etc/init/network-interface.conf ... Installing new version of config file /etc/init/network-interface-security.conf ... Setting up sysvinit-utils (2.87dsf-4ubuntu19) ... Setting up sysv-rc (2.87dsf-4ubuntu19) ... Setting up initscripts (2.87dsf-4ubuntu19) ... Setting up libdrm2 (2.4.21-1ubuntu2.1) ... Setting up libdrm-intel1 (2.4.21-1ubuntu2.1) ... Setting up libdrm-nouveau1 (2.4.21-1ubuntu2.1) ... Setting up libdrm-radeon1 (2.4.21-1ubuntu2.1) ... Setting up udev (162-2.2) ... Removing 'local diversion of /sbin/udevadm to /sbin/udevadm.upgrade' update-initramfs: deferring update (trigger activated) Setting up libplymouth2 (0.8.2-2ubuntu5.1) ... Setting up plymouth (0.8.2-2ubuntu5.1) ... update-initramfs: deferring update (trigger activated) Setting up libudev0 (162-2.2) ... Setting up libkrb5support0 (1.8.1+dfsg-5ubuntu0.2) ... Setting up libk5crypto3 (1.8.1+dfsg-5ubuntu0.2) ... Setting up libkrb5-3 (1.8.1+dfsg-5ubuntu0.2) ... Setting up libgssapi-krb5-2 (1.8.1+dfsg-5ubuntu0.2) ... Setting up libldap-2.4-2 (2.4.23-0ubuntu3.4) ... Setting up libdpkg-perl (1.15.8.4ubuntu3.1) ... Setting up dpkg-dev (1.15.8.4ubuntu3.1) ... Setting up openssl (0.9.8o-1ubuntu4.3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '9104a2a6755e804c098d2bd63e011ff2840520ce', 'amd64', 'maverick', '--nolog', '--batch', '--archive=ubuntu', '--dist=maverick', '--purpose=PPA', '--architecture=amd64', '--comp=main', 'r-base_2.12.1-1~ppa1~maverick1.dsc'] Initiating build 9104a2a6755e804c098d2bd63e011ff2840520ce with 2 processor cores. Automatic build of r-base_2.12.1-1~ppa1~maverick1 on papaya by sbuild/amd64 1.170.5 Build started at 20110114-0329 ****************************************************************************** r-base_2.12.1-1~ppa1~maverick1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.5-dev, tk8.5-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texi2html, texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, xdg-utils, zlib1g-dev, libpng12-dev, libjpeg62-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff4-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, openjdk-6-jdk [!arm !hppa !kfreebsd-i386 !kfreebsd-amd64 !hurd-i386 !mips] Checking for already installed source dependencies... gcc: already installed (4:4.4.4-1ubuntu2 >= 4:4.1.0 is satisfied) g++: already installed (4:4.4.4-1ubuntu2 >= 4:4.1.0 is satisfied) gfortran: missing libblas-dev: missing liblapack-dev: missing tcl8.5-dev: missing tk8.5-dev: missing bison: missing groff-base: missing libncurses5-dev: missing libreadline-dev: missing debhelper: missing texi2html: missing texinfo: missing libbz2-dev: missing liblzma-dev: missing libpcre3-dev: missing xdg-utils: missing zlib1g-dev: missing libpng12-dev: missing libjpeg62-dev: missing libx11-dev: missing libxt-dev: missing x11proto-core-dev: missing libpango1.0-dev: missing libcairo2-dev: missing libtiff4-dev: missing xvfb: missing xauth: missing xfonts-base: missing texlive-base: missing texlive-latex-base: missing texlive-generic-recommended: missing texlive-fonts-recommended: missing texlive-extra-utils: missing texlive-latex-recommended: missing texlive-latex-extra: missing openjdk-6-jdk: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install gfortran libblas-dev liblapack-dev tcl8.5-dev tk8.5-dev bison groff-base libncurses5-dev libreadline-dev debhelper texi2html texinfo libbz2-dev liblzma-dev libpcre3-dev xdg-utils zlib1g-dev libpng12-dev libjpeg62-dev libx11-dev libxt-dev x11proto-core-dev libpango1.0-dev libcairo2-dev libtiff4-dev xvfb xauth xfonts-base texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-extra-utils texlive-latex-recommended texlive-latex-extra openjdk-6-jdk Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils ca-certificates-java defoma ed file fontconfig fontconfig-config gettext gettext-base gfortran-4.4 html2text intltool-debian java-common libaccess-bridge-java libaccess-bridge-java-jni libasound2 libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libblas3gf libcairo-gobject2 libcairo2 libcroco3 libcups2 libdatrie1 libexpat1 libexpat1-dev libflac8 libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev libgdk-pixbuf2.0-0 libgfortran3 libgif4 libglib2.0-bin libglib2.0-data libglib2.0-dev libgtk2.0-0 libgtk2.0-common libice-dev libice6 libjasper1 libjpeg62 libkpathsea5 liblapack3gf liblcms1 libmagic1 libnewt0.52 libnspr4-0d libnss3-1d libogg0 libpango1.0-0 libpango1.0-common libpcrecpp0 libpixman-1-0 libpixman-1-dev libpoppler7 libpopt0 libpthread-stubs0 libpthread-stubs0-dev libpulse0 libpython2.6 libreadline6-dev libsm-dev libsm6 libsndfile1 libsqlite3-0 libthai-data libthai0 libtiff4 libtiffxx0c2 libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-atom1 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont1 libxft-dev libxft2 libxi6 libxinerama1 libxkbfile1 libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxrender1 libxss-dev libxss1 libxt6 libxtst6 luatex m4 man-db mime-support openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib pkg-config po-debconf preview-latex-style python python2.6 shared-mime-info tcl8.5 tex-common texlive-binaries texlive-common texlive-doc-base texlive-pictures tk8.5 ttf-dejavu-core tzdata-java ucf whiptail x11-common x11-xkb-utils x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev xfonts-encodings xfonts-utils xkb-data xserver-common xtrans-dev Suggested packages: bison-doc wamerican wordlist whois vacation dh-make defoma-doc psfontmgr x-ttcidfont-conf dfontmgr libfont-freetype-perl gettext-doc gfortran-multilib gfortran-doc gfortran-4.4-multilib gfortran-4.4-doc libgfortran3-dbg groff default-jre equivs libasound2-plugins libcairo2-doc libcairo-script-interpreter2 cups-common libglib2.0-doc python-subunit librsvg2-common gvfs libjasper-runtime liblcms-utils liblzma-doc ttf-japanese-gothic ttf-japanese-mincho ttf-thryomanes ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp libpango1.0-doc imagemagick pulseaudio less www-browser openjdk-6-demo openjdk-6-source visualvm icedtea6-plugin libnss-mdns sun-java6-fonts ttf-sazanami-gothic ttf-kochi-gothic ttf-sazanami-mincho ttf-kochi-mincho ttf-wqy-microhei ttf-wqy-zenhei ttf-indic-fonts-core ttf-telugu-fonts ttf-oriya-fonts ttf-kannada-fonts ttf-bengali-fonts libmail-box-perl python-doc python-tk python-profiler python2.6-doc python2.6-profiler tclreadline tcl8.5-doc latex2html texinfo-doc-nonfree perl-tk ghostscript xpdf-reader pdf-viewer gv postscript-viewer dvidvi fragmaster latexmk purifyeps xindy texpower tk8.5-doc gvfs-bin xfs xserver Recommended packages: curl wget lynx libatk1.0-data hicolor-icon-theme libgtk2.0-bin libfribidi0 tcpd xml-core texlive-luatex ttf-dejavu-extra icedtea-6-jre-cacao libmail-sendmail-perl doc-base lmodern lacheck texlive-fonts-recommended-doc tipa texlive-latex-base-doc texlive-latex-extra-doc texlive-latex-recommended-doc prosper latex-beamer latex-xcolor texlive-pictures-doc pgf xterm x-terminal-emulator x11-utils x11-xserver-utils libgl1-mesa-dri The following NEW packages will be installed: bison bsdmainutils ca-certificates-java debhelper defoma ed file fontconfig fontconfig-config gettext gettext-base gfortran gfortran-4.4 groff-base html2text intltool-debian java-common libaccess-bridge-java libaccess-bridge-java-jni libasound2 libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libblas-dev libblas3gf libbz2-dev libcairo-gobject2 libcairo2 libcairo2-dev libcroco3 libcups2 libdatrie1 libexpat1 libexpat1-dev libflac8 libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev libgdk-pixbuf2.0-0 libgfortran3 libgif4 libglib2.0-bin libglib2.0-data libglib2.0-dev libgtk2.0-0 libgtk2.0-common libice-dev libice6 libjasper1 libjpeg62 libjpeg62-dev libkpathsea5 liblapack-dev liblapack3gf liblcms1 liblzma-dev libmagic1 libncurses5-dev libnewt0.52 libnspr4-0d libnss3-1d libogg0 libpango1.0-0 libpango1.0-common libpango1.0-dev libpcre3-dev libpcrecpp0 libpixman-1-0 libpixman-1-dev libpng12-dev libpoppler7 libpopt0 libpthread-stubs0 libpthread-stubs0-dev libpulse0 libpython2.6 libreadline-dev libreadline6-dev libsm-dev libsm6 libsndfile1 libsqlite3-0 libthai-data libthai0 libtiff4 libtiff4-dev libtiffxx0c2 libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-atom1 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont1 libxft-dev libxft2 libxi6 libxinerama1 libxkbfile1 libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxrender1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 luatex m4 man-db mime-support openjdk-6-jdk openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib pkg-config po-debconf preview-latex-style python python2.6 shared-mime-info tcl8.5 tcl8.5-dev tex-common texi2html texinfo texlive-base texlive-binaries texlive-common texlive-doc-base texlive-extra-utils texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.5 tk8.5-dev ttf-dejavu-core tzdata-java ucf whiptail x11-common x11-xkb-utils x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base xfonts-encodings xfonts-utils xkb-data xserver-common xtrans-dev xvfb zlib1g-dev 0 upgraded, 188 newly installed, 0 to remove and 0 not upgraded. Need to get 165MB of archives. After this operation, 483MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! x11-common libice6 x11proto-core-dev libice-dev libxau6 libxdmcp6 libxcb1 libx11-data libx11-6 libxau-dev libxdmcp-dev x11proto-input-dev x11proto-kb-dev xtrans-dev libpthread-stubs0 libpthread-stubs0-dev libxcb1-dev libx11-dev libxext6 libsm6 libxt6 libxmu6 libxpm4 libxaw7 libxkbfile1 x11-xkb-utils libmagic1 file libexpat1 libnewt0.52 libpopt0 libsqlite3-0 mime-support python2.6 python ucf whiptail xkb-data bsdmainutils ed ttf-dejavu-core fontconfig-config gettext-base groff-base libfreetype6 libfontconfig1 libpixman-1-0 libxcb-render0 libxcb-shm0 libxrender1 libcairo2 libxml2 libxmuu1 man-db xauth m4 bison openjdk-6-jre-lib tzdata-java java-common libavahi-common-data libavahi-common3 libavahi-client3 libcups2 liblcms1 libjpeg62 libnspr4-0d libnss3-1d openjdk-6-jre-headless ca-certificates-java html2text libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper defoma fontconfig libgfortran3 gfortran-4.4 gfortran libpython2.6 libasound2 libgif4 libogg0 libflac8 libvorbis0a libvorbisenc2 libsndfile1 libwrap0 libx11-xcb1 libxcb-atom1 libxi6 libxtst6 libpulse0 libatk1.0-0 libgtk2.0-common libjasper1 libtiff4 libgdk-pixbuf2.0-0 libpango1.0-common libdatrie1 libthai-data libthai0 libxft2 libpango1.0-0 libxfixes3 libxcomposite1 libxcursor1 libxdamage1 libxinerama1 libxrandr2 shared-mime-info libgtk2.0-0 libaccess-bridge-java-jni openjdk-6-jre libaccess-bridge-java libblas3gf libblas-dev libbz2-dev libcairo-gobject2 libexpat1-dev zlib1g-dev libfreetype6-dev pkg-config libfontconfig1-dev x11proto-render-dev libxrender-dev libpng12-dev libsm-dev libpixman-1-dev libxcb-render0-dev libxcb-shm0-dev libglib2.0-data libglib2.0-bin libglib2.0-dev libcairo2-dev libfontenc1 libjpeg62-dev libkpathsea5 liblapack3gf liblapack-dev libncurses5-dev libxft-dev libpango1.0-dev libpcrecpp0 libpcre3-dev libpoppler7 libreadline6-dev libreadline-dev libtiffxx0c2 libtiff4-dev x11proto-xext-dev libxext-dev libxfont1 libxss1 x11proto-scrnsaver-dev libxss-dev libxt-dev luatex openjdk-6-jdk tex-common preview-latex-style tcl8.5 tcl8.5-dev texi2html texinfo texlive-common texlive-doc-base texlive-binaries texlive-base texlive-extra-utils texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-pictures texlive-latex-extra texlive-latex-recommended tk8.5 tk8.5-dev xdg-utils xfonts-encodings xfonts-utils xfonts-base xserver-common xvfb liblzma-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ maverick/main x11-common all 1:7.5+6ubuntu3 [309kB] Get:2 http://ppa.launchpad.net/maverick-bleed/ppa/ubuntu/ maverick/main libvorbis0a amd64 1.3.1-1ubuntu1~ppa1~maverick1 [105kB] Get:3 http://ftpmaster.internal/ubuntu/ maverick/main libice6 amd64 2:1.0.6-1 [54.3kB] Get:4 http://ftpmaster.internal/ubuntu/ maverick/main x11proto-core-dev all 7.0.17-1 [95.2kB] Get:5 http://ftpmaster.internal/ubuntu/ maverick/main libice-dev amd64 2:1.0.6-1 [67.1kB] Get:6 http://ftpmaster.internal/ubuntu/ maverick/main libxau6 amd64 1:1.0.6-1 [16.8kB] Get:7 http://ftpmaster.internal/ubuntu/ maverick/main libxdmcp6 amd64 1:1.0.3-2 [19.2kB] Get:8 http://ftpmaster.internal/ubuntu/ maverick/main libxcb1 amd64 1.6-1 [43.8kB] Get:9 http://ftpmaster.internal/ubuntu/ maverick/main libx11-data all 2:1.3.3-3ubuntu1 [215kB] Get:10 http://ppa.launchpad.net/maverick-bleed/ppa/ubuntu/ maverick/main libvorbisenc2 amd64 1.3.1-1ubuntu1~ppa1~maverick1 [140kB] Get:11 http://ftpmaster.internal/ubuntu/ maverick/main libx11-6 amd64 2:1.3.3-3ubuntu1 [842kB] Get:12 http://ftpmaster.internal/ubuntu/ maverick/main libxau-dev amd64 1:1.0.6-1 [20.4kB] Get:13 http://ftpmaster.internal/ubuntu/ maverick/main libxdmcp-dev amd64 1:1.0.3-2 [22.8kB] Get:14 http://ftpmaster.internal/ubuntu/ maverick/main x11proto-input-dev all 2.0-2 [62.5kB] Get:15 http://ftpmaster.internal/ubuntu/ maverick/main x11proto-kb-dev all 1.0.4-1 [27.3kB] Get:16 http://ftpmaster.internal/ubuntu/ maverick/main xtrans-dev all 1.2.5-1 [68.5kB] Get:17 http://ftpmaster.internal/ubuntu/ maverick/main libpthread-stubs0 amd64 0.3-2 [3202B] Get:18 http://ftpmaster.internal/ubuntu/ maverick/main libpthread-stubs0-dev amd64 0.3-2 [2412B] Get:19 http://ftpmaster.internal/ubuntu/ maverick/main libxcb1-dev amd64 1.6-1 [81.1kB] Get:20 http://ftpmaster.internal/ubuntu/ maverick/main libx11-dev amd64 2:1.3.3-3ubuntu1 [3506kB] Get:21 http://ftpmaster.internal/ubuntu/ maverick/main libxext6 amd64 2:1.1.2-1 [45.3kB] Get:22 http://ftpmaster.internal/ubuntu/ maverick/main libsm6 amd64 2:1.1.1-1 [25.4kB] Get:23 http://ftpmaster.internal/ubuntu/ maverick/main libxt6 amd64 1:1.0.7-1 [195kB] Get:24 http://ftpmaster.internal/ubuntu/ maverick/main libxmu6 amd64 2:1.0.5-1 [57.5kB] Get:25 http://ftpmaster.internal/ubuntu/ maverick/main libxpm4 amd64 1:3.5.8-1 [44.7kB] Get:26 http://ftpmaster.internal/ubuntu/ maverick/main libxaw7 amd64 2:1.0.7-1 [212kB] Get:27 http://ftpmaster.internal/ubuntu/ maverick/main libxkbfile1 amd64 1:1.0.6-2 [78.4kB] Get:28 http://ftpmaster.internal/ubuntu/ maverick/main x11-xkb-utils amd64 7.5+5 [196kB] Get:29 http://ftpmaster.internal/ubuntu/ maverick/main libmagic1 amd64 5.03-5ubuntu1 [392kB] Get:30 http://ftpmaster.internal/ubuntu/ maverick/main file amd64 5.03-5ubuntu1 [48.0kB] Get:31 http://ftpmaster.internal/ubuntu/ maverick/main libexpat1 amd64 2.0.1-7ubuntu1 [138kB] Get:32 http://ftpmaster.internal/ubuntu/ maverick/main libnewt0.52 amd64 0.52.11-1 [59.4kB] Get:33 http://ftpmaster.internal/ubuntu/ maverick/main libpopt0 amd64 1.16-1 [35.1kB] Get:34 http://ftpmaster.internal/ubuntu/ maverick-updates/main libsqlite3-0 amd64 3.7.2-1ubuntu0.1 [394kB] Get:35 http://ftpmaster.internal/ubuntu/ maverick/main mime-support all 3.48-1ubuntu2 [34.7kB] Get:36 http://ftpmaster.internal/ubuntu/ maverick/main python2.6 amd64 2.6.6-5ubuntu1 [2438kB] Get:37 http://ftpmaster.internal/ubuntu/ maverick-updates/main python all 2.6.6-2ubuntu2 [172kB] Get:38 http://ftpmaster.internal/ubuntu/ maverick/main ucf all 3.0025 [68.1kB] Get:39 http://ftpmaster.internal/ubuntu/ maverick/main whiptail amd64 0.52.11-1 [40.5kB] Get:40 http://ftpmaster.internal/ubuntu/ maverick/main xkb-data all 1.8-1ubuntu8 [446kB] Get:41 http://ftpmaster.internal/ubuntu/ maverick/main bsdmainutils amd64 8.0.11ubuntu1 [205kB] Get:42 http://ftpmaster.internal/ubuntu/ maverick/main ed amd64 1.4-1build1 [62.1kB] Get:43 http://ftpmaster.internal/ubuntu/ maverick/main ttf-dejavu-core all 2.31-1 [1450kB] Get:44 http://ftpmaster.internal/ubuntu/ maverick/main fontconfig-config all 2.8.0-2ubuntu1 [205kB] Get:45 http://ftpmaster.internal/ubuntu/ maverick/main gettext-base amd64 0.18.1.1-1ubuntu2 [99.2kB] Get:46 http://ftpmaster.internal/ubuntu/ maverick/main groff-base amd64 1.20.1-10 [1130kB] Get:47 http://ftpmaster.internal/ubuntu/ maverick-security/main libfreetype6 amd64 2.4.2-2ubuntu0.1 [375kB] Get:48 http://ftpmaster.internal/ubuntu/ maverick/main libfontconfig1 amd64 2.8.0-2ubuntu1 [285kB] Get:49 http://ftpmaster.internal/ubuntu/ maverick/main libpixman-1-0 amd64 0.18.4-1 [275kB] Get:50 http://ftpmaster.internal/ubuntu/ maverick/main libxcb-render0 amd64 1.6-1 [15.7kB] Get:51 http://ftpmaster.internal/ubuntu/ maverick/main libxcb-shm0 amd64 1.6-1 [9242B] Get:52 http://ftpmaster.internal/ubuntu/ maverick/main libxrender1 amd64 1:0.9.6-1 [30.8kB] Get:53 http://ftpmaster.internal/ubuntu/ maverick-updates/main libcairo2 amd64 1.10.0-1ubuntu3 [938kB] Get:54 http://ftpmaster.internal/ubuntu/ maverick-security/main libxml2 amd64 2.7.7.dfsg-4ubuntu0.1 [869kB] Get:55 http://ftpmaster.internal/ubuntu/ maverick/main libxmuu1 amd64 2:1.0.5-1 [15.6kB] Get:56 http://ftpmaster.internal/ubuntu/ maverick/main man-db amd64 2.5.7-4 [1281kB] Get:57 http://ftpmaster.internal/ubuntu/ maverick/main xauth amd64 1:1.0.4-1 [33.8kB] Get:58 http://ftpmaster.internal/ubuntu/ maverick/main m4 amd64 1.4.14-3 [290kB] Get:59 http://ftpmaster.internal/ubuntu/ maverick/main bison amd64 1:2.4.1.dfsg-3 [493kB] Get:60 http://ftpmaster.internal/ubuntu/ maverick-security/main openjdk-6-jre-lib all 6b20-1.9.2-0ubuntu2 [6155kB] Get:61 http://ftpmaster.internal/ubuntu/ maverick-updates/main tzdata-java all 2010o-0ubuntu0.10.10 [144kB] Get:62 http://ftpmaster.internal/ubuntu/ maverick/main java-common all 0.38 [66.0kB] Get:63 http://ftpmaster.internal/ubuntu/ maverick/main libavahi-common-data amd64 0.6.27-2ubuntu3 [35.5kB] Get:64 http://ftpmaster.internal/ubuntu/ maverick/main libavahi-common3 amd64 0.6.27-2ubuntu3 [25.1kB] Get:65 http://ftpmaster.internal/ubuntu/ maverick/main libavahi-client3 amd64 0.6.27-2ubuntu3 [56.7kB] Get:66 http://ftpmaster.internal/ubuntu/ maverick-security/main libcups2 amd64 1.4.4-6ubuntu2.3 [232kB] Get:67 http://ftpmaster.internal/ubuntu/ maverick-security/main liblcms1 amd64 1.18.dfsg-1ubuntu2.10.10.1 [110kB] Get:68 http://ftpmaster.internal/ubuntu/ maverick/main libjpeg62 amd64 6b-16.1 [94.6kB] Get:69 http://ftpmaster.internal/ubuntu/ maverick/main libnspr4-0d amd64 4.8.6-0ubuntu1 [134kB] Get:70 http://ftpmaster.internal/ubuntu/ maverick-security/main libnss3-1d amd64 3.12.8-0ubuntu0.10.10.1 [1230kB] Get:71 http://ftpmaster.internal/ubuntu/ maverick-security/main openjdk-6-jre-headless amd64 6b20-1.9.2-0ubuntu2 [25.6MB] Get:72 http://ftpmaster.internal/ubuntu/ maverick/main ca-certificates-java all 20100412 [101kB] Get:73 http://ftpmaster.internal/ubuntu/ maverick/main html2text amd64 1.3.2a-15 [104kB] Get:74 http://ftpmaster.internal/ubuntu/ maverick/main libcroco3 amd64 0.6.2-1 [101kB] Get:75 http://ftpmaster.internal/ubuntu/ maverick/main libunistring0 amd64 0.9.3-1 [438kB] Get:76 http://ftpmaster.internal/ubuntu/ maverick/main gettext amd64 0.18.1.1-1ubuntu2 [1317kB] Get:77 http://ftpmaster.internal/ubuntu/ maverick/main intltool-debian all 0.35.0+20060710.1 [31.6kB] Get:78 http://ftpmaster.internal/ubuntu/ maverick/main po-debconf all 1.0.16 [224kB] Get:79 http://ftpmaster.internal/ubuntu/ maverick/main debhelper all 8.0.0ubuntu1 [460kB] Get:80 http://ftpmaster.internal/ubuntu/ maverick/main defoma all 0.11.11ubuntu1 [101kB] Get:81 http://ftpmaster.internal/ubuntu/ maverick/main fontconfig amd64 2.8.0-2ubuntu1 [158kB] Get:82 http://ftpmaster.internal/ubuntu/ maverick/main libgfortran3 amd64 4.5.1-7ubuntu2 [287kB] Get:83 http://ftpmaster.internal/ubuntu/ maverick/main gfortran-4.4 amd64 4.4.4-14ubuntu5 [4549kB] Get:84 http://ftpmaster.internal/ubuntu/ maverick/main gfortran amd64 4:4.4.4-1ubuntu2 [1200B] Get:85 http://ftpmaster.internal/ubuntu/ maverick/main libpython2.6 amd64 2.6.6-5ubuntu1 [1072kB] Get:86 http://ftpmaster.internal/ubuntu/ maverick-updates/main libasound2 amd64 1.0.23-1ubuntu2.1 [437kB] Get:87 http://ftpmaster.internal/ubuntu/ maverick/main libgif4 amd64 4.1.6-9 [41.4kB] Get:88 http://ftpmaster.internal/ubuntu/ maverick/main libogg0 amd64 1.2.0~dfsg-1 [17.5kB] Get:89 http://ftpmaster.internal/ubuntu/ maverick/main libflac8 amd64 1.2.1-3 [150kB] Get:90 http://ftpmaster.internal/ubuntu/ maverick/main libsndfile1 amd64 1.0.21-2 [233kB] Get:91 http://ftpmaster.internal/ubuntu/ maverick/main libwrap0 amd64 7.6.q-19 [51.2kB] Get:92 http://ftpmaster.internal/ubuntu/ maverick/main libx11-xcb1 amd64 2:1.3.3-3ubuntu1 [90.3kB] Get:93 http://ftpmaster.internal/ubuntu/ maverick/main libxcb-atom1 amd64 0.3.6-1build1 [10.3kB] Get:94 http://ftpmaster.internal/ubuntu/ maverick/main libxi6 amd64 2:1.3-4 [55.9kB] Get:95 http://ftpmaster.internal/ubuntu/ maverick/main libxtst6 amd64 2:1.1.0-3 [20.0kB] Get:96 http://ftpmaster.internal/ubuntu/ maverick-updates/main libpulse0 amd64 1:0.9.22~0.9.21+stable-queue-32-g8478-0ubuntu21.1 [280kB] Get:97 http://ftpmaster.internal/ubuntu/ maverick/main libatk1.0-0 amd64 1.32.0-0ubuntu1 [57.3kB] Get:98 http://ftpmaster.internal/ubuntu/ maverick/main libgtk2.0-common all 2.22.0-0ubuntu1 [500kB] Get:99 http://ftpmaster.internal/ubuntu/ maverick/main libjasper1 amd64 1.900.1-7 [154kB] Get:100 http://ftpmaster.internal/ubuntu/ maverick/main libtiff4 amd64 3.9.4-2 [149kB] Get:101 http://ftpmaster.internal/ubuntu/ maverick/main libgdk-pixbuf2.0-0 amd64 2.22.0-0ubuntu1 [192kB] Get:102 http://ftpmaster.internal/ubuntu/ maverick/main libpango1.0-common all 1.28.1-1ubuntu3 [113kB] Get:103 http://ftpmaster.internal/ubuntu/ maverick/main libdatrie1 amd64 0.2.3-1 [26.0kB] Get:104 http://ftpmaster.internal/ubuntu/ maverick/main libthai-data all 0.1.14-2 [197kB] Get:105 http://ftpmaster.internal/ubuntu/ maverick/main libthai0 amd64 0.1.14-2 [41.7kB] Get:106 http://ftpmaster.internal/ubuntu/ maverick/main libxft2 amd64 2.1.14-2ubuntu1 [56.3kB] Get:107 http://ftpmaster.internal/ubuntu/ maverick/main libpango1.0-0 amd64 1.28.1-1ubuntu3 [321kB] Get:108 http://ftpmaster.internal/ubuntu/ maverick/main libxfixes3 amd64 1:4.0.5-1 [19.2kB] Get:109 http://ftpmaster.internal/ubuntu/ maverick/main libxcomposite1 amd64 1:0.4.2-1 [15.6kB] Get:110 http://ftpmaster.internal/ubuntu/ maverick/main libxcursor1 amd64 1:1.1.10-2 [25.6kB] Get:111 http://ftpmaster.internal/ubuntu/ maverick/main libxdamage1 amd64 1:1.1.3-1 [14.2kB] Get:112 http://ftpmaster.internal/ubuntu/ maverick/main libxinerama1 amd64 2:1.1-3 [12.4kB] Get:113 http://ftpmaster.internal/ubuntu/ maverick/main libxrandr2 amd64 2:1.3.0-3 [28.4kB] Get:114 http://ftpmaster.internal/ubuntu/ maverick/main shared-mime-info amd64 0.71-3 [401kB] Get:115 http://ftpmaster.internal/ubuntu/ maverick/main libgtk2.0-0 amd64 2.22.0-0ubuntu1 [2235kB] Get:116 http://ftpmaster.internal/ubuntu/ maverick/main libaccess-bridge-java-jni amd64 1.26.2-5 [8788B] Get:117 http://ftpmaster.internal/ubuntu/ maverick-security/main openjdk-6-jre amd64 6b20-1.9.2-0ubuntu2 [267kB] Get:118 http://ftpmaster.internal/ubuntu/ maverick/main libaccess-bridge-java all 1.26.2-5 [410kB] Get:119 http://ftpmaster.internal/ubuntu/ maverick/main libblas3gf amd64 1.2-7 [229kB] Get:120 http://ftpmaster.internal/ubuntu/ maverick/main libblas-dev amd64 1.2-7 [253kB] Get:121 http://ftpmaster.internal/ubuntu/ maverick/main libbz2-dev amd64 1.0.5-4ubuntu1 [33.6kB] Get:122 http://ftpmaster.internal/ubuntu/ maverick-updates/main libcairo-gobject2 amd64 1.10.0-1ubuntu3 [583kB] Get:123 http://ftpmaster.internal/ubuntu/ maverick/main libexpat1-dev amd64 2.0.1-7ubuntu1 [220kB] Get:124 http://ftpmaster.internal/ubuntu/ maverick/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3ubuntu1 [194kB] Get:125 http://ftpmaster.internal/ubuntu/ maverick-security/main libfreetype6-dev amd64 2.4.2-2ubuntu0.1 [746kB] Get:126 http://ftpmaster.internal/ubuntu/ maverick/main pkg-config amd64 0.25-1 [59.7kB] Get:127 http://ftpmaster.internal/ubuntu/ maverick/main libfontconfig1-dev amd64 2.8.0-2ubuntu1 [657kB] Get:128 http://ftpmaster.internal/ubuntu/ maverick/main x11proto-render-dev all 2:0.11-1 [7404B] Get:129 http://ftpmaster.internal/ubuntu/ maverick/main libxrender-dev amd64 1:0.9.6-1 [39.0kB] Get:130 http://ftpmaster.internal/ubuntu/ maverick/main libpng12-dev amd64 1.2.44-1 [273kB] Get:131 http://ftpmaster.internal/ubuntu/ maverick/main libsm-dev amd64 2:1.1.1-1 [28.3kB] Get:132 http://ftpmaster.internal/ubuntu/ maverick/main libpixman-1-dev amd64 0.18.4-1 [302kB] Get:133 http://ftpmaster.internal/ubuntu/ maverick/main libxcb-render0-dev amd64 1.6-1 [23.4kB] Get:134 http://ftpmaster.internal/ubuntu/ maverick/main libxcb-shm0-dev amd64 1.6-1 [10.7kB] Get:135 http://ftpmaster.internal/ubuntu/ maverick/main libglib2.0-data all 2.26.0-0ubuntu1 [972B] Get:136 http://ftpmaster.internal/ubuntu/ maverick/main libglib2.0-bin amd64 2.26.0-0ubuntu1 [347kB] Get:137 http://ftpmaster.internal/ubuntu/ maverick/main libglib2.0-dev amd64 2.26.0-0ubuntu1 [1540kB] Get:138 http://ftpmaster.internal/ubuntu/ maverick-updates/main libcairo2-dev amd64 1.10.0-1ubuntu3 [1142kB] Get:139 http://ftpmaster.internal/ubuntu/ maverick/main libfontenc1 amd64 1:1.0.5-2 [20.6kB] Get:140 http://ftpmaster.internal/ubuntu/ maverick/main libjpeg62-dev amd64 6b-16.1 [199kB] Get:141 http://ftpmaster.internal/ubuntu/ maverick/main libkpathsea5 amd64 2009-7 [133kB] Get:142 http://ftpmaster.internal/ubuntu/ maverick/main liblapack3gf amd64 3.2.1-8 [4434kB] Get:143 http://ftpmaster.internal/ubuntu/ maverick/main liblapack-dev amd64 3.2.1-8 [4817kB] Get:144 http://ftpmaster.internal/ubuntu/ maverick/main libncurses5-dev amd64 5.7+20100626-0ubuntu1 [1618kB] Get:145 http://ftpmaster.internal/ubuntu/ maverick/main libxft-dev amd64 2.1.14-2ubuntu1 [72.4kB] Get:146 http://ftpmaster.internal/ubuntu/ maverick/main libpango1.0-dev amd64 1.28.1-1ubuntu3 [470kB] Get:147 http://ftpmaster.internal/ubuntu/ maverick/main libpcrecpp0 amd64 8.02-1 [108kB] Get:148 http://ftpmaster.internal/ubuntu/ maverick/main libpcre3-dev amd64 8.02-1 [284kB] Get:149 http://ftpmaster.internal/ubuntu/ maverick-security/main libpoppler7 amd64 0.14.3-0ubuntu1.1 [783kB] Get:150 http://ftpmaster.internal/ubuntu/ maverick/main libreadline6-dev amd64 6.1-3 [257kB] Get:151 http://ftpmaster.internal/ubuntu/ maverick/main libreadline-dev amd64 6.1-3 [904B] Get:152 http://ftpmaster.internal/ubuntu/ maverick/main libtiffxx0c2 amd64 3.9.4-2 [6324B] Get:153 http://ftpmaster.internal/ubuntu/ maverick/main libtiff4-dev amd64 3.9.4-2 [270kB] Get:154 http://ftpmaster.internal/ubuntu/ maverick/main x11proto-xext-dev all 7.1.1-2 [27.2kB] Get:155 http://ftpmaster.internal/ubuntu/ maverick/main libxext-dev amd64 2:1.1.2-1 [108kB] Get:156 http://ftpmaster.internal/ubuntu/ maverick/main libxfont1 amd64 1:1.4.2-1 [157kB] Get:157 http://ftpmaster.internal/ubuntu/ maverick/main libxss1 amd64 1:1.2.0-2 [14.0kB] Get:158 http://ftpmaster.internal/ubuntu/ maverick/main x11proto-scrnsaver-dev all 1.2.0-2 [4856B] Get:159 http://ftpmaster.internal/ubuntu/ maverick/main libxss-dev amd64 1:1.2.0-2 [19.9kB] Get:160 http://ftpmaster.internal/ubuntu/ maverick/main libxt-dev amd64 1:1.0.7-1 [525kB] Get:161 http://ftpmaster.internal/ubuntu/ maverick/main luatex amd64 0.60.1-1build2 [2196kB] Get:162 http://ftpmaster.internal/ubuntu/ maverick-security/main openjdk-6-jdk amd64 6b20-1.9.2-0ubuntu2 [10.9MB] Get:163 http://ftpmaster.internal/ubuntu/ maverick/main tex-common all 2.08 [725kB] Get:164 http://ftpmaster.internal/ubuntu/ maverick/main preview-latex-style all 11.85-1ubuntu1 [123kB] Get:165 http://ftpmaster.internal/ubuntu/ maverick/main tcl8.5 amd64 8.5.8-2build1 [1593kB] Get:166 http://ftpmaster.internal/ubuntu/ maverick/main tcl8.5-dev amd64 8.5.8-2build1 [1056kB] Get:167 http://ftpmaster.internal/ubuntu/ maverick/main texi2html all 1.82-1 [445kB] Get:168 http://ftpmaster.internal/ubuntu/ maverick/main texinfo amd64 4.13a.dfsg.1-5ubuntu1 [553kB] Get:169 http://ftpmaster.internal/ubuntu/ maverick/main texlive-common all 2009-10 [100kB] Get:170 http://ftpmaster.internal/ubuntu/ maverick/main texlive-doc-base all 2009-2 [1339kB] Get:171 http://ftpmaster.internal/ubuntu/ maverick/main texlive-binaries amd64 2009-7 [8080kB] Get:172 http://ftpmaster.internal/ubuntu/ maverick/main texlive-base all 2009-10 [14.7MB] Get:173 http://ftpmaster.internal/ubuntu/ maverick/main texlive-extra-utils all 2009-9ubuntu1 [1583kB] Get:174 http://ftpmaster.internal/ubuntu/ maverick/main texlive-fonts-recommended all 2009-10 [7166kB] Get:175 http://ftpmaster.internal/ubuntu/ maverick/main texlive-generic-recommended all 2009-10 [1720kB] Get:176 http://ftpmaster.internal/ubuntu/ maverick/main texlive-latex-base all 2009-10 [1342kB] Get:177 http://ftpmaster.internal/ubuntu/ maverick/main texlive-pictures all 2009-10 [865kB] Get:178 http://ftpmaster.internal/ubuntu/ maverick/main texlive-latex-extra all 2009-9ubuntu1 [4724kB] Get:179 http://ftpmaster.internal/ubuntu/ maverick/main texlive-latex-recommended all 2009-10 [6587kB] Get:180 http://ftpmaster.internal/ubuntu/ maverick/main tk8.5 amd64 8.5.8-1 [1168kB] Get:181 http://ftpmaster.internal/ubuntu/ maverick/main tk8.5-dev amd64 8.5.8-1 [986kB] Get:182 http://ftpmaster.internal/ubuntu/ maverick-updates/main xdg-utils all 1.0.2+cvs20100307-1ubuntu0.1 [64.0kB] Get:183 http://ftpmaster.internal/ubuntu/ maverick/main xfonts-encodings all 1:1.0.3-1 [584kB] Get:184 http://ftpmaster.internal/ubuntu/ maverick/main xfonts-utils amd64 1:7.5+2 [99.3kB] Get:185 http://ftpmaster.internal/ubuntu/ maverick/main xfonts-base all 1:1.0.1 [6161kB] Get:186 http://ftpmaster.internal/ubuntu/ maverick-updates/main xserver-common all 2:1.9.0-0ubuntu7.1 [87.0kB] Get:187 http://ftpmaster.internal/ubuntu/ maverick-updates/main xvfb amd64 2:1.9.0-0ubuntu7.1 [912kB] Get:188 http://ftpmaster.internal/ubuntu/ maverick/main liblzma-dev amd64 4.999.9beta+20100527-1 [232kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 165MB in 6s (24.8MB/s) Selecting previously deselected package x11-common. (Reading database ... 13456 files and directories currently installed.) Unpacking x11-common (from .../x11-common_1%3a7.5+6ubuntu3_all.deb) ... Selecting previously deselected package libice6. Unpacking libice6 (from .../libice6_2%3a1.0.6-1_amd64.deb) ... Selecting previously deselected package x11proto-core-dev. Unpacking x11proto-core-dev (from .../x11proto-core-dev_7.0.17-1_all.deb) ... Setting up x11-common (1:7.5+6ubuntu3) ... Selecting previously deselected package libice-dev. (Reading database ... 13577 files and directories currently installed.) Unpacking libice-dev (from .../libice-dev_2%3a1.0.6-1_amd64.deb) ... Selecting previously deselected package libxau6. Unpacking libxau6 (from .../libxau6_1%3a1.0.6-1_amd64.deb) ... Selecting previously deselected package libxdmcp6. Unpacking libxdmcp6 (from .../libxdmcp6_1%3a1.0.3-2_amd64.deb) ... Selecting previously deselected package libxcb1. Unpacking libxcb1 (from .../libxcb1_1.6-1_amd64.deb) ... Selecting previously deselected package libx11-data. Unpacking libx11-data (from .../libx11-data_2%3a1.3.3-3ubuntu1_all.deb) ... Selecting previously deselected package libx11-6. Unpacking libx11-6 (from .../libx11-6_2%3a1.3.3-3ubuntu1_amd64.deb) ... Selecting previously deselected package libxau-dev. Unpacking libxau-dev (from .../libxau-dev_1%3a1.0.6-1_amd64.deb) ... Selecting previously deselected package libxdmcp-dev. Unpacking libxdmcp-dev (from .../libxdmcp-dev_1%3a1.0.3-2_amd64.deb) ... Selecting previously deselected package x11proto-input-dev. Unpacking x11proto-input-dev (from .../x11proto-input-dev_2.0-2_all.deb) ... Selecting previously deselected package x11proto-kb-dev. Unpacking x11proto-kb-dev (from .../x11proto-kb-dev_1.0.4-1_all.deb) ... Selecting previously deselected package xtrans-dev. Unpacking xtrans-dev (from .../xtrans-dev_1.2.5-1_all.deb) ... Selecting previously deselected package libpthread-stubs0. Unpacking libpthread-stubs0 (from .../libpthread-stubs0_0.3-2_amd64.deb) ... Selecting previously deselected package libpthread-stubs0-dev. Unpacking libpthread-stubs0-dev (from .../libpthread-stubs0-dev_0.3-2_amd64.deb) ... Selecting previously deselected package libxcb1-dev. Unpacking libxcb1-dev (from .../libxcb1-dev_1.6-1_amd64.deb) ... Selecting previously deselected package libx11-dev. Unpacking libx11-dev (from .../libx11-dev_2%3a1.3.3-3ubuntu1_amd64.deb) ... Selecting previously deselected package libxext6. Unpacking libxext6 (from .../libxext6_2%3a1.1.2-1_amd64.deb) ... Selecting previously deselected package libsm6. Unpacking libsm6 (from .../libsm6_2%3a1.1.1-1_amd64.deb) ... Selecting previously deselected package libxt6. Unpacking libxt6 (from .../libxt6_1%3a1.0.7-1_amd64.deb) ... Selecting previously deselected package libxmu6. Unpacking libxmu6 (from .../libxmu6_2%3a1.0.5-1_amd64.deb) ... Selecting previously deselected package libxpm4. Unpacking libxpm4 (from .../libxpm4_1%3a3.5.8-1_amd64.deb) ... Selecting previously deselected package libxaw7. Unpacking libxaw7 (from .../libxaw7_2%3a1.0.7-1_amd64.deb) ... Selecting previously deselected package libxkbfile1. Unpacking libxkbfile1 (from .../libxkbfile1_1%3a1.0.6-2_amd64.deb) ... Selecting previously deselected package x11-xkb-utils. Unpacking x11-xkb-utils (from .../x11-xkb-utils_7.5+5_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.03-5ubuntu1_amd64.deb) ... Selecting previously deselected package file. Unpacking file (from .../file_5.03-5ubuntu1_amd64.deb) ... Selecting previously deselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7ubuntu1_amd64.deb) ... Selecting previously deselected package libnewt0.52. Unpacking libnewt0.52 (from .../libnewt0.52_0.52.11-1_amd64.deb) ... Selecting previously deselected package libpopt0. Unpacking libpopt0 (from .../libpopt0_1.16-1_amd64.deb) ... Selecting previously deselected package libsqlite3-0. Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.2-1ubuntu0.1_amd64.deb) ... Selecting previously deselected package mime-support. Unpacking mime-support (from .../mime-support_3.48-1ubuntu2_all.deb) ... Selecting previously deselected package python2.6. Unpacking python2.6 (from .../python2.6_2.6.6-5ubuntu1_amd64.deb) ... Selecting previously deselected package python. Unpacking python (from .../python_2.6.6-2ubuntu2_all.deb) ... Selecting previously deselected package ucf. Unpacking ucf (from .../archives/ucf_3.0025_all.deb) ... Moving old data out of the way Selecting previously deselected package whiptail. Unpacking whiptail (from .../whiptail_0.52.11-1_amd64.deb) ... Selecting previously deselected package xkb-data. Unpacking xkb-data (from .../xkb-data_1.8-1ubuntu8_all.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.0.11ubuntu1_amd64.deb) ... Selecting previously deselected package ed. Unpacking ed (from .../ed_1.4-1build1_amd64.deb) ... Selecting previously deselected package ttf-dejavu-core. Unpacking ttf-dejavu-core (from .../ttf-dejavu-core_2.31-1_all.deb) ... Selecting previously deselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.8.0-2ubuntu1_all.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-1ubuntu2_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.20.1-10_amd64.deb) ... Selecting previously deselected package libfreetype6. Unpacking libfreetype6 (from .../libfreetype6_2.4.2-2ubuntu0.1_amd64.deb) ... Selecting previously deselected package libfontconfig1. Unpacking libfontconfig1 (from .../libfontconfig1_2.8.0-2ubuntu1_amd64.deb) ... Selecting previously deselected package libpixman-1-0. Unpacking libpixman-1-0 (from .../libpixman-1-0_0.18.4-1_amd64.deb) ... Selecting previously deselected package libxcb-render0. Unpacking libxcb-render0 (from .../libxcb-render0_1.6-1_amd64.deb) ... Selecting previously deselected package libxcb-shm0. Unpacking libxcb-shm0 (from .../libxcb-shm0_1.6-1_amd64.deb) ... Selecting previously deselected package libxrender1. Unpacking libxrender1 (from .../libxrender1_1%3a0.9.6-1_amd64.deb) ... Selecting previously deselected package libcairo2. Unpacking libcairo2 (from .../libcairo2_1.10.0-1ubuntu3_amd64.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4ubuntu0.1_amd64.deb) ... Selecting previously deselected package libxmuu1. Unpacking libxmuu1 (from .../libxmuu1_2%3a1.0.5-1_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.5.7-4_amd64.deb) ... Selecting previously deselected package xauth. Unpacking xauth (from .../xauth_1%3a1.0.4-1_amd64.deb) ... Selecting previously deselected package m4. Unpacking m4 (from .../archives/m4_1.4.14-3_amd64.deb) ... Selecting previously deselected package bison. Unpacking bison (from .../bison_1%3a2.4.1.dfsg-3_amd64.deb) ... Selecting previously deselected package openjdk-6-jre-lib. Unpacking openjdk-6-jre-lib (from .../openjdk-6-jre-lib_6b20-1.9.2-0ubuntu2_all.deb) ... Selecting previously deselected package tzdata-java. Unpacking tzdata-java (from .../tzdata-java_2010o-0ubuntu0.10.10_all.deb) ... Selecting previously deselected package java-common. Unpacking java-common (from .../java-common_0.38_all.deb) ... Selecting previously deselected package libavahi-common-data. Unpacking libavahi-common-data (from .../libavahi-common-data_0.6.27-2ubuntu3_amd64.deb) ... Selecting previously deselected package libavahi-common3. Unpacking libavahi-common3 (from .../libavahi-common3_0.6.27-2ubuntu3_amd64.deb) ... Selecting previously deselected package libavahi-client3. Unpacking libavahi-client3 (from .../libavahi-client3_0.6.27-2ubuntu3_amd64.deb) ... Selecting previously deselected package libcups2. Unpacking libcups2 (from .../libcups2_1.4.4-6ubuntu2.3_amd64.deb) ... Selecting previously deselected package liblcms1. Unpacking liblcms1 (from .../liblcms1_1.18.dfsg-1ubuntu2.10.10.1_amd64.deb) ... Selecting previously deselected package libjpeg62. Unpacking libjpeg62 (from .../libjpeg62_6b-16.1_amd64.deb) ... Selecting previously deselected package libnspr4-0d. Unpacking libnspr4-0d (from .../libnspr4-0d_4.8.6-0ubuntu1_amd64.deb) ... Selecting previously deselected package libnss3-1d. Unpacking libnss3-1d (from .../libnss3-1d_3.12.8-0ubuntu0.10.10.1_amd64.deb) ... Selecting previously deselected package openjdk-6-jre-headless. Unpacking openjdk-6-jre-headless (from .../openjdk-6-jre-headless_6b20-1.9.2-0ubuntu2_amd64.deb) ... Selecting previously deselected package ca-certificates-java. Unpacking ca-certificates-java (from .../ca-certificates-java_20100412_all.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-1_amd64.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-1ubuntu2_amd64.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.0.0ubuntu1_all.deb) ... Selecting previously deselected package defoma. Unpacking defoma (from .../defoma_0.11.11ubuntu1_all.deb) ... Selecting previously deselected package fontconfig. Unpacking fontconfig (from .../fontconfig_2.8.0-2ubuntu1_amd64.deb) ... Selecting previously deselected package libgfortran3. Unpacking libgfortran3 (from .../libgfortran3_4.5.1-7ubuntu2_amd64.deb) ... Selecting previously deselected package gfortran-4.4. Unpacking gfortran-4.4 (from .../gfortran-4.4_4.4.4-14ubuntu5_amd64.deb) ... Selecting previously deselected package gfortran. Unpacking gfortran (from .../gfortran_4%3a4.4.4-1ubuntu2_amd64.deb) ... Selecting previously deselected package libpython2.6. Unpacking libpython2.6 (from .../libpython2.6_2.6.6-5ubuntu1_amd64.deb) ... Selecting previously deselected package libasound2. Unpacking libasound2 (from .../libasound2_1.0.23-1ubuntu2.1_amd64.deb) ... Selecting previously deselected package libgif4. Unpacking libgif4 (from .../libgif4_4.1.6-9_amd64.deb) ... Selecting previously deselected package libogg0. Unpacking libogg0 (from .../libogg0_1.2.0~dfsg-1_amd64.deb) ... Selecting previously deselected package libflac8. Unpacking libflac8 (from .../libflac8_1.2.1-3_amd64.deb) ... Selecting previously deselected package libvorbis0a. Unpacking libvorbis0a (from .../libvorbis0a_1.3.1-1ubuntu1~ppa1~maverick1_amd64.deb) ... Selecting previously deselected package libvorbisenc2. Unpacking libvorbisenc2 (from .../libvorbisenc2_1.3.1-1ubuntu1~ppa1~maverick1_amd64.deb) ... Selecting previously deselected package libsndfile1. Unpacking libsndfile1 (from .../libsndfile1_1.0.21-2_amd64.deb) ... Selecting previously deselected package libwrap0. Unpacking libwrap0 (from .../libwrap0_7.6.q-19_amd64.deb) ... Selecting previously deselected package libx11-xcb1. Unpacking libx11-xcb1 (from .../libx11-xcb1_2%3a1.3.3-3ubuntu1_amd64.deb) ... Selecting previously deselected package libxcb-atom1. Unpacking libxcb-atom1 (from .../libxcb-atom1_0.3.6-1build1_amd64.deb) ... Selecting previously deselected package libxi6. Unpacking libxi6 (from .../libxi6_2%3a1.3-4_amd64.deb) ... Selecting previously deselected package libxtst6. Unpacking libxtst6 (from .../libxtst6_2%3a1.1.0-3_amd64.deb) ... Selecting previously deselected package libpulse0. Unpacking libpulse0 (from .../libpulse0_1%3a0.9.22~0.9.21+stable-queue-32-g8478-0ubuntu21.1_amd64.deb) ... Selecting previously deselected package libatk1.0-0. Unpacking libatk1.0-0 (from .../libatk1.0-0_1.32.0-0ubuntu1_amd64.deb) ... Selecting previously deselected package libgtk2.0-common. Unpacking libgtk2.0-common (from .../libgtk2.0-common_2.22.0-0ubuntu1_all.deb) ... Selecting previously deselected package libjasper1. Unpacking libjasper1 (from .../libjasper1_1.900.1-7_amd64.deb) ... Selecting previously deselected package libtiff4. Unpacking libtiff4 (from .../libtiff4_3.9.4-2_amd64.deb) ... Selecting previously deselected package libgdk-pixbuf2.0-0. Unpacking libgdk-pixbuf2.0-0 (from .../libgdk-pixbuf2.0-0_2.22.0-0ubuntu1_amd64.deb) ... Selecting previously deselected package libpango1.0-common. Unpacking libpango1.0-common (from .../libpango1.0-common_1.28.1-1ubuntu3_all.deb) ... Selecting previously deselected package libdatrie1. Unpacking libdatrie1 (from .../libdatrie1_0.2.3-1_amd64.deb) ... Selecting previously deselected package libthai-data. Unpacking libthai-data (from .../libthai-data_0.1.14-2_all.deb) ... Selecting previously deselected package libthai0. Unpacking libthai0 (from .../libthai0_0.1.14-2_amd64.deb) ... Selecting previously deselected package libxft2. Unpacking libxft2 (from .../libxft2_2.1.14-2ubuntu1_amd64.deb) ... Selecting previously deselected package libpango1.0-0. Unpacking libpango1.0-0 (from .../libpango1.0-0_1.28.1-1ubuntu3_amd64.deb) ... Selecting previously deselected package libxfixes3. Unpacking libxfixes3 (from .../libxfixes3_1%3a4.0.5-1_amd64.deb) ... Selecting previously deselected package libxcomposite1. Unpacking libxcomposite1 (from .../libxcomposite1_1%3a0.4.2-1_amd64.deb) ... Selecting previously deselected package libxcursor1. Unpacking libxcursor1 (from .../libxcursor1_1%3a1.1.10-2_amd64.deb) ... Selecting previously deselected package libxdamage1. Unpacking libxdamage1 (from .../libxdamage1_1%3a1.1.3-1_amd64.deb) ... Selecting previously deselected package libxinerama1. Unpacking libxinerama1 (from .../libxinerama1_2%3a1.1-3_amd64.deb) ... Selecting previously deselected package libxrandr2. Unpacking libxrandr2 (from .../libxrandr2_2%3a1.3.0-3_amd64.deb) ... Selecting previously deselected package shared-mime-info. Unpacking shared-mime-info (from .../shared-mime-info_0.71-3_amd64.deb) ... Selecting previously deselected package libgtk2.0-0. Unpacking libgtk2.0-0 (from .../libgtk2.0-0_2.22.0-0ubuntu1_amd64.deb) ... Selecting previously deselected package libaccess-bridge-java-jni. Unpacking libaccess-bridge-java-jni (from .../libaccess-bridge-java-jni_1.26.2-5_amd64.deb) ... Selecting previously deselected package openjdk-6-jre. Unpacking openjdk-6-jre (from .../openjdk-6-jre_6b20-1.9.2-0ubuntu2_amd64.deb) ... Selecting previously deselected package libaccess-bridge-java. Unpacking libaccess-bridge-java (from .../libaccess-bridge-java_1.26.2-5_all.deb) ... Selecting previously deselected package libblas3gf. Unpacking libblas3gf (from .../libblas3gf_1.2-7_amd64.deb) ... Selecting previously deselected package libblas-dev. Unpacking libblas-dev (from .../libblas-dev_1.2-7_amd64.deb) ... Selecting previously deselected package libbz2-dev. Unpacking libbz2-dev (from .../libbz2-dev_1.0.5-4ubuntu1_amd64.deb) ... Selecting previously deselected package libcairo-gobject2. Unpacking libcairo-gobject2 (from .../libcairo-gobject2_1.10.0-1ubuntu3_amd64.deb) ... Selecting previously deselected package libexpat1-dev. Unpacking libexpat1-dev (from .../libexpat1-dev_2.0.1-7ubuntu1_amd64.deb) ... Selecting previously deselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3ubuntu1_amd64.deb) ... Selecting previously deselected package libfreetype6-dev. Unpacking libfreetype6-dev (from .../libfreetype6-dev_2.4.2-2ubuntu0.1_amd64.deb) ... Selecting previously deselected package pkg-config. Unpacking pkg-config (from .../pkg-config_0.25-1_amd64.deb) ... Selecting previously deselected package libfontconfig1-dev. Unpacking libfontconfig1-dev (from .../libfontconfig1-dev_2.8.0-2ubuntu1_amd64.deb) ... Selecting previously deselected package x11proto-render-dev. Unpacking x11proto-render-dev (from .../x11proto-render-dev_2%3a0.11-1_all.deb) ... Selecting previously deselected package libxrender-dev. Unpacking libxrender-dev (from .../libxrender-dev_1%3a0.9.6-1_amd64.deb) ... Selecting previously deselected package libpng12-dev. Unpacking libpng12-dev (from .../libpng12-dev_1.2.44-1_amd64.deb) ... Selecting previously deselected package libsm-dev. Unpacking libsm-dev (from .../libsm-dev_2%3a1.1.1-1_amd64.deb) ... Selecting previously deselected package libpixman-1-dev. Unpacking libpixman-1-dev (from .../libpixman-1-dev_0.18.4-1_amd64.deb) ... Selecting previously deselected package libxcb-render0-dev. Unpacking libxcb-render0-dev (from .../libxcb-render0-dev_1.6-1_amd64.deb) ... Selecting previously deselected package libxcb-shm0-dev. Unpacking libxcb-shm0-dev (from .../libxcb-shm0-dev_1.6-1_amd64.deb) ... Selecting previously deselected package libglib2.0-data. Unpacking libglib2.0-data (from .../libglib2.0-data_2.26.0-0ubuntu1_all.deb) ... Selecting previously deselected package libglib2.0-bin. Unpacking libglib2.0-bin (from .../libglib2.0-bin_2.26.0-0ubuntu1_amd64.deb) ... Selecting previously deselected package libglib2.0-dev. Unpacking libglib2.0-dev (from .../libglib2.0-dev_2.26.0-0ubuntu1_amd64.deb) ... Selecting previously deselected package libcairo2-dev. Unpacking libcairo2-dev (from .../libcairo2-dev_1.10.0-1ubuntu3_amd64.deb) ... Selecting previously deselected package libfontenc1. Unpacking libfontenc1 (from .../libfontenc1_1%3a1.0.5-2_amd64.deb) ... Selecting previously deselected package libjpeg62-dev. Unpacking libjpeg62-dev (from .../libjpeg62-dev_6b-16.1_amd64.deb) ... Selecting previously deselected package libkpathsea5. Unpacking libkpathsea5 (from .../libkpathsea5_2009-7_amd64.deb) ... Selecting previously deselected package liblapack3gf. Unpacking liblapack3gf (from .../liblapack3gf_3.2.1-8_amd64.deb) ... Selecting previously deselected package liblapack-dev. Unpacking liblapack-dev (from .../liblapack-dev_3.2.1-8_amd64.deb) ... Selecting previously deselected package libncurses5-dev. Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100626-0ubuntu1_amd64.deb) ... Selecting previously deselected package libxft-dev. Unpacking libxft-dev (from .../libxft-dev_2.1.14-2ubuntu1_amd64.deb) ... Selecting previously deselected package libpango1.0-dev. Unpacking libpango1.0-dev (from .../libpango1.0-dev_1.28.1-1ubuntu3_amd64.deb) ... Selecting previously deselected package libpcrecpp0. Unpacking libpcrecpp0 (from .../libpcrecpp0_8.02-1_amd64.deb) ... Selecting previously deselected package libpcre3-dev. Unpacking libpcre3-dev (from .../libpcre3-dev_8.02-1_amd64.deb) ... Selecting previously deselected package libpoppler7. Unpacking libpoppler7 (from .../libpoppler7_0.14.3-0ubuntu1.1_amd64.deb) ... Selecting previously deselected package libreadline6-dev. Unpacking libreadline6-dev (from .../libreadline6-dev_6.1-3_amd64.deb) ... Selecting previously deselected package libreadline-dev. Unpacking libreadline-dev (from .../libreadline-dev_6.1-3_amd64.deb) ... Selecting previously deselected package libtiffxx0c2. Unpacking libtiffxx0c2 (from .../libtiffxx0c2_3.9.4-2_amd64.deb) ... Selecting previously deselected package libtiff4-dev. Unpacking libtiff4-dev (from .../libtiff4-dev_3.9.4-2_amd64.deb) ... Selecting previously deselected package x11proto-xext-dev. Unpacking x11proto-xext-dev (from .../x11proto-xext-dev_7.1.1-2_all.deb) ... Selecting previously deselected package libxext-dev. Unpacking libxext-dev (from .../libxext-dev_2%3a1.1.2-1_amd64.deb) ... Selecting previously deselected package libxfont1. Unpacking libxfont1 (from .../libxfont1_1%3a1.4.2-1_amd64.deb) ... Selecting previously deselected package libxss1. Unpacking libxss1 (from .../libxss1_1%3a1.2.0-2_amd64.deb) ... Selecting previously deselected package x11proto-scrnsaver-dev. Unpacking x11proto-scrnsaver-dev (from .../x11proto-scrnsaver-dev_1.2.0-2_all.deb) ... Selecting previously deselected package libxss-dev. Unpacking libxss-dev (from .../libxss-dev_1%3a1.2.0-2_amd64.deb) ... Selecting previously deselected package libxt-dev. Unpacking libxt-dev (from .../libxt-dev_1%3a1.0.7-1_amd64.deb) ... Selecting previously deselected package luatex. Unpacking luatex (from .../luatex_0.60.1-1build2_amd64.deb) ... Selecting previously deselected package openjdk-6-jdk. Unpacking openjdk-6-jdk (from .../openjdk-6-jdk_6b20-1.9.2-0ubuntu2_amd64.deb) ... Selecting previously deselected package tex-common. Unpacking tex-common (from .../tex-common_2.08_all.deb) ... Selecting previously deselected package preview-latex-style. Unpacking preview-latex-style (from .../preview-latex-style_11.85-1ubuntu1_all.deb) ... Selecting previously deselected package tcl8.5. Unpacking tcl8.5 (from .../tcl8.5_8.5.8-2build1_amd64.deb) ... Selecting previously deselected package tcl8.5-dev. Unpacking tcl8.5-dev (from .../tcl8.5-dev_8.5.8-2build1_amd64.deb) ... Selecting previously deselected package texi2html. Unpacking texi2html (from .../texi2html_1.82-1_all.deb) ... Selecting previously deselected package texinfo. Unpacking texinfo (from .../texinfo_4.13a.dfsg.1-5ubuntu1_amd64.deb) ... Selecting previously deselected package texlive-common. Unpacking texlive-common (from .../texlive-common_2009-10_all.deb) ... Selecting previously deselected package texlive-doc-base. Unpacking texlive-doc-base (from .../texlive-doc-base_2009-2_all.deb) ... Selecting previously deselected package texlive-binaries. Unpacking texlive-binaries (from .../texlive-binaries_2009-7_amd64.deb) ... Selecting previously deselected package texlive-base. Unpacking texlive-base (from .../texlive-base_2009-10_all.deb) ... Selecting previously deselected package texlive-extra-utils. Unpacking texlive-extra-utils (from .../texlive-extra-utils_2009-9ubuntu1_all.deb) ... Selecting previously deselected package texlive-fonts-recommended. Unpacking texlive-fonts-recommended (from .../texlive-fonts-recommended_2009-10_all.deb) ... Selecting previously deselected package texlive-generic-recommended. Unpacking texlive-generic-recommended (from .../texlive-generic-recommended_2009-10_all.deb) ... Selecting previously deselected package texlive-latex-base. Unpacking texlive-latex-base (from .../texlive-latex-base_2009-10_all.deb) ... Selecting previously deselected package texlive-pictures. Unpacking texlive-pictures (from .../texlive-pictures_2009-10_all.deb) ... Selecting previously deselected package texlive-latex-extra. Unpacking texlive-latex-extra (from .../texlive-latex-extra_2009-9ubuntu1_all.deb) ... Selecting previously deselected package texlive-latex-recommended. Unpacking texlive-latex-recommended (from .../texlive-latex-recommended_2009-10_all.deb) ... Selecting previously deselected package tk8.5. Unpacking tk8.5 (from .../tk8.5_8.5.8-1_amd64.deb) ... Selecting previously deselected package tk8.5-dev. Unpacking tk8.5-dev (from .../tk8.5-dev_8.5.8-1_amd64.deb) ... Selecting previously deselected package xdg-utils. Unpacking xdg-utils (from .../xdg-utils_1.0.2+cvs20100307-1ubuntu0.1_all.deb) ... Selecting previously deselected package xfonts-encodings. Unpacking xfonts-encodings (from .../xfonts-encodings_1%3a1.0.3-1_all.deb) ... Selecting previously deselected package xfonts-utils. Unpacking xfonts-utils (from .../xfonts-utils_1%3a7.5+2_amd64.deb) ... Selecting previously deselected package xfonts-base. Unpacking xfonts-base (from .../xfonts-base_1%3a1.0.1_all.deb) ... Selecting previously deselected package xserver-common. Unpacking xserver-common (from .../xserver-common_2%3a1.9.0-0ubuntu7.1_all.deb) ... Selecting previously deselected package xvfb. Unpacking xvfb (from .../xvfb_2%3a1.9.0-0ubuntu7.1_amd64.deb) ... Selecting previously deselected package liblzma-dev. Unpacking liblzma-dev (from .../liblzma-dev_4.999.9beta+20100527-1_amd64.deb) ... Processing triggers for libglib2.0-0 ... No schema files found: doing nothing. Setting up libice6 (2:1.0.6-1) ... Setting up x11proto-core-dev (7.0.17-1) ... Setting up libice-dev (2:1.0.6-1) ... Setting up libxau6 (1:1.0.6-1) ... Setting up libxdmcp6 (1:1.0.3-2) ... Setting up libxcb1 (1.6-1) ... Setting up libx11-data (2:1.3.3-3ubuntu1) ... Setting up libx11-6 (2:1.3.3-3ubuntu1) ... Setting up libxau-dev (1:1.0.6-1) ... Setting up libxdmcp-dev (1:1.0.3-2) ... Setting up x11proto-input-dev (2.0-2) ... Setting up x11proto-kb-dev (1.0.4-1) ... Setting up xtrans-dev (1.2.5-1) ... Setting up libpthread-stubs0 (0.3-2) ... Setting up libpthread-stubs0-dev (0.3-2) ... Setting up libxcb1-dev (1.6-1) ... Setting up libx11-dev (2:1.3.3-3ubuntu1) ... Setting up libxext6 (2:1.1.2-1) ... Setting up libsm6 (2:1.1.1-1) ... Setting up libxt6 (1:1.0.7-1) ... Setting up libxmu6 (2:1.0.5-1) ... Setting up libxpm4 (1:3.5.8-1) ... Setting up libxaw7 (2:1.0.7-1) ... Setting up libxkbfile1 (1:1.0.6-2) ... Setting up x11-xkb-utils (7.5+5) ... Setting up libmagic1 (5.03-5ubuntu1) ... Setting up file (5.03-5ubuntu1) ... Setting up libexpat1 (2.0.1-7ubuntu1) ... Setting up libnewt0.52 (0.52.11-1) ... Setting up libpopt0 (1.16-1) ... Setting up libsqlite3-0 (3.7.2-1ubuntu0.1) ... Setting up mime-support (3.48-1ubuntu2) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.6 (2.6.6-5ubuntu1) ... Setting up python (2.6.6-2ubuntu2) ... Setting up ucf (3.0025) ... Setting up whiptail (0.52.11-1) ... Setting up xkb-data (1.8-1ubuntu8) ... Setting up bsdmainutils (8.0.11ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up ed (1.4-1build1) ... Setting up ttf-dejavu-core (2.31-1) ... Setting up fontconfig-config (2.8.0-2ubuntu1) ... Setting up gettext-base (0.18.1.1-1ubuntu2) ... Setting up groff-base (1.20.1-10) ... Setting up libfreetype6 (2.4.2-2ubuntu0.1) ... Setting up libfontconfig1 (2.8.0-2ubuntu1) ... Setting up libpixman-1-0 (0.18.4-1) ... Setting up libxcb-render0 (1.6-1) ... Setting up libxcb-shm0 (1.6-1) ... Setting up libxrender1 (1:0.9.6-1) ... Setting up libcairo2 (1.10.0-1ubuntu3) ... Setting up libxml2 (2.7.7.dfsg-4ubuntu0.1) ... Setting up libxmuu1 (2:1.0.5-1) ... Setting up man-db (2.5.7-4) ... Building database of manual pages ... Setting up xauth (1:1.0.4-1) ... Setting up m4 (1.4.14-3) ... Setting up bison (1:2.4.1.dfsg-3) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode. Setting up tzdata-java (2010o-0ubuntu0.10.10) ... Setting up java-common (0.38) ... Setting up libavahi-common-data (0.6.27-2ubuntu3) ... Setting up libavahi-common3 (0.6.27-2ubuntu3) ... Setting up libavahi-client3 (0.6.27-2ubuntu3) ... Setting up libcups2 (1.4.4-6ubuntu2.3) ... Setting up liblcms1 (1.18.dfsg-1ubuntu2.10.10.1) ... Setting up libjpeg62 (6b-16.1) ... Setting up libnspr4-0d (4.8.6-0ubuntu1) ... Setting up libnss3-1d (3.12.8-0ubuntu0.10.10.1) ... Setting up html2text (1.3.2a-15) ... Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-1) ... Setting up gettext (0.18.1.1-1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16) ... Setting up debhelper (8.0.0ubuntu1) ... Setting up defoma (0.11.11ubuntu1) ... Setting up fontconfig (2.8.0-2ubuntu1) ... Updating font configuration of fontconfig... Cleaning up category cid.. Cleaning up category truetype.. Cleaning up category type1.. Updating category type1.. Updating category truetype.. Updating category cid.. Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libgfortran3 (4.5.1-7ubuntu2) ... Setting up gfortran-4.4 (4.4.4-14ubuntu5) ... Setting up gfortran (4:4.4.4-1ubuntu2) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode. Setting up libpython2.6 (2.6.6-5ubuntu1) ... Setting up libasound2 (1.0.23-1ubuntu2.1) ... Setting up libgif4 (4.1.6-9) ... Setting up libogg0 (1.2.0~dfsg-1) ... Setting up libflac8 (1.2.1-3) ... Setting up libvorbis0a (1.3.1-1ubuntu1~ppa1~maverick1) ... Setting up libvorbisenc2 (1.3.1-1ubuntu1~ppa1~maverick1) ... Setting up libsndfile1 (1.0.21-2) ... Setting up libwrap0 (7.6.q-19) ... Setting up libx11-xcb1 (2:1.3.3-3ubuntu1) ... Setting up libxcb-atom1 (0.3.6-1build1) ... Setting up libxi6 (2:1.3-4) ... Setting up libxtst6 (2:1.1.0-3) ... Setting up libpulse0 (1:0.9.22~0.9.21+stable-queue-32-g8478-0ubuntu21.1) ... Setting up libatk1.0-0 (1.32.0-0ubuntu1) ... Setting up libgtk2.0-common (2.22.0-0ubuntu1) ... Setting up libjasper1 (1.900.1-7) ... Setting up libtiff4 (3.9.4-2) ... Setting up libgdk-pixbuf2.0-0 (2.22.0-0ubuntu1) ... Setting up libpango1.0-common (1.28.1-1ubuntu3) ... Cleaning up font configuration of pango... Updating font configuration of pango... Cleaning up category xfont.. Updating category xfont.. *** You don't have any defomized font packages. *** So we are trying to force to generate pangox.aliases... Setting up libdatrie1 (0.2.3-1) ... Setting up libthai-data (0.1.14-2) ... Setting up libthai0 (0.1.14-2) ... Setting up libxft2 (2.1.14-2ubuntu1) ... Setting up libpango1.0-0 (1.28.1-1ubuntu3) ... Setting up libxfixes3 (1:4.0.5-1) ... Setting up libxcomposite1 (1:0.4.2-1) ... Setting up libxcursor1 (1:1.1.10-2) ... Setting up libxdamage1 (1:1.1.3-1) ... Setting up libxinerama1 (2:1.1-3) ... Setting up libxrandr2 (2:1.3.0-3) ... Setting up shared-mime-info (0.71-3) ... Setting up libgtk2.0-0 (2.22.0-0ubuntu1) ... Setting up libblas3gf (1.2-7) ... update-alternatives: using /usr/lib/libblas/libblas.so.3gf to provide /usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode. Setting up libblas-dev (1.2-7) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode. Setting up libbz2-dev (1.0.5-4ubuntu1) ... Setting up libcairo-gobject2 (1.10.0-1ubuntu3) ... Setting up libexpat1-dev (2.0.1-7ubuntu1) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3ubuntu1) ... Setting up libfreetype6-dev (2.4.2-2ubuntu0.1) ... Setting up pkg-config (0.25-1) ... Setting up libfontconfig1-dev (2.8.0-2ubuntu1) ... Setting up x11proto-render-dev (2:0.11-1) ... Setting up libxrender-dev (1:0.9.6-1) ... Setting up libpng12-dev (1.2.44-1) ... Setting up libsm-dev (2:1.1.1-1) ... Setting up libpixman-1-dev (0.18.4-1) ... Setting up libxcb-render0-dev (1.6-1) ... Setting up libxcb-shm0-dev (1.6-1) ... Setting up libglib2.0-data (2.26.0-0ubuntu1) ... Setting up libglib2.0-bin (2.26.0-0ubuntu1) ... Setting up libglib2.0-dev (2.26.0-0ubuntu1) ... Setting up libcairo2-dev (1.10.0-1ubuntu3) ... Setting up libfontenc1 (1:1.0.5-2) ... Setting up libjpeg62-dev (6b-16.1) ... Setting up libkpathsea5 (2009-7) ... Setting up liblapack3gf (3.2.1-8) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode. Setting up liblapack-dev (3.2.1-8) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode. Setting up libncurses5-dev (5.7+20100626-0ubuntu1) ... Setting up libxft-dev (2.1.14-2ubuntu1) ... Setting up libpango1.0-dev (1.28.1-1ubuntu3) ... Setting up libpcrecpp0 (8.02-1) ... Setting up libpcre3-dev (8.02-1) ... Setting up libpoppler7 (0.14.3-0ubuntu1.1) ... Setting up libreadline6-dev (6.1-3) ... Setting up libreadline-dev (6.1-3) ... Setting up libtiffxx0c2 (3.9.4-2) ... Setting up libtiff4-dev (3.9.4-2) ... Setting up x11proto-xext-dev (7.1.1-2) ... Setting up libxext-dev (2:1.1.2-1) ... Setting up libxfont1 (1:1.4.2-1) ... Setting up libxss1 (1:1.2.0-2) ... Setting up x11proto-scrnsaver-dev (1.2.0-2) ... Setting up libxss-dev (1:1.2.0-2) ... Setting up libxt-dev (1:1.0.7-1) ... Setting up luatex (0.60.1-1build2) ... texlive-base is not ready, cannot create formats Setting up tex-common (2.08) ... Creating config file /etc/texmf/texmf.d/05TeXMF.cnf with new version Creating config file /etc/texmf/texmf.d/15Plain.cnf with new version Creating config file /etc/texmf/texmf.d/45TeXinputs.cnf with new version Creating config file /etc/texmf/texmf.d/55Fonts.cnf with new version Creating config file /etc/texmf/texmf.d/65BibTeX.cnf with new version Creating config file /etc/texmf/texmf.d/75DviPS.cnf with new version Creating config file /etc/texmf/texmf.d/80DVIPDFMx.cnf with new version Creating config file /etc/texmf/texmf.d/85Misc.cnf with new version Creating config file /etc/texmf/texmf.d/90TeXDoc.cnf with new version Creating config file /etc/texmf/texmf.d/95NonPath.cnf with new version Creating config file /etc/texmf/updmap.d/00updmap.cfg with new version Creating config file /etc/texmf/texmf.cnf with new version Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up preview-latex-style (11.85-1ubuntu1) ... Setting up tcl8.5 (8.5.8-2build1) ... update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode. Setting up tcl8.5-dev (8.5.8-2build1) ... Setting up texi2html (1.82-1) ... Setting up texinfo (4.13a.dfsg.1-5ubuntu1) ... Running mktexlsr. This may take some time. ... done. Setting up texlive-common (2009-10) ... Setting up texlive-doc-base (2009-2) ... Setting up texlive-binaries (2009-7) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode. update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode. Building format(s) --refresh. This may take some time... done. Setting up tk8.5 (8.5.8-1) ... update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode. Setting up tk8.5-dev (8.5.8-1) ... Setting up xdg-utils (1.0.2+cvs20100307-1ubuntu0.1) ... Setting up xfonts-encodings (1:1.0.3-1) ... Setting up xfonts-utils (1:7.5+2) ... Setting up xfonts-base (1:1.0.1) ... Setting up xserver-common (2:1.9.0-0ubuntu7.1) ... Setting up xvfb (2:1.9.0-0ubuntu7.1) ... Setting up liblzma-dev (4.999.9beta+20100527-1) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2009-10) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Building e-tex based formats --byhyphen /var/lib/texmf/tex/generic/config/language.def. This may take some time... done. Setting up texlive-generic-recommended (2009-10) ... Setting up texlive-latex-base (2009-10) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Setting up texlive-pictures (2009-10) ... Setting up texlive-extra-utils (2009-9ubuntu1) ... Setting up texlive-fonts-recommended (2009-10) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Setting up texlive-latex-extra (2009-9ubuntu1) ... Setting up texlive-latex-recommended (2009-10) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Setting up ca-certificates-java (20100412) ... creating /etc/ssl/certs/java/cacerts... done. Setting up openjdk-6-jre-headless (6b20-1.9.2-0ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/java to provide /usr/bin/java (java) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode. Setting up openjdk-6-jre-lib (6b20-1.9.2-0ubuntu2) ... Setting up libaccess-bridge-java (1.26.2-5) ... Setting up libaccess-bridge-java-jni (1.26.2-5) ... Setting up openjdk-6-jre (6b20-1.9.2-0ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/javaws to provide /usr/bin/javaws (javaws) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/pluginappletviewer to provide /usr/bin/pluginappletviewer (pluginappletviewer) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode. Setting up openjdk-6-jdk (6b20-1.9.2-0ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/apt to provide /usr/bin/apt (apt) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jar to provide /usr/bin/jar (jar) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/javac to provide /usr/bin/javac (javac) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/javah to provide /usr/bin/javah (javah) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/javap to provide /usr/bin/javap (javap) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jps to provide /usr/bin/jps (jps) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode. Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.12.1-0ubuntu10.1 make_3.81-8 dpkg-dev_1.15.8.4ubuntu3.1 gcc-4.4_4.4.4-14ubuntu5 g++-4.4_4.4.4-14ubuntu5 binutils_2.20.51.20100908-0ubuntu2 libstdc++6-4.4-dev_4.4.4-14ubuntu5 libstdc++6_4.5.1-7ubuntu2 ------------------------------------------------------------------------------ gpgv: Signature made Fri Jan 14 02:08:33 2011 UTC using DSA key ID CC964518 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./r-base_2.12.1-1~ppa1~maverick1.dsc dpkg-source: info: extracting r-base in r-base-2.12.1 dpkg-source: info: unpacking r-base_2.12.1.orig.tar.gz dpkg-source: info: applying r-base_2.12.1-1~ppa1~maverick1.diff.gz dpkg-source: info: upstream files that have been modified: r-base-2.12.1/configure r-base-2.12.1/m4/R.m4 dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions dpkg-buildpackage: source package r-base dpkg-buildpackage: source version 2.12.1-1~ppa1~maverick1 dpkg-source --before-build r-base-2.12.1 dpkg-buildpackage: host architecture amd64 /usr/bin/fakeroot debian/rules clean *** clean *** dh_testdir dh_testroot rm -f configure-stamp \ build-stamp build-indep-stamp build-arch-stamp \ make-stamp make-arch-stamp make-indep-stamp \ install-indep-stamp install-arch-stamp \ check-stamp [ ! -f Makefile ] || /usr/bin/make distclean rm -f `find . -name "*~"` rm -rf debian/tmp debian/files* core debian/substvars rm -f doc/html/function.html doc/html/packages.html rm -f modules/*.so src/unix/Rscript dh_clean debian/rules build *** configure *** #automake #autoconf dh_testdir R_PAPERSIZE=letter \ R_BROWSER=xdg-open \ PAGER=/usr/bin/pager \ PERL=/usr/bin/perl \ R_UNZIPCMD=/usr/bin/unzip \ R_ZIPCMD=/usr/bin/zip \ R_PRINTCMD=/usr/bin/lpr \ LIBnn=lib \ AWK=/usr/bin/awk \ CC=gcc \ CXX=g++ \ F77=gfortran \ FC=gfortran \ CFLAGS="-std=gnu99 -O3 -pipe -g" \ CXXFLAGS="-O3 -pipe -g" \ FFLAGS="-O3 -pipe -g" \ FCFLAGS="-O3 -pipe -g" \ CPPFLAGS= \ LDFLAGS= \ FLIBS= \ rsharedir=/usr/share/R/share \ rincludedir=/usr/share/R/include \ rdocdir=/usr/share/R/doc \ ./configure --prefix=/usr \ --with-cairo \ --with-jpeglib \ --with-readline \ --with-tcltk \ --with-system-bzlib \ --with-system-pcre \ --with-system-zlib \ --mandir=/usr/share/man \ --infodir=/usr/share/info \ --datadir=/usr/share/R/share \ --includedir=/usr/share/R/include \ --with-blas \ --with-lapack \ --enable-R-profiling \ --enable-R-shlib \ --enable-memory-profiling \ --without-recommended-packages \ --build x86_64-linux-gnu checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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... missing checking for working autoconf... missing checking for working automake... missing checking for working autoheader... missing checking for gawk... /usr/bin/awk checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking for bison... bison -y checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for tr... /usr/bin/tr checking for which... /usr/bin/which checking for /usr/bin/pager... /usr/bin/pager checking for /usr/bin/perl... /usr/bin/perl checking whether perl version is at least 5.8.0... yes checking for gtar... no checking for gnutar... no checking for tar... /bin/tar checking for tex... /usr/bin/tex checking for latex... /usr/bin/latex 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... yes checking for install-info... /usr/sbin/install-info checking for texi2dvi... /usr/bin/texi2dvi checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip checking for bzip2... /bin/bzip2 using default browser ... xdg-open checking for acroread... no checking for acroread4... no checking for xdg-open... /usr/bin/xdg-open checking for pkg-config... /usr/bin/pkg-config checking for gcc... 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking whether gcc needs -traditional... no checking how to run the C preprocessor... gcc -E defining F77 to be gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc accepts -fvisibility... yes checking whether gfortran 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 gcc... gcc checking whether we are using the GNU Objective C compiler... no checking whether gcc accepts -g... no checking for Objective C++ compiler... trying some possibilities checking whether g++ can compile ObjC++... no checking whether can compile ObjC++... no no working 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 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... 3458764513820540925 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 objdump... objdump checking how to recognize dependent libraries... pass_all checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU Fortran 77 compiler... (cached) yes checking whether gfortran accepts -g... (cached) yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the 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 g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the 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 gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for 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 whether time.h and sys/time.h may both be included... 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 locale.h usability... yes checking locale.h presence... yes checking for locale.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 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/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/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... 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 time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) 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 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 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 gcc option to accept ISO C99... none needed checking for 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 long double... 16 checking size of size_t... 8 checking whether we can compute C Make dependencies... yes, using gcc -MM checking whether gcc supports -c -o FILE.lo... yes checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5 -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../.. -lgfortranbegin -lgfortran -lm checking how to get verbose linking output from gcc... -v checking for C libraries of gcc... -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5 -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../.. -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 gfortran appends underscores to external names... yes checking whether gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether gfortran and gcc agree on int and double... yes checking whether gfortran and gcc agree on double complex... yes checking whether g++ accepts -M for generating dependencies... yes checking whether we can compute ObjC Make dependencies... no checking whether C runtime needs -D__NO_MATH_INLINES... no checking for xmkmf... no checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether rint exists and is declared... yes checking for fseeko... yes checking for ftello... yes checking for isblank... 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 sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether va_copy exists and is declared... yes checking whether __va_copy exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether setenv exists and is declared... yes checking whether system exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether strcoll exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether times exists and is declared... yes checking whether time exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether getuid 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 for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for acosh... yes checking for asinh... yes checking for atanh... yes checking for mkdtemp... yes checking for snprintf... yes checking for strdup... yes checking for strncasecmp... yes checking for vsnprintf... yes checking whether acosh is declared... yes checking whether asinh is declared... yes checking whether atanh is declared... yes checking whether mkdtemp is declared... yes checking whether snprintf is declared... yes checking whether strdup is declared... yes checking whether strncasecmp is declared... yes checking whether vsnprintf is declared... yes checking for library containing connect... none required checking for library containing gethostbyname... none required checking for library containing xdr_string... none required checking for __setfpucw... no checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking whether mktime sets errno... no checking whether C99 double complex is supported... checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for double complex... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking whether cacosh exists and is declared... yes checking whether casinh exists and is declared... yes checking whether catanh exists and is declared... yes checking whether C99 double complex is compatible with Rcomplex... yes yes checking for cblas_cdotu_sub in vecLib framework... no checking for dgemm_... no checking for ATL_xerbla in -latlas... no checking for dgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for dgemm_ in -lblas... (cached) yes checking for dgemm_ in -lessl... no checking for dgemm_ in -lblas... (cached) yes checking whether double complex BLAS can be used... yes checking whether the BLAS is complete... yes checking for zgeev_... no checking for zgeev_ in -llapack... yes checking iconv.h usability... yes checking iconv.h presence... yes checking for iconv.h... yes checking for iconv... yes checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes checking for iconvlist... no checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking wctype.h usability... yes checking wctype.h presence... yes checking for wctype.h... yes checking whether mbrtowc exists and is declared... yes checking whether wcrtomb exists and is declared... yes checking whether wcscoll exists and is declared... yes checking whether wcsftime exists and is declared... yes checking whether wcstod exists and is declared... yes checking whether mbstowcs exists and is declared... yes checking whether wcstombs exists and is declared... yes checking whether wctrans exists and is declared... yes checking whether iswblank exists and is declared... yes checking whether wctype exists and is declared... yes checking whether iswctype exists and is declared... yes checking for wctrans_t... yes checking for mbstate_t... yes checking for ICU... no checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking for XtToolkitInitialize in -lXt... yes using X11 ... yes checking for KeySym... yes checking X11/Xmu/Atoms.h usability... no checking X11/Xmu/Atoms.h presence... no checking for X11/Xmu/Atoms.h... no checking whether pkg-config knows about cairo and pango... yes checking whether cairo including pango is >= 1.2 and works... yes checking for tclConfig.sh... no checking for tclConfig.sh in library (sub)directories... /usr/lib/tcl8.5/tclConfig.sh checking for tkConfig.sh... no checking for tkConfig.sh in library (sub)directories... /usr/lib/tk8.5/tkConfig.sh checking tcl.h usability... yes checking tcl.h presence... yes checking for tcl.h... yes checking tk.h usability... yes checking tk.h presence... yes checking for tk.h... yes checking whether compiling/linking Tcl/Tk code works... yes checking for BSD networking... yes checking if jpeglib version >= 6b... yes checking for jpeg_destroy_compress in -ljpeg... yes checking for main in -lz... yes checking if libpng version >= 1.0.5... yes checking for png_create_write_struct in -lpng... yes checking tiffio.h usability... yes checking tiffio.h presence... yes checking for tiffio.h... yes checking for TIFFOpen in -ltiff... yes checking rpc/types.h usability... yes checking rpc/types.h presence... yes checking for rpc/types.h... yes checking for rpc/xdr.h... yes checking for XDR support... yes checking for gzeof in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version == 1.2.3... yes checking whether zlib support needs to be compiled... no checking for BZ2_bzlibVersion in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking if bzip2 version >= 1.0.6... yes checking whether bzip2 support needs to be compiled... no checking for lzma_version_number in -llzma... yes checking lzma.h usability... yes checking lzma.h presence... yes checking for lzma.h... yes checking if lzma version >= 4.999... yes checking for pcre_fullinfo in -lpcre... yes checking pcre.h usability... yes checking pcre.h presence... yes checking for pcre.h... yes checking pcre/pcre.h usability... no checking pcre/pcre.h presence... no checking for pcre/pcre.h... no checking if PCRE version >= 7.6... yes checking whether PCRE support needs to be compiled... no checking whether leap seconds are treated according to POSIX... yes checking for setitimer... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking whether KERN_USRSTACK sysctl is supported... no checking for visible __lib_stack_end... yes checking for paperconf... false checking for java... /usr/bin/java checking for javac... /usr/bin/javac checking for javah... /usr/bin/javah checking for jar... /usr/bin/jar checking whether Java compiler works... yes checking whether Java compiler works for version 1.4... yes checking whether Java interpreter works... yes checking Java environment... /usr/lib/jvm/java-6-openjdk/jre checking for cached Java settings... no checking whether JNI programs can be compiled... yes checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking whether we are using the GNU Fortran compiler... (cached) yes checking whether gfortran accepts -g... (cached) yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking whether NLS is requested... yes checking whether make sets $(MAKE)... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for msgfmt... /usr/bin/msgfmt checking for gmsgfmt... /usr/bin/msgfmt checking for xgettext... /usr/bin/xgettext checking for msgmerge... /usr/bin/msgmerge checking whether we are using the GNU C Library 2 or newer... yes checking for ranlib... (cached) ranlib checking for simple visibility declarations... yes checking for inline... inline checking for stdint.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... yes checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... yes checking for iconv declaration... install-shextern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 2.4.1, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... (cached) yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for shared library run path origin... done checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc using as R_SHELL for scripts ... /bin/bash 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/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile.in config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/bzip2/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/pcre/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/extra/xz/Makefile config.status: creating src/extra/zlib/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/modules/vfonts/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/Rdiff config.status: creating src/scripts/Sd2Rd config.status: creating src/scripts/f77_f2c config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tests/Native/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing po-directories commands config.status: creating po/POTFILES config.status: creating po/Makefile config.status: executing stamp-h commands R is now configured for x86_64-pc-linux-gnu Source directory: . Installation directory: /usr C compiler: gcc -std=gnu99 -O3 -pipe -g Fortran 77 compiler: gfortran -O3 -pipe -g C++ compiler: g++ -O3 -pipe -g Fortran 90/95 compiler: gfortran -O3 -pipe -g Obj-C compiler: Interfaces supported: X11, tcltk External libraries: readline, BLAS(generic), LAPACK(generic), lzma Additional capabilities: PNG, JPEG, TIFF, NLS, cairo Options enabled: shared R library, R profiling, memory profiling, Java Recommended packages: no touch configure-stamp *** make-arch *** /usr/bin/make CFLAGS="-std=gnu99 -O3 -pipe -g" \ CXXFLAGS="-O3 -pipe -g" \ FFLAGS="-O3 -pipe -g" \ FCFLAGS="-O3 -pipe -g" \ CC=gcc \ CXX=g++ \ F77=gfortran \ LDFLAGS="-Wl,-O1" \ R make[1]: Entering directory `/build/buildd/r-base-2.12.1' make[2]: Entering directory `/build/buildd/r-base-2.12.1/m4' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/m4' make[2]: Entering directory `/build/buildd/r-base-2.12.1/tools' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/tools' make[2]: Entering directory `/build/buildd/r-base-2.12.1/doc' make[3]: Entering directory `/build/buildd/r-base-2.12.1/doc/html' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/doc/html' make[3]: Entering directory `/build/buildd/r-base-2.12.1/doc/manual' make[3]: Nothing to be done for `R'. make[3]: Leaving directory `/build/buildd/r-base-2.12.1/doc/manual' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/doc' make[2]: Entering directory `/build/buildd/r-base-2.12.1/etc' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/etc' make[2]: Entering directory `/build/buildd/r-base-2.12.1/share' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/share' make[2]: Entering directory `/build/buildd/r-base-2.12.1/src' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/scripts' creating src/scripts/R.fe make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/scripts' mkdir -p -- ../../bin make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/scripts' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/scripts' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/include' mkdir -p -- ../../include make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/include/R_ext' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/include' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/extra' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[5]: Entering directory `/build/buildd/r-base-2.12.1/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-parse.d from tre-parse.c making tre-stack.d from tre-stack.c making xmalloc.d from xmalloc.c make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/tre' gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c regerror.c -o regerror.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c regexec.c -o regexec.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c tre-stack.c -o tre-stack.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -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[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/appl' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/appl' making bakslv.d from bakslv.c making binning.d from binning.c making cpoly.d from cpoly.c making cumsum.d from cumsum.c making fft.d from fft.c making fmin.d from fmin.c making integrate.d from integrate.c making interv.d from interv.c making lbfgsb.d from lbfgsb.c making machar.d from machar.c making maxcol.d from maxcol.c making pretty.d from pretty.c making rcont.d from rcont.c making rowsum.d from rowsum.c making stem.d from stem.c making strsignif.d from strsignif.c making tabulate.d from tabulate.c making uncmin.d from uncmin.c making zeroin.d from zeroin.c make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/appl' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/appl' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c bakslv.c -o bakslv.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c binning.c -o binning.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c cpoly.c -o cpoly.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c cumsum.c -o cumsum.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c fft.c -o fft.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c fmin.c -o fmin.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c integrate.c -o integrate.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c interv.c -o interv.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c lbfgsb.c -o lbfgsb.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c machar.c -o machar.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c maxcol.c -o maxcol.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pretty.c -o pretty.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rcont.c -o rcont.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rowsum.c -o rowsum.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c stem.c -o stem.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c strsignif.c -o strsignif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c tabulate.c -o tabulate.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c uncmin.c -o uncmin.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c zeroin.c -o zeroin.o gfortran -fpic -O3 -pipe -g -c ch2inv.f -o ch2inv.o gfortran -fpic -O3 -pipe -g -c chol.f -o chol.o gfortran -fpic -O3 -pipe -g -c dchdc.f -o dchdc.o gfortran -fpic -O3 -pipe -g -c dpbfa.f -o dpbfa.o gfortran -fpic -O3 -pipe -g -c dpbsl.f -o dpbsl.o gfortran -fpic -O3 -pipe -g -c dpoco.f -o dpoco.o gfortran -fpic -O3 -pipe -g -c dpodi.f -o dpodi.o gfortran -fpic -O3 -pipe -g -c dpofa.f -o dpofa.o gfortran -fpic -O3 -pipe -g -c dposl.f -o dposl.o gfortran -fpic -O3 -pipe -g -c dqrdc.f -o dqrdc.o gfortran -fpic -O3 -pipe -g -c dqrdc2.f -o dqrdc2.o gfortran -fpic -O3 -pipe -g -c dqrls.f -o dqrls.o gfortran -fpic -O3 -pipe -g -c dqrsl.f -o dqrsl.o gfortran -fpic -O3 -pipe -g -c dqrutl.f -o dqrutl.o gfortran -fpic -O3 -pipe -g -c dsvdc.f -o dsvdc.o gfortran -fpic -O3 -pipe -g -c dtrco.f -o dtrco.o gfortran -fpic -O3 -pipe -g -c dtrsl.f -o dtrsl.o gfortran -fpic -O3 -pipe -g -c eigen.f -o eigen.o rm -f libappl.a ar cr libappl.a bakslv.o binning.o cpoly.o cumsum.o fft.o fmin.o integrate.o interv.o lbfgsb.o machar.o maxcol.o pretty.o rcont.o rowsum.o stem.o strsignif.o tabulate.o uncmin.o zeroin.o ch2inv.o chol.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 eigen.o ranlib libappl.a make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/appl' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/appl' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath' make[4]: Entering directory `/build/buildd/r-base-2.12.1/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 fround.d from fround.c making ftrunc.d from ftrunc.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 bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.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 dlnorm.d from dlnorm.c making plnorm.d from plnorm.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 qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.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[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c mlutils.c -o mlutils.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c d1mach.c -o d1mach.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c i1mach.c -o i1mach.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c fmax2.c -o fmax2.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c fmin2.c -o fmin2.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c fprec.c -o fprec.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c fround.c -o fround.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c ftrunc.c -o ftrunc.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c sign.c -o sign.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c fsign.c -o fsign.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c imax2.c -o imax2.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c imin2.c -o imin2.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c chebyshev.c -o chebyshev.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c log1p.c -o log1p.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c expm1.c -o expm1.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c lgammacor.c -o lgammacor.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c gammalims.c -o gammalims.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c stirlerr.c -o stirlerr.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c bd0.c -o bd0.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c gamma.c -o gamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c lgamma.c -o lgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c gamma_cody.c -o gamma_cody.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c beta.c -o beta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c lbeta.c -o lbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c polygamma.c -o polygamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c bessel_i.c -o bessel_i.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c bessel_j.c -o bessel_j.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c bessel_k.c -o bessel_k.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c bessel_y.c -o bessel_y.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c choose.c -o choose.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c snorm.c -o snorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c sexp.c -o sexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dgamma.c -o dgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pgamma.c -o pgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qgamma.c -o qgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rgamma.c -o rgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dbeta.c -o dbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pbeta.c -o pbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qbeta.c -o qbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rbeta.c -o rbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dunif.c -o dunif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c punif.c -o punif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qunif.c -o qunif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c runif.c -o runif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dnorm.c -o dnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pnorm.c -o pnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qnorm.c -o qnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rnorm.c -o rnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dlnorm.c -o dlnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c plnorm.c -o plnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qlnorm.c -o qlnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rlnorm.c -o rlnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c df.c -o df.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pf.c -o pf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qf.c -o qf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rf.c -o rf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dnf.c -o dnf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dt.c -o dt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pt.c -o pt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qt.c -o qt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rt.c -o rt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dnt.c -o dnt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dchisq.c -o dchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pchisq.c -o pchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qchisq.c -o qchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rchisq.c -o rchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rnchisq.c -o rnchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dbinom.c -o dbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pbinom.c -o pbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qbinom.c -o qbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rbinom.c -o rbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rmultinom.c -o rmultinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dcauchy.c -o dcauchy.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pcauchy.c -o pcauchy.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qcauchy.c -o qcauchy.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rcauchy.c -o rcauchy.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dexp.c -o dexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pexp.c -o pexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qexp.c -o qexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rexp.c -o rexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dgeom.c -o dgeom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pgeom.c -o pgeom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qgeom.c -o qgeom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rgeom.c -o rgeom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dhyper.c -o dhyper.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c phyper.c -o phyper.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qhyper.c -o qhyper.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rhyper.c -o rhyper.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dnbinom.c -o dnbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pnbinom.c -o pnbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qnbinom.c -o qnbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rnbinom.c -o rnbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dpois.c -o dpois.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c ppois.c -o ppois.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qpois.c -o qpois.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rpois.c -o rpois.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dweibull.c -o dweibull.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pweibull.c -o pweibull.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qweibull.c -o qweibull.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rweibull.c -o rweibull.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dlogis.c -o dlogis.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c plogis.c -o plogis.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qlogis.c -o qlogis.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rlogis.c -o rlogis.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dnchisq.c -o dnchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pnchisq.c -o pnchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qnchisq.c -o qnchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dnbeta.c -o dnbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pnbeta.c -o pnbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qnbeta.c -o qnbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pnf.c -o pnf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c pnt.c -o pnt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qnf.c -o qnf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qnt.c -o qnt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c ptukey.c -o ptukey.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qtukey.c -o qtukey.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c toms708.c -o toms708.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c wilcox.c -o wilcox.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -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 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[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' config.status: creating src/unix/Makefile make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' making dynload.d from dynload.c making edit.d from edit.c making stubs.d from stubs.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 making aqua.d from aqua.c making Rembedded.d from Rembedded.c make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dynload.c -o dynload.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c edit.c -o edit.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c stubs.c -o stubs.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c system.c -o system.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c sys-unix.c -o sys-unix.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c sys-std.c -o sys-std.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c X11.c -o X11.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c aqua.c -o aqua.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c Rembedded.c -o Rembedded.o rm -rf libunix.a ar cr libunix.a dynload.o edit.o stubs.o system.o sys-unix.o sys-std.o X11.o aqua.o Rembedded.o ranlib libunix.a make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -DR_HOME='"/build/buildd/r-base-2.12.1"' -o Rscript \ ./Rscript.c make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/main' config.status: creating src/main/Makefile make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/main' making CConverters.d from CConverters.c 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 base.d from base.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 cov.d from cov.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 deriv.d from deriv.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 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 fourier.d from fourier.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.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 model.d from model.c making names.d from names.c making objects.d from objects.c making optim.d from optim.c making optimize.d from optimize.c making options.d from options.c making par.d from par.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 size.d from size.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 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 acosh.d from acosh.c making asinh.d from asinh.c making atanh.d from atanh.c making mkdtemp.d from mkdtemp.c making snprintf.d from snprintf.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c making vsnprintf.d from vsnprintf.c making xspline.d from xspline.c make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/main' gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c CConverters.c -o CConverters.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c CommandLineArgs.c -o CommandLineArgs.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c Rdynload.c -o Rdynload.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c Renviron.c -o Renviron.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c RNG.c -o RNG.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c agrep.c -o agrep.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c apply.c -o apply.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c arithmetic.c -o arithmetic.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c array.c -o array.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c attrib.c -o attrib.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c base.c -o base.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c bind.c -o bind.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c builtin.c -o builtin.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c character.c -o character.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c coerce.c -o coerce.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c colors.c -o colors.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c complex.c -o complex.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c connections.c -o connections.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c context.c -o context.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c cov.c -o cov.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c cum.c -o cum.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dcf.c -o dcf.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c datetime.c -o datetime.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c debug.c -o debug.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c deparse.c -o deparse.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c deriv.c -o deriv.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c devices.c -o devices.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dotcode.c -o dotcode.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dounzip.c -o dounzip.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dstruct.c -o dstruct.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c duplicate.c -o duplicate.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c engine.c -o engine.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c envir.c -o envir.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c errors.c -o errors.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c eval.c -o eval.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c format.c -o format.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c fourier.c -o fourier.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c gevents.c -o gevents.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c gram.c -o gram.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c gram-ex.c -o gram-ex.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c gramLatex.c -o gramLatex.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c gramRd.c -o gramRd.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c graphics.c -o graphics.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c grep.c -o grep.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c identical.c -o identical.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c inlined.c -o inlined.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c inspect.c -o inspect.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c internet.c -o internet.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c iosupport.c -o iosupport.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c lapack.c -o lapack.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c list.c -o list.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c localecharset.c -o localecharset.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c logic.c -o logic.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c main.c -o main.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c mapply.c -o mapply.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c match.c -o match.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c memory.c -o memory.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c model.c -o model.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c names.c -o names.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c objects.c -o objects.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c optim.c -o optim.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c optimize.c -o optimize.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c options.c -o options.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c par.c -o par.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c paste.c -o paste.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c platform.c -o platform.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c plot.c -o plot.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c plot3d.c -o plot3d.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c plotmath.c -o plotmath.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c print.c -o print.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c printarray.c -o printarray.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c printvector.c -o printvector.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c printutils.c -o printutils.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c qsort.c -o qsort.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c random.c -o random.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c raw.c -o raw.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c registration.c -o registration.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c relop.c -o relop.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rlocale.c -o rlocale.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c saveload.c -o saveload.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c scan.c -o scan.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c seq.c -o seq.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c serialize.c -o serialize.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c size.c -o size.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c sort.c -o sort.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c source.c -o source.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c split.c -o split.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c sprintf.c -o sprintf.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c startup.c -o startup.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c subassign.c -o subassign.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c subscript.c -o subscript.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c subset.c -o subset.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c summary.c -o summary.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c sysutils.c -o sysutils.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c unique.c -o unique.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c util.c -o util.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c version.c -o version.o gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c vfonts.c -o vfonts.o gfortran -fpic -O3 -pipe -g -c xxxpr.f -o xxxpr.o gcc -shared -Wl,-O1 -o libR.so CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o gramLatex.o gramRd.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 model.o names.o objects.o optim.o optimize.o options.o par.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 size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o ../unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a ../extra/tre/libtre.a -lblas -lgfortran -lm -lreadline -lpcre -llzma -lbz2 -lz -ldl -lm make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/main' mkdir -p -- /build/buildd/r-base-2.12.1/bin/exec mkdir -p -- /build/buildd/r-base-2.12.1/lib make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/main' gcc -I../../src/extra -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c Rmain.c -o Rmain.o gcc -Wl,--export-dynamic -Wl,-O1 -o R.bin Rmain.o -L../../lib -lR make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/main' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/modules' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/internet' making Rhttpd.d from Rhttpd.c making Rsock.d from Rsock.c making internet.d from internet.c making nanoftp.d from nanoftp.c making nanohttp.d from nanohttp.c making sock.d from sock.c making sockconn.d from sockconn.c make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/internet' gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c internet.c -o internet.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c nanoftp.c -o nanoftp.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c nanohttp.c -o nanohttp.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c sock.c -o sock.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -shared -Wl,-O1 -o internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o sockconn.o -L../../../lib -lR make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/internet' mkdir -p -- /build/buildd/r-base-2.12.1/modules make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/lapack' making Lapack.d from Lapack.c make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/lapack' gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c Lapack.c -o Lapack.o gcc -shared -Wl,-O1 -o lapack.so Lapack.o -L../../../lib -lR -llapack -lblas -lgfortran -lm make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c g_alab_her.c -o g_alab_her.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c g_cntrlify.c -o g_cntrlify.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c g_fontdb.c -o g_fontdb.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c g_her_glyph.c -o g_her_glyph.o gcc -shared -Wl,-O1 -o vfonts.so g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o -L../../../lib -lR -lm make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/X11' making dataentry.d from dataentry.c making devX11.d from devX11.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/X11' gcc -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c dataentry.c -o dataentry.o gcc -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c devX11.c -o devX11.o gcc -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rotated.c -o rotated.o gcc -I. -I../../../src/include -I../../../src/include -pthread -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c rbitmap.c -o rbitmap.o gcc -shared -Wl,-O1 -o R_X11.so dataentry.o devX11.o rotated.o rbitmap.o -lSM -lICE -pthread -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -lX11 -lpng12 -lz -lcairo -lX11 -lXt -ltiff -ljpeg -lpng -lz -L../../../lib -lR -lm make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/library' mkdir -p -- ../../library make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/profile' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/base' building package 'base' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/base' mkdir -p -- ../../../library/base/demo mkdir -p -- ../../../library/base/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/base' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/base' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools' mkdir -p -- ../../../library/tools/R mkdir -p -- ../../../library/tools/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools' make[6]: Entering directory `/build/buildd/r-base-2.12.1/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 gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c text.c -o text.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c init.c -o init.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c Rmd5.c -o Rmd5.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c md5.c -o md5.o gcc -shared -Wl,-O1 -o tools.so text.o init.o Rmd5.o md5.o -L../../../../lib -lR make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/po mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/utils' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/utils' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/utils' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/utils' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/po mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' making chull.d from chull.c making devNull.d from devNull.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c making devQuartz.d from devQuartz.c making init.d from init.c gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c chull.c -o chull.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c devNull.c -o devNull.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c devPicTeX.c -o devPicTeX.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c devPS.c -o devPS.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c devQuartz.c -o devQuartz.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -c init.c -o init.o gcc -shared -Wl,-O1 -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o -L../../../../lib -lR make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/graphics' mkdir -p -- ../../../library/graphics/R mkdir -p -- ../../../library/graphics/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/graphics' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/graphics' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/graphics' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/graphics' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats' mkdir -p -- ../../../library/stats/R mkdir -p -- ../../../library/stats/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats' make[6]: Entering directory `/build/buildd/r-base-2.12.1/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 Trunmed.d from Trunmed.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 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 gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c init.c -o init.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c kmeans.c -o kmeans.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c ansari.c -o ansari.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c bandwidths.c -o bandwidths.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c chisqsim.c -o chisqsim.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c d2x2xk.c -o d2x2xk.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c fexact.c -o fexact.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c kendall.c -o kendall.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c ks.c -o ks.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c line.c -o line.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c smooth.c -o smooth.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c prho.c -o prho.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c swilk.c -o swilk.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c ksmooth.c -o ksmooth.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c loessc.c -o loessc.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c monoSpl.c -o monoSpl.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c isoreg.c -o isoreg.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c Srunmed.c -o Srunmed.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c Trunmed.c -o Trunmed.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c dblcen.c -o dblcen.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c distance.c -o distance.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c hclust-utils.c -o hclust-utils.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c nls.c -o nls.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c HoltWinters.c -o HoltWinters.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c PPsum.c -o PPsum.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c arima.c -o arima.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c burg.c -o burg.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c filter.c -o filter.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c mAR.c -o mAR.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c pacf.c -o pacf.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c starma.c -o starma.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c port.c -o port.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c family.c -o family.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c sbart.c -o sbart.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c approx.c -o approx.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c loglin.c -o loglin.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c lowess.c -o lowess.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c massdist.c -o massdist.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c splines.c -o splines.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c bsplvd.f -o bsplvd.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c bvalue.f -o bvalue.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c bvalus.f -o bvalus.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c loessf.f -o loessf.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c ppr.f -o ppr.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c qsbart.f -o qsbart.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c sgram.f -o sgram.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c sinerp.f -o sinerp.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c sslvrg.f -o sslvrg.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c stxwx.f -o stxwx.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c hclust.f -o hclust.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c kmns.f -o kmns.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c eureka.f -o eureka.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c stl.f -o stl.o gfortran -fpic -O3 -pipe -g -ffloat-store -c portsrc.f -o portsrc.o gfortran -fvisibility=hidden -fpic -O3 -pipe -g -c lminfl.f -o lminfl.o gcc -shared -Wl,-O1 -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 Trunmed.o dblcen.o distance.o hclust-utils.o nls.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 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 -lblas -lgfortran -lm -L../../../../lib -lR make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/datasets' mkdir -p -- ../../../library/datasets/R make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/datasets' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods' mkdir -p -- ../../../library/methods/R mkdir -p -- ../../../library/methods/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods' make[6]: Entering directory `/build/buildd/r-base-2.12.1/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 gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c do_substitute_direct.c -o do_substitute_direct.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c init.c -o init.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c slot.c -o slot.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c class_support.c -o class_support.o gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c tests.c -o tests.o gcc -shared -Wl,-O1 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o -L../../../../lib -lR make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods' dumping R code in package 'methods' initializing class and method definitions ...done make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid' mkdir -p -- ../../../library/grid/R mkdir -p -- ../../../library/grid/doc mkdir -p -- ../../../library/grid/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid' make[6]: Entering directory `/build/buildd/r-base-2.12.1/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 gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c gpar.c -o gpar.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c grid.c -o grid.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c just.c -o just.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c layout.c -o layout.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c matrix.c -o matrix.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c register.c -o register.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c state.c -o state.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c unit.c -o unit.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c util.c -o util.o gcc -I../../../../include -fvisibility=hidden -fpic -std=gnu99 -O3 -pipe -g -c viewport.c -o viewport.o gcc -shared -Wl,-O1 -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[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines' mkdir -p -- ../../../library/splines/R mkdir -p -- ../../../library/splines/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines/src' making splines.d from splines.c gcc -I../../../../include -fpic -std=gnu99 -O3 -pipe -g -c splines.c -o splines.o gcc -shared -Wl,-O1 -o splines.so splines.o -L../../../../lib -lR make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats4' mkdir -p -- ../../../library/stats4/R mkdir -p -- ../../../library/stats4/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats4' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats4' Creating a new generic function for "coef" in "stats4" Creating a new generic function for "summary" in "stats4" Creating a new generic function for "profile" in "stats4" Creating a new generic function for "plot" in "stats4" Creating a new generic function for "confint" in "stats4" Creating a new generic function for "logLik" in "stats4" Creating a new generic function for "vcov" in "stats4" Creating a new generic function for "update" in "stats4" make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats4' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats4' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec mkdir -p -- ../../../library/tcltk/po make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' making init.d from init.c making tcltk.d from tcltk.c making tcltk_unix.d from tcltk_unix.c gcc -I../../../../include -I/usr/include/tcl8.5 -I/usr/include/tcl8.5 -fpic -std=gnu99 -O3 -pipe -g -c init.c -o init.o gcc -I../../../../include -I/usr/include/tcl8.5 -I/usr/include/tcl8.5 -fpic -std=gnu99 -O3 -pipe -g -c tcltk.c -o tcltk.o gcc -I../../../../include -I/usr/include/tcl8.5 -I/usr/include/tcl8.5 -fpic -std=gnu99 -O3 -pipe -g -c tcltk_unix.c -o tcltk_unix.o gcc -shared -Wl,-O1 -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib -ltcl8.5 -L/usr/lib -ltk8.5 -lX11 -lXss -lXext -lm -L../../../../lib -lR make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/base' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src' make[2]: Entering directory `/build/buildd/r-base-2.12.1/tests' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/tests' make[2]: Entering directory `/build/buildd/r-base-2.12.1/po' make[3]: Entering directory `/build/buildd/r-base-2.12.1/po' installing translations: mkdir -p -- ../share/locale/en/LC_MESSAGES en mkdir -p -- ../share/locale/en_GB/LC_MESSAGES en_GB mkdir -p -- ../share/locale/es/LC_MESSAGES es mkdir -p -- ../share/locale/fr/LC_MESSAGES fr mkdir -p -- ../share/locale/de/LC_MESSAGES de mkdir -p -- ../share/locale/it/LC_MESSAGES it mkdir -p -- ../share/locale/ja/LC_MESSAGES ja mkdir -p -- ../share/locale/ko/LC_MESSAGES ko mkdir -p -- ../share/locale/nn/LC_MESSAGES nn mkdir -p -- ../share/locale/pt_BR/LC_MESSAGES pt_BR mkdir -p -- ../share/locale/ru/LC_MESSAGES ru mkdir -p -- ../share/locale/zh_CN/LC_MESSAGES zh_CN mkdir -p -- ../share/locale/zh_TW/LC_MESSAGES zh_TW mkdir -p -- ../share/locale/en@quot/LC_MESSAGES en@quot make[3]: Leaving directory `/build/buildd/r-base-2.12.1/po' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/po' you should 'make docs' now ... make[1]: Leaving directory `/build/buildd/r-base-2.12.1' (cd src/nmath/standalone; \ /usr/bin/make CFLAGS="-std=gnu99 -O3 -pipe -g -D_REENTRANT" \ CXXFLAGS="-O3 -pipe -g -D_REENTRANT" \ FFLAGS="-O3 -pipe -g -D_REENTRANT" \ CC=gcc \ CXX=g++ \ F77=gfortran \ libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.1 \ shared static ) make[1]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' (cd ../../include; /usr/bin/make Rmath.h) make[2]: Entering directory `/build/buildd/r-base-2.12.1/src/include' make[2]: `Rmath.h' is up to date. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src/include' Copying source files make[2]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' 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 fround.d from fround.c making ftrunc.d from ftrunc.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 bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.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 dlnorm.d from dlnorm.c making plnorm.d from plnorm.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 qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.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 making std_unif.d from std_unif.c make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' make[2]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c mlutils.c -o mlutils.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c d1mach.c -o d1mach.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c i1mach.c -o i1mach.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fmax2.c -o fmax2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fmin2.c -o fmin2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fprec.c -o fprec.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fround.c -o fround.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c ftrunc.c -o ftrunc.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c sign.c -o sign.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fsign.c -o fsign.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c imax2.c -o imax2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c imin2.c -o imin2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c chebyshev.c -o chebyshev.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c log1p.c -o log1p.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c expm1.c -o expm1.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c lgammacor.c -o lgammacor.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c gammalims.c -o gammalims.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c stirlerr.c -o stirlerr.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bd0.c -o bd0.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c gamma.c -o gamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c lgamma.c -o lgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c beta.c -o beta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c lbeta.c -o lbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c polygamma.c -o polygamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bessel_i.c -o bessel_i.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bessel_j.c -o bessel_j.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bessel_k.c -o bessel_k.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bessel_y.c -o bessel_y.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c choose.c -o choose.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c snorm.c -o snorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c sexp.c -o sexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dgamma.c -o dgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pgamma.c -o pgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qgamma.c -o qgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rgamma.c -o rgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dbeta.c -o dbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pbeta.c -o pbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qbeta.c -o qbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rbeta.c -o rbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dunif.c -o dunif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c punif.c -o punif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qunif.c -o qunif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c runif.c -o runif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnorm.c -o dnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnorm.c -o pnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnorm.c -o qnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rnorm.c -o rnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dlnorm.c -o dlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c plnorm.c -o plnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qlnorm.c -o qlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rlnorm.c -o rlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c df.c -o df.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pf.c -o pf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qf.c -o qf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rf.c -o rf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnf.c -o dnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dt.c -o dt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pt.c -o pt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qt.c -o qt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rt.c -o rt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnt.c -o dnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dchisq.c -o dchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pchisq.c -o pchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qchisq.c -o qchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rchisq.c -o rchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rnchisq.c -o rnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dbinom.c -o dbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pbinom.c -o pbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qbinom.c -o qbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rbinom.c -o rbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rmultinom.c -o rmultinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dcauchy.c -o dcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pcauchy.c -o pcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qcauchy.c -o qcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rcauchy.c -o rcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dexp.c -o dexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pexp.c -o pexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qexp.c -o qexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rexp.c -o rexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dgeom.c -o dgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pgeom.c -o pgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qgeom.c -o qgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rgeom.c -o rgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dhyper.c -o dhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c phyper.c -o phyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qhyper.c -o qhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rhyper.c -o rhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnbinom.c -o dnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnbinom.c -o pnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnbinom.c -o qnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rnbinom.c -o rnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dpois.c -o dpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c ppois.c -o ppois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qpois.c -o qpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rpois.c -o rpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dweibull.c -o dweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pweibull.c -o pweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qweibull.c -o qweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rweibull.c -o rweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dlogis.c -o dlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c plogis.c -o plogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qlogis.c -o qlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rlogis.c -o rlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnchisq.c -o dnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnchisq.c -o pnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnchisq.c -o qnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnbeta.c -o dnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnbeta.c -o pnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnbeta.c -o qnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnf.c -o pnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnt.c -o pnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnf.c -o qnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnt.c -o qnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c ptukey.c -o ptukey.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qtukey.c -o qtukey.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c toms708.c -o toms708.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c wilcox.c -o wilcox.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c signrank.c -o signrank.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -c std_unif.c -o std_unif.lo gcc -shared -o libRmath.so -Wl,-soname,libRmath.so.1 mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo expm1.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' make[2]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c mlutils.c -o mlutils.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c d1mach.c -o d1mach.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c i1mach.c -o i1mach.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fmax2.c -o fmax2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fmin2.c -o fmin2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fprec.c -o fprec.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fround.c -o fround.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c ftrunc.c -o ftrunc.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c sign.c -o sign.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c fsign.c -o fsign.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c imax2.c -o imax2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c imin2.c -o imin2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c chebyshev.c -o chebyshev.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c log1p.c -o log1p.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c expm1.c -o expm1.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c lgammacor.c -o lgammacor.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c gammalims.c -o gammalims.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c stirlerr.c -o stirlerr.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bd0.c -o bd0.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c gamma.c -o gamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c lgamma.c -o lgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c beta.c -o beta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c lbeta.c -o lbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c polygamma.c -o polygamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bessel_i.c -o bessel_i.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bessel_j.c -o bessel_j.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bessel_k.c -o bessel_k.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c bessel_y.c -o bessel_y.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c choose.c -o choose.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c snorm.c -o snorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c sexp.c -o sexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dgamma.c -o dgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pgamma.c -o pgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qgamma.c -o qgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rgamma.c -o rgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dbeta.c -o dbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pbeta.c -o pbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qbeta.c -o qbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rbeta.c -o rbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dunif.c -o dunif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c punif.c -o punif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qunif.c -o qunif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c runif.c -o runif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnorm.c -o dnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnorm.c -o pnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnorm.c -o qnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rnorm.c -o rnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dlnorm.c -o dlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c plnorm.c -o plnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qlnorm.c -o qlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rlnorm.c -o rlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c df.c -o df.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pf.c -o pf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qf.c -o qf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rf.c -o rf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnf.c -o dnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dt.c -o dt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pt.c -o pt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qt.c -o qt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rt.c -o rt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnt.c -o dnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dchisq.c -o dchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pchisq.c -o pchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qchisq.c -o qchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rchisq.c -o rchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rnchisq.c -o rnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dbinom.c -o dbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pbinom.c -o pbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qbinom.c -o qbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rbinom.c -o rbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rmultinom.c -o rmultinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dcauchy.c -o dcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pcauchy.c -o pcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qcauchy.c -o qcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rcauchy.c -o rcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dexp.c -o dexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pexp.c -o pexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qexp.c -o qexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rexp.c -o rexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dgeom.c -o dgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pgeom.c -o pgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qgeom.c -o qgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rgeom.c -o rgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dhyper.c -o dhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c phyper.c -o phyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qhyper.c -o qhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rhyper.c -o rhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnbinom.c -o dnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnbinom.c -o pnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnbinom.c -o qnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rnbinom.c -o rnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dpois.c -o dpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c ppois.c -o ppois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qpois.c -o qpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rpois.c -o rpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dweibull.c -o dweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pweibull.c -o pweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qweibull.c -o qweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rweibull.c -o rweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dlogis.c -o dlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c plogis.c -o plogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qlogis.c -o qlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c rlogis.c -o rlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnchisq.c -o dnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnchisq.c -o pnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnchisq.c -o qnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c dnbeta.c -o dnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnbeta.c -o pnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnbeta.c -o qnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnf.c -o pnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c pnt.c -o pnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnf.c -o qnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qnt.c -o qnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c ptukey.c -o ptukey.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c qtukey.c -o qtukey.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c toms708.c -o toms708.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c wilcox.c -o wilcox.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c signrank.c -o signrank.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -std=gnu99 -O3 -pipe -g -D_REENTRANT -c std_unif.c -o std_unif.o ar cr libRmath.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 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 std_unif.o ranlib libRmath.a make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' make[1]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' /usr/bin/make docs R_CMD_BUILD_HELP_OPTS="--txt --example" make[1]: Entering directory `/build/buildd/r-base-2.12.1' make[2]: Entering directory `/build/buildd/r-base-2.12.1/m4' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/m4' make[2]: Entering directory `/build/buildd/r-base-2.12.1/tools' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/tools' make[2]: Entering directory `/build/buildd/r-base-2.12.1/doc' make[3]: Entering directory `/build/buildd/r-base-2.12.1/doc/html' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/doc/html' make[3]: Entering directory `/build/buildd/r-base-2.12.1/doc/manual' make[3]: Nothing to be done for `R'. make[3]: Leaving directory `/build/buildd/r-base-2.12.1/doc/manual' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/doc' make[2]: Entering directory `/build/buildd/r-base-2.12.1/etc' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/etc' make[2]: Entering directory `/build/buildd/r-base-2.12.1/share' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/share' make[2]: Entering directory `/build/buildd/r-base-2.12.1/src' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/scripts' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/scripts' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/scripts' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/scripts' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/include' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/include/R_ext' make[4]: Nothing to be done for `R'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/include/R_ext' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/include' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/extra' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[5]: `libtre.a' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/appl' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/appl' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/appl' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/appl' make[4]: `libappl.a' is up to date. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/appl' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/appl' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath' make[4]: `libnmath.a' is up to date. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' make[4]: `libunix.a' is up to date. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -DR_HOME='"/build/buildd/r-base-2.12.1"' -o Rscript \ ./Rscript.c make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/main' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/main' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/main' /build/buildd/r-base-2.12.1/lib/libR.so is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/main' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/main' /build/buildd/r-base-2.12.1/bin/exec/R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/modules' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[5]: `internet.so' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[5]: `lapack.so' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[5]: `vfonts.so' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[5]: `Makedeps' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[5]: `R_X11.so' is up to date. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/library' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/profile' building system startup profile make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/profile' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/base' building package 'base' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/base' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/base' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/base' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools' building package 'tools' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tools' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/utils' building package 'utils' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/utils' all.R is unchanged make[5]: Nothing to be done for `iconvlist'. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/utils' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/utils' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/utils' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/utils' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices' building package 'grDevices' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grDevices' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/graphics' building package 'graphics' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/graphics' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/graphics' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/graphics' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/graphics' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/graphics' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats' building package 'stats' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/datasets' building package 'datasets' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/datasets' all.R is unchanged ../../../library/datasets/R/datasets is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/datasets' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/datasets' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods' building package 'methods' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/methods' make[5]: Nothing to be done for `RfilesLazy'. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/methods' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid' building package 'grid' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/grid' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/grid' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines' building package 'splines' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[7]: `Makedeps' is up to date. make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[7]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/splines' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/splines' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats4' building package 'stats4' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats4' all.R is unchanged make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats4' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/stats4' make[5]: Nothing to be done for `Rfiles'. make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats4' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/stats4' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk' make[5]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[6]: Entering directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[5]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk/src' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/tcltk' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library/base' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src' make[2]: Entering directory `/build/buildd/r-base-2.12.1/tests' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/tests' make[2]: Entering directory `/build/buildd/r-base-2.12.1/po' make[3]: Entering directory `/build/buildd/r-base-2.12.1/po' installing translations: en en_GB es fr de it ja ko nn pt_BR ru zh_CN zh_TW en@quot make[3]: Leaving directory `/build/buildd/r-base-2.12.1/po' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/po' you should 'make docs' now ... make[2]: Entering directory `/build/buildd/r-base-2.12.1/doc' creating NEWS creating NEWS.pdf make[3]: Entering directory `/build/buildd/r-base-2.12.1/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-data.html creating doc/manual/R-exts.html creating doc/manual/R-intro.html creating doc/manual/R-ints.html creating doc/manual/R-lang.html make[4]: Entering directory `/build/buildd/r-base-2.12.1/doc/html' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/doc/html' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/doc/manual' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/doc' make[2]: Entering directory `/build/buildd/r-base-2.12.1/src/library' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/library' installing parsed Rd make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/library' building/updating package metadata ... make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/library' writing package indices make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/library' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[1]: Leaving directory `/build/buildd/r-base-2.12.1' touch make-arch-stamp /usr/bin/fakeroot debian/rules binary-arch *** check *** xvfb-run make check-all make[1]: Entering directory `/build/buildd/r-base-2.12.1' make[2]: Entering directory `/build/buildd/r-base-2.12.1/tests' make[3]: Entering directory `/build/buildd/r-base-2.12.1/tests' make[4]: Entering directory `/build/buildd/r-base-2.12.1/tests/Examples' Collecting examples for package 'base' Extracting from parsed Rd's ........................................ Running examples in package 'base' Collecting examples for package 'tools' Extracting from parsed Rd's .... Running examples in package 'tools' Comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... 454c454 < character(0) --- > [1] "Matrix" "nlme" "mgcv" 785c785 < character(0) --- > [1] "lattice" 794c794 < character(0) --- > [1] "R (>= 2.11.0)" Collecting examples for package 'utils' Extracting from parsed Rd's ............ Running examples in package 'utils' Error: testing 'utils' failed Execution halted make[4]: *** [test-Examples-Base] Error 1 make[4]: Leaving directory `/build/buildd/r-base-2.12.1/tests/Examples' make[3]: *** [test-Examples] Error 2 make[3]: Leaving directory `/build/buildd/r-base-2.12.1/tests' make[2]: *** [test-all-basics] Error 1 make[2]: Leaving directory `/build/buildd/r-base-2.12.1/tests' make[1]: *** [check-all] Error 2 make[1]: Leaving directory `/build/buildd/r-base-2.12.1' make: [check-stamp] Error 2 (ignored) touch check-stamp *** install-arch *** dh_testdir dh_testroot dh_prep -a dh_installdirs -A /build/buildd/r-base-2.12.1/debian/r-base-core /usr/bin/make DESTDIR=/build/buildd/r-base-2.12.1/debian/r-base-core install make[1]: Entering directory `/build/buildd/r-base-2.12.1' make[2]: Entering directory `/build/buildd/r-base-2.12.1/m4' make[2]: Nothing to be done for `install'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/m4' make[2]: Entering directory `/build/buildd/r-base-2.12.1/tools' make[2]: Nothing to be done for `install'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/tools' make[2]: Entering directory `/build/buildd/r-base-2.12.1/doc' installing doc ... mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/man/man1 make[3]: Entering directory `/build/buildd/r-base-2.12.1/doc/html' installing doc/html ... mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc/html make[3]: Leaving directory `/build/buildd/r-base-2.12.1/doc/html' make[3]: Entering directory `/build/buildd/r-base-2.12.1/doc/manual' installing doc/manual ... mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc/manual make[3]: Leaving directory `/build/buildd/r-base-2.12.1/doc/manual' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/doc' make[2]: Entering directory `/build/buildd/r-base-2.12.1/etc' mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/etc installing etc ... make[2]: Leaving directory `/build/buildd/r-base-2.12.1/etc' make[2]: Entering directory `/build/buildd/r-base-2.12.1/share' installing share ... mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/R mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/encodings mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/java mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/licenses mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/make mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/sh mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/texmf mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/texmf/tex/latex make[2]: Leaving directory `/build/buildd/r-base-2.12.1/share' make[2]: Entering directory `/build/buildd/r-base-2.12.1/src' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/scripts' mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/bin make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/scripts' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/include' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/include/R_ext' mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/include/R_ext make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/include/R_ext' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/include' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/extra' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/blas' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/blas' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/bzip2' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/bzip2' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/pcre' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/pcre' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/tre' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/xdr' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/xdr' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/xz' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/xz' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/zlib' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/zlib' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/extra/intl' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra/intl' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/extra' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/appl' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/appl' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath' make[3]: Nothing to be done for `install'. make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -DR_HOME='"/usr/lib/R"' -o Rscript \ ./Rscript.c mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/pkgconfig make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/main' mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/bin/exec mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/lib make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/main' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/main' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/modules' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/internet' mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/modules make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/internet' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/lapack' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/vfonts' make[4]: Entering directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[4]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules/X11' make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/modules' make[3]: Entering directory `/build/buildd/r-base-2.12.1/src/library' mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/library installing packages ... building HTML index ... make[3]: Leaving directory `/build/buildd/r-base-2.12.1/src/library' make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src' make[2]: Entering directory `/build/buildd/r-base-2.12.1/tests' make[2]: Nothing to be done for `install'. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/tests' make[2]: Entering directory `/build/buildd/r-base-2.12.1/po' installing translations: mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/en/LC_MESSAGES en mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/en_GB/LC_MESSAGES en_GB mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/es/LC_MESSAGES es mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/fr/LC_MESSAGES fr mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/de/LC_MESSAGES de mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/it/LC_MESSAGES it mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/ja/LC_MESSAGES ja mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/ko/LC_MESSAGES ko mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/nn/LC_MESSAGES nn mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/pt_BR/LC_MESSAGES pt_BR mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/ru/LC_MESSAGES ru mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/zh_CN/LC_MESSAGES zh_CN mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/zh_TW/LC_MESSAGES zh_TW mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/locale/en@quot/LC_MESSAGES en@quot make[2]: Leaving directory `/build/buildd/r-base-2.12.1/po' make[1]: Leaving directory `/build/buildd/r-base-2.12.1' (cd src/unix; \ rm -vf Rscript /build/buildd/r-base-2.12.1/debian/r-base-core/usr/bin/Rscript; \ /usr/bin/make CFLAGS="-std=gnu99 -O3 -pipe -g -D_REENTRANT" \ CXXFLAGS="-O3 -pipe -g -D_REENTRANT" \ FFLAGS="-O3 -pipe -g -D_REENTRANT" \ CC=gcc \ CXX=g++ \ F77=gfortran \ RHOME=/usr/lib/R \ DESTDIR=/build/buildd/r-base-2.12.1/debian/r-base-core \ install-Rscript ) removed `Rscript' removed `/build/buildd/r-base-2.12.1/debian/r-base-core/usr/bin/Rscript' make[1]: Entering directory `/build/buildd/r-base-2.12.1/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fpic -std=gnu99 -O3 -pipe -g -D_REENTRANT -DR_HOME='"/usr/lib/R"' -o Rscript \ ./Rscript.c make[1]: Leaving directory `/build/buildd/r-base-2.12.1/src/unix' #ls -ltr /build/buildd/r-base-2.12.1/debian/r-base-core/usr/bin/ #strings src/unix/Rscript cp -vax src/unix/Rscript /build/buildd/r-base-2.12.1/debian/r-base-core/usr/bin/ `src/unix/Rscript' -> `/build/buildd/r-base-2.12.1/debian/r-base-core/usr/bin/Rscript' #ls -ltr /build/buildd/r-base-2.12.1/debian/r-base-core/usr/bin/ #strings /build/buildd/r-base-2.12.1/debian/r-base-core/usr/bin/Rscript (cd src/nmath/standalone; \ /usr/bin/make DESTDIR=/build/buildd/r-base-2.12.1/debian/r-base-core install ) make[1]: Entering directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' make[2]: Entering directory `/build/buildd/r-base-2.12.1/src/include' make[2]: `Rmath.h' is up to date. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/src/include' /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged make[1]: Leaving directory `/build/buildd/r-base-2.12.1/src/nmath/standalone' chmod a+x /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/share/sh/echo.sh rm -v /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/COPYING removed `/build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/COPYING' (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/; \ ln -s ../../share/common-licenses/GPL-2 COPYING) rm -v /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc/COPYING \ /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc/COPYING.LIB removed `/build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc/COPYING' removed `/build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc/COPYING.LIB' (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc; \ ln -s ../../../share/common-licenses/GPL-2 COPYING; \ ln -s ../../../share/common-licenses/LGPL-2.1 COPYING.LIB ) # edd 03 Oct 2006 use link into /usr/share/, not /usr/lib/ (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/texmf/tex/latex && \ ln -s ../../../R/share/texmf R) dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html dh_movefiles --sourcedir=debian/r-base-core -pr-base-html dh_movefiles --sourcedir=debian/r-base-core -pr-base-latex make prefix=/build/buildd/r-base-2.12.1/debian/r-base-core/usr \ rdocdir=/build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/R/doc \ install-pdf make[1]: Entering directory `/build/buildd/r-base-2.12.1' make[2]: Entering directory `/build/buildd/r-base-2.12.1/doc/manual' creating doc/manual/version.tex collecting LaTeX docs for package 'base' ... Converting parsed Rd's to LaTeX ........................................ collecting LaTeX docs for package 'datasets' ... Converting parsed Rd's to LaTeX ........ collecting LaTeX docs for package 'grDevices' ... Converting parsed Rd's to LaTeX ...... collecting LaTeX docs for package 'graphics' ... Converting parsed Rd's to LaTeX ....... collecting LaTeX docs for package 'grid' ... Converting parsed Rd's to LaTeX ........ collecting LaTeX docs for package 'methods' ... Converting parsed Rd's to LaTeX ....... collecting LaTeX docs for package 'splines' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'stats' ... Converting parsed Rd's to LaTeX .............................. collecting LaTeX docs for package 'stats4' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'tcltk' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'tools' ... Converting parsed Rd's to LaTeX .... collecting LaTeX docs for package 'utils' ... Converting parsed Rd's to LaTeX ............ PDF/LaTeX documentation: reference index ... This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/bm.sty) (/usr/share/texmf-texlive/tex/latex/base/alltt.sty) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (../../share/texmf/tex/latex/upquote.sty (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))) NOT loading ae (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) NOT loading lmodern (/usr/share/texmf-texlive/tex/latex/graphics/color.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 332. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 332. ) (/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/base/makeidx.sty) Writing index file refman.idx No file refman.aux. (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-texlive/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fonts/m ap/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd) [1] Underfull \hbox (badness 2443) in paragraph at lines 71--77 []\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 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 2334) in paragraph at lines 71--77 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is Underfull \hbox (badness 3407) in paragraph at lines 71--77 \T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er- wise, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 1960) in paragraph at lines 77--85 []\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 . It Underfull \hbox (badness 1189) in paragraph at lines 77--85 \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, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 1661) in paragraph at lines 77--85 \T1/pcr/m/n/10 double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m/n /10 1.110223e-16\T1/ptm/m/n/10 . As [2] [3] [4] Underfull \hbox (badness 10000) in paragraph at lines 224--228 \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.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 261--264 [][][]\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, [5] Underfull \hbox (badness 2359) in paragraph at lines 305--308 []\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 [6] [7] [8] [9] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [10] [11] Overfull \hbox (0.78088pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE)[] [12] [13] [14] [15] Underfull \hbox (badness 1838) in paragraph at lines 933--936 []\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 [16] [17] [18] [19] [20] [21] [22] [23] Underfull \hbox (badness 2865) in paragraph at lines 1448--1451 []\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 [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1596--1598 []\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 [26] [27] Underfull \hbox (badness 10000) in paragraph at lines 1742--1744 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [28] [29] [30] [31] [32] [33] [34] [35] Underfull \hbox (badness 5878) in paragraph at lines 2233--2238 []\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 2233--2238 \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 [36] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 2432--2435 [39] Underfull \hbox (badness 10000) in paragraph at lines 2466--2468 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 forwardsolve(L, b) \T1/ptm/m/n/10 is just a wrap-per for \T1/pcr/m/n/10 backsolve(L, b, [40] [41] [42] Underfull \vbox (badness 3803) has occurred while \output is active [43] [44] [45] [46] [47] [48] Underfull \hbox (badness 10000) in paragraph at lines 3016--3018 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Underfull \hbox (badness 2521) in paragraph at lines 4046--4048 []\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 [66] [67] [68] [69] [70] Underfull \hbox (badness 1270) in paragraph at lines 4366--4374 []\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 \T1/pcr/m/n/10 c("first", [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2443) in paragraph at lines 4874--4881 []\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 : / / [79] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4904--4904 []\T1/pcr/m/n/9 z <- c(32:126, 160:255) # range of most 8-bit charsets, Latin- 1 in Unicode[] [80] [81] [82] [83] Underfull \hbox (badness 1635) in paragraph at lines 5180--5183 []\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 5184--5187 []\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 5201--5214 []\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 5215--5223 []\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 [84] [85] [86] [87] Underfull \hbox (badness 2158) in paragraph at lines 5424--5428 \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 [88] Underfull \hbox (badness 10000) in paragraph at lines 5506--5514 []\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 [89] [90] Underfull \hbox (badness 1067) in paragraph at lines 5698--5705 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [91] [92] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5803--5803 []\T1/pcr/m/n/9 ## fifo example -- may fail, e.g. on Cygwin, even with OS supp ort for fifos[] Underfull \vbox (badness 10000) has occurred while \output is active [93] [94] [95] [96] [97] [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6296--6298 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [101] [102] [103] [104] [105] [106] Underfull \hbox (badness 8132) in paragraph at lines 6666--6670 []\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 6666--6670 \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 [107] Underfull \hbox (badness 10000) in paragraph at lines 6685--6696 []\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 2875) in paragraph at lines 6685--6696 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional=TRUE)\T1/ptm/m/n/10 . As that i s a generic func-tion, meth-ods can be Overfull \hbox (4.63962pt too wide) in paragraph at lines 6717--6721 []\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") [108] [109] [110] [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 5802) in paragraph at lines 7298--7302 []\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 [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 7422--7426 \T1/pcr/m/n/10 trace("plot", browser, exit=browser, signature = c("track", [119] [120] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7550--7550 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO ! "); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 7567--7567 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] [121] [122] Underfull \hbox (badness 4254) in paragraph at lines 7697--7701 []\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 [123] [124] Underfull \hbox (badness 1603) in paragraph at lines 7844--7847 []\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 [125] Overfull \hbox (60.78088pt too wide) in paragraph at lines 7873--7873 []\T1/pcr/m/n/10 detach(name, pos = 2, unload = FALSE, character.only = FALSE, force = FALSE)[] [126] [127] [128] [129] [130] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8194--8194 []\T1/pcr/m/n/10 ## Group methods, notably for round(), signif(), floor(), cei ling(),[] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 2150) in paragraph at lines 8991--8994 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [143] Underfull \hbox (badness 5316) in paragraph at lines 9004--9012 \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 9013--9015 []\T1/pcr/m/n/10 duplicated(x, fromLast=TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than [144] [145] [146] Underfull \hbox (badness 10000) in paragraph at lines 9214--9217 []\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 [147] [148] [149] [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 5288) in paragraph at lines 9865--9867 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [156] Underfull \hbox (badness 3039) in paragraph at lines 9875--9878 []\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 Underfull \hbox (badness 10000) in paragraph at lines 9934--9936 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [157] [158] [159] Underfull \vbox (badness 3803) has occurred while \output is active [160] Underfull \hbox (badness 10000) in paragraph at lines 10159--10161 []\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 10342--10352 []\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 10342--10352 \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] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] Underfull \hbox (badness 2165) in paragraph at lines 11588--11590 []\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 \T1/pcr /m/n/10 fsep = [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 11791--11795 [][][]\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 , [186] Overfull \hbox (30.78088pt too wide) in paragraph at lines 11836--11836 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [187] Underfull \hbox (badness 10000) in paragraph at lines 11897--11900 [][][]\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 (0.78088pt too wide) in paragraph at lines 11918--11918 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE)[] [188] Underfull \hbox (badness 3965) in paragraph at lines 11944--11948 []\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] [191] [192] [193] [194] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12353--12353 [] \T1/pcr/m/n/10 decimal.mark = ".", zero.print = NULL, drop0trailing = FAL SE, ...)[] [195] Underfull \hbox (badness 1168) in paragraph at lines 12393--12397 []\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 12393--12397 \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 12479--12482 [][][]\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 , [197] [198] [199] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12647--12647 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA, ...)[] Underfull \hbox (badness 2790) in paragraph at lines 12653--12656 []\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 1024) in paragraph at lines 12684--12688 []\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 12750--12758 []\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] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] Underfull \hbox (badness 2418) in paragraph at lines 13701--13705 \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 13708--13711 []\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 [217] Underfull \hbox (badness 2326) in paragraph at lines 13737--13744 [][][]\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 , [218] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13837--13837 []\T1/pcr/m/n/9 ## Not run: ## for translation, those strings should appear in R-pkg.pot as[] [219] [220] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13978--13978 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE,[] [221] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13981--13981 []\T1/pcr/m/n/10 grepl(pattern, x, ignore.case = FALSE, perl = FALSE, fixed = FALSE,[] Underfull \hbox (badness 1867) in paragraph at lines 14000--14007 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] Underfull \hbox (badness 2285) in paragraph at lines 14871--14873 []\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 (24.78088pt too wide) in paragraph at lines 14901--14901 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE)[] [235] [236] [237] Underfull \hbox (badness 1072) in paragraph at lines 15084--15087 []\T1/ptm/m/n/10 Sometimes it is bet-ter to use a con-struc-tion such as \T1/pc r/m/n/10 (tmp <- yes; tmp[!test] <- [238] [239] [240] [241] Underfull \hbox (badness 10000) in paragraph at lines 15311--15313 []\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 [242] Underfull \hbox (badness 4217) in paragraph at lines 15395--15404 [][][]\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 15410--15426 [][][]\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 , [243] [244] [245] [246] [247] [248] [249] [250] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15912--15912 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [251] [252] [253] Underfull \hbox (badness 4739) in paragraph at lines 16035--16037 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [254] [255] [256] [257] [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16512--16514 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [262] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16559--16559 []\T1/pcr/m/n/9 vapply(i39, fivenum, c(Min.=0, "1st Qu."=0, Median=0, "3rd Qu. "=0, Max.=0))[] Underfull \hbox (badness 1975) in paragraph at lines 16575--16578 []\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 [263] [264] [265] [266] Underfull \hbox (badness 10000) in paragraph at lines 16835--16839 []\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 [267] [268] Underfull \hbox (badness 10000) in paragraph at lines 16990--16994 []\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 16990--16994 [][]\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 [269] Underfull \hbox (badness 1221) in paragraph at lines 17038--17043 []\T1/ptm/m/n/10 Normally \T1/pcr/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of loaded pack-ages, but \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 o r \T1/pcr/m/n/10 FALSE [270] Underfull \hbox (badness 10000) in paragraph at lines 17125--17131 [][][]\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 library.dynam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 data[][][]\T1/ptm/m/n/10 , [271] [272] Underfull \hbox (badness 10000) in paragraph at lines 17260--17264 []\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 [273] Underfull \hbox (badness 1264) in paragraph at lines 17309--17313 []\T1/phv/m/n/10 R \T1/ptm/m/n/10 is dis-tributed un-der the terms of the GNU G EN-ERAL PUB-LIC LI-CENSE Ver-sion 2, [274] [275] [276] [277] Underfull \hbox (badness 3343) in paragraph at lines 17523--17527 [][][]\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 17606--17606 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] [279] [280] Underfull \hbox (badness 6380) in paragraph at lines 17732--17737 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 10000) in paragraph at lines 17764--17767 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC _CTYPE"\T1/ptm/m/n/10 , [281] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17832--17832 []\T1/pcr/m/n/9 Sys.setlocale("LC_COLLATE", "C") # turn off locale-specific sorting, usually[] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18697--18697 []\T1/pcr/m/n/9 ## Simple version: intersect <- function(x, y) y[match(x, y, nomatch = 0)][] [296] [297] Underfull \hbox (badness 1655) in paragraph at lines 18813--18817 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] Underfull \hbox (badness 4366) in paragraph at lines 19405--19411 \T1/pcr/m/n/10 www . bzip . org/$[][]\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 . Overfull \hbox (60.78088pt too wide) in paragraph at lines 19444--19444 []\T1/pcr/m/n/10 R --min-vsize=vl --max-vsize=vu --min-nsize=nl --max-nsize=nu --max-ppsize=N[] [308] [309] [310] [311] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19694--19694 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19695--19695 [] \T1/pcr/m/n/10 sort = TRUE, suffixes = c(".x",".y"), incomparables = N ULL, ...)[] [312] [313] [314] [315] [316] [317] [318] [319] Underfull \hbox (badness 3849) in paragraph at lines 20216--20221 []\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 [320] [321] [322] [323] Underfull \hbox (badness 1609) in paragraph at lines 20439--20441 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of \T1/pcr/m/n/10 c("bytes", "chars", [324] [325] [326] [327] [328] [329] [330] [331] [332] Underfull \hbox (badness 10000) in paragraph at lines 21003--21009 []\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 21003--21009 \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] Underfull \hbox (badness 8189) in paragraph at lines 21188--21194 []\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 [][]mode [][][] [335] [336] [337] Underfull \hbox (badness 1694) in paragraph at lines 21371--21374 []\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] [341] Underfull \hbox (badness 1603) in paragraph at lines 21601--21603 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [342] Underfull \hbox (badness 1210) in paragraph at lines 21707--21716 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [343] [344] Underfull \hbox (badness 5475) in paragraph at lines 21802--21810 []\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 21819--21823 []\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 4048) in paragraph at lines 21835--21844 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue \T1/pcr/m/n/10 " [345] [346] Underfull \hbox (badness 3138) in paragraph at lines 22045--22051 []\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 3514) in paragraph at lines 22045--22051 \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- [347] Underfull \hbox (badness 10000) in paragraph at lines 22095--22102 []\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 22104--22111 []\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 2384) in paragraph at lines 22104--22111 \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 CRAN Underfull \hbox (badness 2837) in paragraph at lines 22104--22111 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke \T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 22104--22111 \T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran"; Underfull \hbox (badness 1881) in paragraph at lines 22117--22122 []\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] [352] Underfull \hbox (badness 10000) in paragraph at lines 22408--22411 []\T1/pcr/m/n/10 FUN = "*" \T1/ptm/m/n/10 is han-dled in-ter-nally as a spe-cia l case, \T1/ptm/m/it/10 via \T1/pcr/m/n/10 as.vector(X) %*% [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 23051--23055 []\T1/ptm/m/n/10 This func-tion is al-most never used: \T1/pcr/m/n/10 `name` \T 1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m/n/10 get[][][](name, [364] Underfull \hbox (badness 1796) in paragraph at lines 23114--23117 []\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] [368] [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 7415) in paragraph at lines 24177--24181 []\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 [382] [383] [384] [385] [386] Underfull \hbox (badness 1533) in paragraph at lines 24552--24555 []\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] [388] Underfull \hbox (badness 1337) in paragraph at lines 24649--24652 []\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., [389] Underfull \hbox (badness 1038) in paragraph at lines 24714--24724 []\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 [390] [391] [392] [393] [394] [395] [396] [397] Underfull \hbox (badness 4048) in paragraph at lines 25182--25187 []\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 25182--25187 \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 25182--25187 \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 , [398] [399] [400] [401] [402] [403] [404] [405] [406] [407] [408] Overfull \hbox (153.38951pt too wide) in paragraph at lines 25881--25883 []\T1/ptm/m/n/10 Punctuation char-ac-ters: `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr /m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/1 0 ` \T1/pcr/m/n/10 { | } ~\T1/ptm/m/n/10 '. Overfull \hbox (25.91963pt too wide) in paragraph at lines 25891--25893 []\T1/ptm/m/n/10 Hexadecimal dig-its: `\T1/pcr/m/n/10 0 1 2 3 4 5 6 7 8 9 A B C D E F a b c d e f\T1/ptm/m/n/10 '. [409] [410] [411] Underfull \hbox (badness 5417) in paragraph at lines 26101--26104 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 26105--26107 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 26108--26110 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / w ww . opengroup . org / onlinepubs / [412] [413] [414] [415] Underfull \hbox (badness 10000) in paragraph at lines 26387--26391 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] Underfull \hbox (badness 2302) in paragraph at lines 27340--27347 []\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 27340--27347 \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 2582) in paragraph at lines 27340--27347 \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, but Underfull \hbox (badness 4805) in paragraph at lines 27340--27347 \T1/ptm/m/n/10 in gen-eral it is not. (To scale by the stan-dard de-vi-a-tions with-out cen-ter-ing, use [431] [432] [433] Underfull \hbox (badness 1158) in paragraph at lines 27489--27494 []\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 27516--27520 []\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 27516--27520 \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- [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1803) in paragraph at lines 27904--27907 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length(along.with)\T1/ptm/m/n/10 . Underfull \hbox (badness 2809) in paragraph at lines 27908--27914 []\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 [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] Underfull \hbox (badness 4303) in paragraph at lines 28673--28676 []\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 [452] [453] [454] [455] [456] [457] [458] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29111--29111 []\T1/pcr/m/n/9 is.unsorted(x, strictly=TRUE) #-> TRUE : is not (and cannot be ) sorted strictly[] [459] [460] [461] [462] [463] [464] [465] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29565--29565 []\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)[] [466] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29580--29580 []\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 29929--29931 []\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 29989--29989 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known")[] [473] [474] Underfull \hbox (badness 6526) in paragraph at lines 30139--30149 []\T1/ptm/m/n/10 Then \T1/phv/m/n/10 R \T1/ptm/m/n/10 searches for the site-wid e startup pro-file un-less the com-mand line op-tion Underfull \hbox (badness 6110) in paragraph at lines 30175--30185 []\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 ' or Underfull \hbox (badness 2635) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the Underfull \hbox (badness 1112) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us- ing [475] Underfull \hbox (badness 7704) in paragraph at lines 30226--30231 \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, e.g. [476] [477] [478] [479] [480] [481] [482] [483] [484] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30818--30818 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [485] [486] [487] [488] [489] Overfull \hbox (6.78088pt too wide) in paragraph at lines 31070--31070 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31113--31113 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [490] [491] [492] [493] [494] [495] [496] [497] Underfull \hbox (badness 10000) in paragraph at lines 31564--31567 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 31611--31611 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision[] [498] [499] [500] [501] [502] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31902--31902 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a=, A=1, b=2:3, "Otherwise: last"),"\n")[] [503] [504] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32030--32030 []\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.[] [505] [506] [507] [508] Underfull \hbox (badness 4036) in paragraph at lines 32230--32233 []\T1/ptm/m/n/10 These set-tings are usu-ally con-trolled by the en-vi-ron-ment vari-ables \T1/pcr/m/n/10 LC_NUMERIC \T1/ptm/m/n/10 and [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 32354--32358 []\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 32369--32372 []\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] [514] [515] Underfull \hbox (badness 1082) in paragraph at lines 32644--32647 []\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] Underfull \hbox (badness 1038) in paragraph at lines 32816--32819 []\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 [518] [519] [520] [521] [522] [523] [524] Overfull \hbox (6.78088pt too wide) in paragraph at lines 33255--33255 []\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c ("no",[] [525] Underfull \hbox (badness 1270) in paragraph at lines 33273--33276 []\T1/ptm/m/n/10 levels to re-move from all fac-tors in \T1/pcr/m/n/10 ...\T1/p tm/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 33341--33344 []\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] [530] Underfull \hbox (badness 10000) in paragraph at lines 33573--33575 []\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 [531] Underfull \hbox (badness 10000) in paragraph at lines 33656--33659 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . [532] [533] Underfull \hbox (badness 5475) in paragraph at lines 33782--33786 [][][]\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 \ [][]$\T1/pcr/m/n/10 http : / / [534] Underfull \hbox (badness 10000) in paragraph at lines 33844--33848 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http : [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 4181) in paragraph at lines 34187--34191 []\T1/ptm/m/n/10 For most Unix-alikes use the Ol-son databases. The system-spec ific de-fault lo-ca-tion Underfull \hbox (badness 2495) in paragraph at lines 34187--34191 \T1/ptm/m/n/10 in the file sys-tem varies, e.g. `\T1/pcr/m/n/10 /usr/share/zone info\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 /usr/etc/zoneinfo\T1/ptm/m/n/10 ', Underfull \hbox (badness 3460) in paragraph at lines 34209--34211 [][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Time _ zone$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / www . twinsun . com / [541] [542] [543] [544] [545] Overfull \hbox (9.78043pt too wide) in paragraph at lines 34519--34519 []\T1/pcr/m/n/9 trace("f", quote(browser(skipCalls=4)), exit = quote(browser(s kipCalls=4)))[] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 1708) in paragraph at lines 34897--34905 []\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 34897--34905 \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 34906--34910 []\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-stead of \T1/pcr/m/n/10 tr y(expr, Underfull \hbox (badness 3977) in paragraph at lines 34906--34910 \T1/pcr/m/n/10 silent=TRUE)\T1/ptm/m/n/10 , some-thing like \T1/pcr/m/n/10 tryC atch(expr, error = function(e) e) \T1/ptm/m/n/10 (or Underfull \hbox (badness 4859) in paragraph at lines 34919--34924 [][][]\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 34978--34990 []\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 34978--34990 \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] [556] [557] [558] [559] [560] [561] [562] [563] Underfull \hbox (badness 1803) in paragraph at lines 35694--35697 []\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 35698--35705 []\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 [564] [565] Underfull \hbox (badness 3668) in paragraph at lines 35828--35830 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [566] [567] [568] [569] [570] Underfull \hbox (badness 6592) in paragraph at lines 36100--36105 []\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] [572] [573] Underfull \vbox (badness 3803) has occurred while \output is active [574] [575] [576] [577] [578] Underfull \hbox (badness 2846) in paragraph at lines 36608--36612 []\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 36635--36635 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 36656--36660 []\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]) (./datasets-pkg.tex Chapter 2. 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 [581] [582] [583] [584] [585] Underfull \vbox (badness 10000) has occurred while \output is active [586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 365--365 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \vbox (badness 10000) has occurred while \output is active [606] Underfull \hbox (badness 10000) in paragraph at lines 1490--1493 []\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 1490--1493 \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 [607] Underfull \vbox (badness 2368) has occurred while \output is active [608] Underfull \hbox (badness 1325) in paragraph at lines 1571--1576 []\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- [609] [610] [611] [612] [613] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1888--1888 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] [614] [615] [616] [617] [618] [619] [620] Overfull \vbox (17.60591pt too high) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \vbox (badness 10000) has occurred while \output is active [634] [635] Underfull \vbox (badness 1365) has occurred while \output is active [636] [637] [638] [639] [640] Underfull \hbox (badness 5175) in paragraph at lines 3452--3455 []\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 3452--3455 \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 . [641] [642] [643] Underfull \vbox (badness 10000) has occurred while \output is active [644] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3698--3698 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3727--3730 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] Overfull \vbox (18.9959pt too high) has occurred while \output is active [656] [657] [658]) (./grDevices-pkg.tex Chapter 3. [659] [660] [661] [662] [663] [664] Overfull \hbox (6.78088pt too wide) in paragraph at lines 367--367 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [665] [666] [667] [668] [669] [670] [671] [672] [673] Underfull \hbox (badness 5175) in paragraph at lines 898--900 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [674] [675] Underfull \hbox (badness 10000) in paragraph at lines 1000--1002 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [676] [677] [678] [679] [680] [681] Underfull \hbox (badness 10000) in paragraph at lines 1424--1426 []\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, if [682] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1505--1505 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [683] Underfull \hbox (badness 1184) in paragraph at lines 1544--1557 []\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 1694) in paragraph at lines 1544--1557 \T1/pcr/m/n/10 "pbmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pgm"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "pgmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pgnm"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "pgnmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pnm"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "pnmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ppm"\T1/ptm/m/n/10 , Underfull \hbox (badness 6493) in paragraph at lines 1544--1557 \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/ptm/ m/n/10 , \T1/pcr/m/n/10 "psmono"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "psgray"\T1/ptm /m/n/10 , [684] [685] Underfull \hbox (badness 10000) in paragraph at lines 1650--1652 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [686] [687] [688] [689] Underfull \hbox (badness 2326) in paragraph at lines 1902--1912 \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 1902--1912 \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 1902--1912 \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 1902--1912 \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 [690] [691] Overfull \hbox (42.18039pt too wide) in paragraph at lines 2028--2028 []\T1/pcr/m/n/9 # This currently only works on the Windows and X11(type="Xlib" ) screen devices...[] [692] [693] [694] [695] Underfull \hbox (badness 10000) in paragraph at lines 2291--2292 [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] Underfull \hbox (badness 10000) in paragraph at lines 2888--2891 [][][]\T1/pcr/m/n/10 colors[][][] \T1/ptm/m/n/10 for the vec-tor of built-in na med col-ors; [][]\T1/pcr/m/n/10 hsv[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gr ay[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 rainbow[][][]\T1/ptm/m/n/10 , [706] [707] [708] [709] [710] [711] Underfull \hbox (badness 5939) in paragraph at lines 3331--3336 []\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 , [712] [713] [714] [715] [716] Underfull \vbox (badness 10000) has occurred while \output is active [717] [718] Underfull \vbox (badness 3803) has occurred while \output is active [719] [720] [721] [722] Underfull \hbox (badness 5077) in paragraph at lines 4011--4017 []\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 [723] [724] [725] Underfull \hbox (badness 1755) in paragraph at lines 4167--4169 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [726] [727] Underfull \hbox (badness 7344) in paragraph at lines 4319--4321 []\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 4330--4335 [][][]\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 [728] [729] Underfull \hbox (badness 2035) in paragraph at lines 4442--4451 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 3735) in paragraph at lines 4442--4451 \T1/ptm/m/n/10 vided: \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica- Underfull \hbox (badness 10000) in paragraph at lines 4442--4451 \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 ), Underfull \hbox (badness 4686) in paragraph at lines 4484--4490 \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 [730] Underfull \hbox (badness 10000) in paragraph at lines 4509--4517 []\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 4509--4517 \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 \hbox (badness 7344) in paragraph at lines 4528--4530 []\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 [731] [732] [733] [734] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4713--4713 []\T1/pcr/m/n/10 quartz(title, width, height, pointsize, family, fontsmooth, a ntialias,[] [735] Underfull \hbox (badness 10000) in paragraph at lines 4804--4806 []\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 [736] [737] [738] [739] [740] Underfull \hbox (badness 10000) in paragraph at lines 5111--5114 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [741] [742] [743] [744] [745] [746] [747] Underfull \hbox (badness 1189) in paragraph at lines 5478--5480 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [748] Underfull \hbox (badness 1132) in paragraph at lines 5546--5548 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and \T1/pcr/m/n/10 "-cronyx- Underfull \hbox (badness 2547) in paragraph at lines 5581--5587 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g. of \T1 /pcr/m/n/10 quote(pi)\T1/ptm/m/n/10 ) have been seen [749] [750] [751] [752] Underfull \hbox (badness 2065) in paragraph at lines 5814--5820 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/pcr/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , Underfull \hbox (badness 1360) in paragraph at lines 5814--5820 \T1/pcr/m/n/10 Narrow"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1 /ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 "Times "\T1/ptm/m/n/10 . Underfull \hbox (badness 1721) in paragraph at lines 5847--5850 []\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 / [753] [754] [755] Underfull \hbox (badness 1231) in paragraph at lines 6009--6011 []\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 [756] [757] [758]) (./graphics-pkg.tex Chapter 4. [759] [760] Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 []\T1/pcr/m/n/10 arrows(x0, y0, x1 = x0, y1 = y0, length = 0.25, angle = 30, c ode = 2,[] [761] Underfull \hbox (badness 2856) in paragraph at lines 175--178 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the point [762] Underfull \hbox (badness 1412) in paragraph at lines 283--288 []\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- [763] [764] [765] [766] Underfull \hbox (badness 2726) in paragraph at lines 462--468 []\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 [767] [768] [769] Underfull \hbox (badness 10000) in paragraph at lines 659--662 []\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 [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1233--1233 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [780] Underfull \hbox (badness 1024) in paragraph at lines 1278--1286 \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 Underfull \hbox (badness 3375) in paragraph at lines 1312--1314 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [781] [782] [783] [784] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1685--1691 [][][]\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 [787] [788] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1815--1815 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns,[] [789] [790] [791] [792] Underfull \hbox (badness 4859) in paragraph at lines 2003--2006 []\T1/ptm/m/n/10 labels and graph-i-cal pa-ram-e-ters can also be spec-i-fied a s ar-gu-ments. [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] Underfull \hbox (badness 1226) in paragraph at lines 2646--2650 \T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr /m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2753 []\T1/ptm/m/n/10 graphical pa-ram-e-ters, or ar-gu-ments to [][]\T1/pcr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [805] [806] [807] [808] Underfull \hbox (badness 1755) in paragraph at lines 2998--3002 []\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] [810] [811] [812] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3241--3241 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [813] [814] [815] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3413--3413 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [816] Underfull \vbox (badness 10000) has occurred while \output is active [817] [818] [819] [820] Underfull \hbox (badness 1867) in paragraph at lines 3723--3727 []\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 3886--3888 []\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] [828] [829] [830] [831] Underfull \hbox (badness 1264) in paragraph at lines 4387--4399 \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] [834] [835] [836] [837] [838] [839] [840] [841] [842] [843] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5259--5259 [] \T1/pcr/m/n/9 col = c("purple", "violetred1", "green3", "cornsilk", "cya n", "white"))[] [844] Underfull \hbox (badness 1052) in paragraph at lines 5313--5317 []\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., \T1/pcr/m/n/10 type = [845] [846] [847] [848] [849] [850] [851] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric vec tor ~ factor[] [852] [853] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5827--5827 [] \T1/pcr/m/n/10 axes = TRUE, labels = FALSE, add = FALSE, ann = TRUE, ...)[] [854] [855] [856] Underfull \hbox (badness 10000) in paragraph at lines 6058--6060 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [857] [858] Underfull \hbox (badness 1028) in paragraph at lines 6151--6153 []\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 [859] [860] Underfull \vbox (badness 3803) has occurred while \output is active [861] [862] Underfull \hbox (badness 10000) in paragraph at lines 6410--6412 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr [863] [864] Underfull \hbox (badness 2600) in paragraph at lines 6503--6505 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6574--6574 [] \T1/pcr/m/n/9 title="Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6583--6583 [] \T1/pcr/m/n/9 title="Overlapping rectangles, one clockwise, other anti-clockwise")[] [866] [867] [868] [869] [870] [871] [872] [873] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7100--7100 [] \T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), space = "Lab")[] [874] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7111--7111 [] \T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints=0 , add=TRUE))[] [875] [876] [877] [878] [879] [880] [881] [882] [883] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7618--7618 []\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 7619--7619 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [884] Underfull \hbox (badness 2080) in paragraph at lines 7721--7726 []\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 [885] Underfull \hbox (badness 1533) in paragraph at lines 7759--7763 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i]==1\T1/ptm/m/n/10 , a (slightly en -larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn. For [886] [887] [888] [889] [890] [891] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8121--8121 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 6691) in paragraph at lines 8147--8150 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) [892] Underfull \hbox (badness 1584) in paragraph at lines 8184--8190 []\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.8232 \HeaderA{units}{Graphical Units}{units} [894] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8290--8290 []\T1/pcr/m/n/10 xspline(x, y = NULL, shape = 0, open = TRUE, repEnds = TRUE, draw = TRUE,[] Underfull \hbox (badness 1205) in paragraph at lines 8297--8299 []\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] [897]) (./grid-pkg.tex [898] Chapter 5. Underfull \vbox (badness 10000) has occurred while \output is active [899] [900] [901] [902] [903] Underfull \hbox (badness 10000) in paragraph at lines 291--297 \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 291--297 \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 [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 888--888 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 890--890 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 892--892 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [914] [915] Underfull \hbox (badness 2781) in paragraph at lines 1037--1040 []\T1/ptm/m/n/10 Both func-tions cre-ate an ar-rows grob (a graph-i-cal ob-ject de-scrib-ing ar-rows), but only [916] [917] [918] [919] Underfull \hbox (badness 3219) in paragraph at lines 1212--1215 []\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 [920] [921] [922] [923] [924] [925] [926] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1652--1652 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [927] [928] Underfull \hbox (badness 2961) in paragraph at lines 1770--1775 []\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 , [929] [930] Underfull \hbox (badness 4479) in paragraph at lines 1858--1861 []\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] Underfull \hbox (badness 2894) in paragraph at lines 1924--1931 []\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 [932] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1969--1969 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [933] [934] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2126--2126 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [935] [936] [937] [938] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2361--2361 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [939] [940] [941] [942] [943] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2670--2670 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [944] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2709--2709 []\T1/pcr/m/n/10 moveToGrob(x = 0, y = 0, default.units = "npc", name = NULL, vp = NULL)[] [945] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2765--2765 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [946] [947] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2890--2890 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2897--2897 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [948] [949] [950] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3090--3090 [] \T1/pcr/m/n/9 title="Nested rectangles, outer clockwise, inn er anti-clockwise")[] [951] Overfull \hbox (58.38037pt too wide) in paragraph at lines 3105--3105 [] \T1/pcr/m/n/9 title="Overlapping rectangles, one clockwise, other anti-clockwise")[] [952] [953] [954] [955] [956] Underfull \hbox (badness 10000) in paragraph at lines 3390--3392 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 1067) in paragraph at lines 3787--3790 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 7256) in paragraph at lines 4026--4028 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] Underfull \hbox (badness 1867) in paragraph at lines 5325--5327 []\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 [991] Underfull \hbox (badness 10000) in paragraph at lines 5362--5368 [][][]\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 , [992] [993] [994] [995] [996] [997]) (./methods-pkg.tex [998] Chapter 6. [999] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459 []\T1/pcr/m/n/10 "namedList" # the alternative to "list" that preserves the na mes attribute[] [1005] [1006] [1007] Underfull \hbox (badness 1281) in paragraph at lines 654--663 []\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 [1008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 732--732 []\T1/pcr/m/n/9 setMethod("f", "B2", function(x) {x@b0 <- 111; c(x@b2, callNex tMethod())})[] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1302--1302 []\T1/pcr/m/n/9 ## the super- and subclasses of "standardGeneric" and "derived DefaultMethod"[] [1017] [1018] [1019] [1020] [1021] [1022] Overfull \hbox (198.78021pt too wide) in paragraph at lines 1714--1714 []\T1/pcr/m/n/9 stopifnot(identical(cc(letters, character(), cd1), paste(lette rs, character(), cd1))) # the "character" method[] Overfull \hbox (355.38004pt too wide) in paragraph at lines 1716--1716 []\T1/pcr/m/n/9 stopifnot(identical(cc(letters, character(), cd2), c(letters, character(), cd2))) # the default, because "vdate" doesn\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 t extend "character"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1718--1718 []\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 1720--1720 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 1726--1726 []\T1/pcr/m/n/9 setMethod("numMax", "numeric", function(...)max(...)) # won\TS 1/pcr/m/n/9 '\T1/pcr/m/n/9 t work for complex data[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 1727--1727 []\T1/pcr/m/n/9 setMethod("numMax", "Number", function(...) paste(...)) # shou ld not be selected w/o complex args[] [1023] Underfull \hbox (badness 10000) in paragraph at lines 1760--1762 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1024] [1025] Underfull \hbox (badness 10000) in paragraph at lines 1903--1908 []\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 [1026] [1027] [1028] [1029] [1030] Underfull \hbox (badness 10000) in paragraph at lines 2257--2261 []\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 [1031] [1032] [1033] Underfull \hbox (badness 3792) in paragraph at lines 2502--2505 []\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 [1034] Underfull \hbox (badness 1194) in paragraph at lines 2533--2537 []\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 [1035] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2589--2589 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1036] [1037] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2824--2824 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1038] [1039] [1040] [1041] [1042] [1043] Underfull \hbox (badness 1552) in paragraph at lines 3181--3183 []\T1/pcr/m/n/10 packageName \T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1044] [1045] [1046] [1047] Underfull \hbox (badness 10000) in paragraph at lines 3405--3409 []\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 [1048] Overfull \hbox (28.78088pt too wide) in paragraph at lines 3519--3528 [] [1049] [1050] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3610--3610 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1051] Underfull \hbox (badness 1394) in paragraph at lines 3681--3686 \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 [1052] [1053] [1054] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3943--3943 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3963--3963 []\T1/pcr/m/n/9 setClass("stringsDated", contains = "character", representatio n(stamp="POSIXt"))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 ## In contrast, a class that simply extends "factor" has no su ch ambiguities[] Underfull \vbox (badness 10000) has occurred while \output is active [1055] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3978--3978 []\T1/pcr/m/n/9 setClass("factorDated", contains = "factor", representation(st amp="POSIXt"))[] [1056] [1057] [1058] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4192--4192 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4193--4193 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1059] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4250--4250 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here)[] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 10000) in paragraph at lines 4722--4731 []\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 [1066] [1067] [1068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4915--4915 []\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 4944--4944 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier fails here)[] Underfull \vbox (badness 10000) has occurred while \output is active [1069] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4958--4958 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] [1070] [1071] Underfull \hbox (badness 10000) in paragraph at lines 5102--5104 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1072] [1073] [1074] [1075] Underfull \hbox (badness 1087) in paragraph at lines 5391--5396 []\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 [1076] [1077] [1078] [1079] [1080] [1081] Underfull \hbox (badness 1248) in paragraph at lines 5860--5864 []\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 5860--5864 \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 [1082] Underfull \hbox (badness 4291) in paragraph at lines 5918--5932 []\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 [1083] [1084] [1085] Underfull \vbox (badness 10000) has occurred while \output is active [1086] [1087]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6272 \aliasA{S4}{S3Part}{S4} [1088] [1089] [1090] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6500--6500 []\T1/pcr/m/n/9 ## two examples extending S3 class "lm", class "xlm" directly and "ylm" indirectly[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6512--6512 []\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 6517--6517 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c ("mlm", "lm")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6526--6526 []\T1/pcr/m/n/9 setClass("dataFrameD", representation(date = "Date"), contains = "data.frame")[] [1091]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.6546 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.6548 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.6549 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.6551 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.6552 \aliasA{Summary}{S4groupGeneric}{Summary} [1092] Underfull \hbox (badness 2050) in paragraph at lines 6612--6616 []\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 6625--6635 []\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 6625--6635 \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 , [1093] [1094] Underfull \hbox (badness 1694) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see [1095] Underfull \hbox (badness 10000) in paragraph at lines 6806--6809 []\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 [1096] [1097] Underfull \hbox (badness 2111) in paragraph at lines 6912--6919 []\T1/ptm/m/n/10 The slots in a class def-i-ni-tion will be the union of all th e slots spec-i-fied di-rectly by [1098] [1099] Underfull \vbox (badness 3803) has occurred while \output is active [1100] [1101] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7236--7236 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(),[] [1102] [1103] Underfull \hbox (badness 2277) in paragraph at lines 7367--7375 []\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 [1104] Underfull \hbox (badness 3128) in paragraph at lines 7408--7413 []\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 [1105] [1106] [1107] Underfull \hbox (badness 1755) in paragraph at lines 7622--7625 []\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the method. For [1108] [1109] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7765--7765 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li nk{setClass})[] [1110] [1111] [1112] [1113] [1114] Overfull \hbox (52.98038pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/9 ## two examples extending S3 class "lm", class "xlm" directly and "ylm" indirectly[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8170--8170 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date = "POSIXt"))[] [1115] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8178--8178 []\T1/pcr/m/n/9 someLetters <- stamped(sample(letters, 10), ISOdatetime(2008, 10, 15, 12, 0, 0))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8181--8181 []\T1/pcr/m/n/9 st # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m /n/9 s class, then calls the S3 print method.[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8192--8192 [] \T1/pcr/m/n/9 prototype(NA, tsp = rep(1,3))) # prototype to be a legal S3 time-series[] [1116] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8281--8281 []\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 8292--8292 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8894--8894 []\T1/pcr/m/n/9 ## if no other attached packages have methods for \TS1/pcr/m/ n/9 `\T1/pcr/m/n/9 +\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 or its group generic[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8895--8895 []\T1/pcr/m/n/9 ## functions, this returns a 16 by 2 matrix of selection patte rns (in R 2.9.0)[] [1126] Underfull \hbox (badness 10000) in paragraph at lines 8956--8958 []\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 8964--8968 []\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 8964--8968 \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 [1127] [1128] [1129] [1130]) (./splines-pkg.tex Chapter 7. 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] Overfull \hbox (20.58041pt too wide) in paragraph at lines 463--463 []\T1/pcr/m/n/9 ispl <- polySpline( interpSpline( weight ~ height, women, bSp line = TRUE ) )[] [1139] [1140] [1141] [1142] [1143] [1144] [1145]) (./stats-pkg.tex [1146] Chapter 8. [1147] 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 , [1148] [1149] [1150] [1151] [1152] [1153] Overfull \hbox (18.78088pt too wide) in paragraph at lines 425--425 [] \T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE)[] [1154] [1155] [1156] [1157] [1158] [1159] Underfull \hbox (badness 1024) in paragraph at lines 803--805 []\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 [1160] [1161] [1162] [1163] [1164] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1138--1138 [] \T1/pcr/m/n/10 c("Pillai", "Wilks", "Hotelling-Lawley", "Roy", "Sph erical"),[] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2566--2566 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(0), ma = numeric(0), lag.max = r, pacf = FALSE)[] [1188] [1189] [1190] [1191] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2802--2802 []\T1/pcr/m/n/9 legend(40,70, c("mean","median"), lty=1,col=c("blue","green"), bg="gray90")[] [1192] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2825--2825 []\T1/pcr/m/n/10 bw.ucv(x, nb = 1000, lower = 0.1 * hmax, upper = hmax, tol = 0.1 * lower)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2827--2827 []\T1/pcr/m/n/10 bw.bcv(x, nb = 1000, lower = 0.1 * hmax, upper = hmax, tol = 0.1 * lower)[] [1193] [1194] Underfull \hbox (badness 10000) in paragraph at lines 2991--2993 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1195] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3038--3038 []\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 3039--3039 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3627--3627 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0)[] [1205] [1206] [1207] [1208] [1209] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3911--3911 []\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 3912--3912 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1210] [1211] [1212] Underfull \hbox (badness 10000) in paragraph at lines 4070--4072 []\T1/ptm/m/n/10 the Pear-son resid-u-als, \T1/pcr/m/n/10 (observed - expected) / [1213] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4122--4122 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1214] [1215] [1216] [1217] Underfull \hbox (badness 3989) in paragraph at lines 4366--4373 []\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 = [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4929--4929 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] [1226] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4947--4947 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter"))[] Underfull \hbox (badness 10000) in paragraph at lines 4979--4981 []\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 , \T1/pcr/m/n/10 m <- [1227] [1228] [1229] Underfull \hbox (badness 1436) in paragraph at lines 5157--5162 []\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 5157--5162 \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 5157--5162 \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 , [1230] [1231] [1232] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5319--5319 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1233] [1234] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5484--5484 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE,[] [1235] [1236] [1237] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5664--5664 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL)[] [1238] [1239] [1240] [1241] [1242] [1243] Underfull \hbox (badness 5954) in paragraph at lines 5993--5995 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1244] Underfull \hbox (badness 2503) in paragraph at lines 6060--6062 []\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 6063--6065 []\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 [1245] [1246] [1247] [1248] [1249] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6354--6354 [] \T1/pcr/m/n/9 ylim = c(0, 1), xlab="", main="R\TS1/pcr/m/n/9 '\T1/pcr/m /n/9 s density() kernels with width = 1")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6363--6363 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1250] [1251] [1252] [1253] [1254] [1255] Underfull \hbox (badness 10000) in paragraph at lines 6730--6734 \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 [1256] Underfull \hbox (badness 6493) in paragraph at lines 6828--6831 []\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 [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] Underfull \hbox (badness 3780) in paragraph at lines 7360--7365 []\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 , ..., \T 1/pcr/m/n/10 x[t- [1266] [1267] [1268] [1269] [1270] Underfull \hbox (badness 1210) in paragraph at lines 7689--7691 []\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 [1271] [1272] [1273] [1274] [1275] [1276] [1277] Underfull \vbox (badness 3803) has occurred while \output is active [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8619--8619 [] \T1/pcr/m/n/9 satisfaction=c("VeryD", "LittleD", "ModerateS" , "VeryS")))[] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] Underfull \hbox (badness 2443) in paragraph at lines 9242--9248 [][][]\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); [1296] [1297] [1298] [1299] [1300] [1301] [1302] Underfull \hbox (badness 4518) in paragraph at lines 9684--9689 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1303] Underfull \hbox (badness 4132) in paragraph at lines 9723--9727 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1304] Underfull \hbox (badness 10000) in paragraph at lines 9826--9829 []\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 [1305] [1306] [1307] Underfull \hbox (badness 2142) in paragraph at lines 10025--10028 []\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 ^^@ [1308] [1309] Underfull \hbox (badness 1708) in paragraph at lines 10106--10109 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: Underfull \hbox (badness 10000) in paragraph at lines 10147--10153 [][][]\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, [1310] [1311] Underfull \hbox (badness 2635) in paragraph at lines 10315--10321 \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 [1312] [1313] [1314] Underfull \hbox (badness 1694) in paragraph at lines 10469--10472 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1315] [1316] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10598--10598 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 10611--10615 []\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 [1317] [1318] [1319] [1320] [1321] [1322] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10907--10907 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]),col=2:4), D EV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.10922 \aliasA{hat}{influence.measures}{hat} [1323] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10976--10976 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10988--10988 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 11034--11039 []\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- [1324] Underfull \hbox (badness 1052) in paragraph at lines 11045--11047 []\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 [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 4518) in paragraph at lines 12485--12490 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1349] [1350] [1351] Underfull \hbox (badness 10000) in paragraph at lines 12679--12683 []\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 , [1352] [1353] [1354] [1355] [1356] Underfull \hbox (badness 1163) in paragraph at lines 12997--13005 \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 , [1357] [1358] Underfull \hbox (badness 4518) in paragraph at lines 13107--13112 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1359] [1360] [1361] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13281--13281 []\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 13282--13282 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1362] Underfull \hbox (badness 10000) in paragraph at lines 13329--13332 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, \T1/pcr/m/n/10 plogis(x) == (1+ [1363] [1364] [1365] [1366] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13606--13606 []\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 13607--13607 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] Underfull \hbox (badness 2726) in paragraph at lines 14092--14095 []\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 , [1375] [1376] [1377] [1378] [1379] Underfull \vbox (badness 10000) has occurred while \output is active [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] Underfull \hbox (badness 1648) in paragraph at lines 14983--14985 []\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, [1390] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15061--15061 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a="contr.sum", b="c ontr.poly"))[] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15612--15612 []\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[] [1400] [1401] [1402] [1403] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15827--15827 []\T1/pcr/m/n/9 persp(x,size, dnb <- outer(x, size, function(x,s) dnbinom(x,s, prob= 0.4)),[] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] Underfull \vbox (badness 10000) has occurred while \output is active [1414] [1415] [1416] [1417] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16680--16680 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1418] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16727--16727 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1419] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16774--16774 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1420] [1421] [1422] [1423] [1424] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17076--17076 [] \T1/pcr/m/n/10 method = c("Nelder-Mead", "BFGS", "CG", "L-BFGS-B", "SA NN"),[] [1425] Underfull \hbox (badness 1248) in paragraph at lines 17182--17185 []\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 17195--17199 \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 [1426] Underfull \hbox (badness 2042) in paragraph at lines 17253--17255 []\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 [1427] [1428] Underfull \vbox (badness 10000) has occurred while \output is active [1429] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17382--17382 [] \T1/pcr/m/n/9 control = list(maxit=30000, temp=2000, trace=TRUE , REPORT=500))[] [1430] Underfull \hbox (badness 2564) in paragraph at lines 17457--17468 []\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 17457--17468 \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 [1431] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17516--17516 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1432] [1433] [1434] [1435] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17791--17791 [] \T1/pcr/m/n/10 alternative = c("two.sided", "less", "greater "), ...)[] Underfull \hbox (badness 1337) in paragraph at lines 17803--17806 []\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 [1436] [1437] [1438] [1439] [1440] [1441] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18119--18119 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1442] [1443] Overfull \hbox (42.78088pt too wide) in paragraph at lines 18207--18207 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s d ist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 18210--18210 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1444] [1445] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18325--18325 []\T1/pcr/m/n/9 plot(lm.SR <- lm(sr ~ pop15 + pop75 + dpi + ddpi, data = LifeC ycleSavings))[] [1446] [1447] [1448] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18512--18512 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 18522--18525 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1449] Underfull \hbox (badness 1107) in paragraph at lines 18580--18582 []\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 [1450] [1451] [1452] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18735--18735 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1453] [1454] [1455] Underfull \hbox (badness 2343) in paragraph at lines 18913--18915 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 6859) in paragraph at lines 19867--19874 [][][]\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 19877--19883 []\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 , [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20835--20835 [] \T1/pcr/m/n/10 cs.ind = 1L:k, tst.ind = k + 1L, zap.ind = integ er(0),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20838--20838 [] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == "Pr(",[] [1488] [1489] [1490] [1491] [1492] [1493] Underfull \hbox (badness 1337) in paragraph at lines 21160--21166 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 10000) in paragraph at lines 21904--21907 []\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 21904--21907 \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 [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] Underfull \hbox (badness 8094) in paragraph at lines 22480--22483 []\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 \T1/pcr/m/n/10 y[j] = [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] Underfull \hbox (badness 1412) in paragraph at lines 23298--23300 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1529] [1530] [1531] [1532] [1533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23657--23657 []\T1/pcr/m/n/9 (s2 <- smooth.spline(y18, control = list(trace=TRUE,tol=1e-6, low= -1.5)))[] [1534] [1535] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23795--23795 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail,[] [1536] [1537] [1538] [1539] [1540] [1541] [1542] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24170--24170 []\T1/pcr/m/n/10 splinefun(x, y = NULL, method = c("fmm", "periodic", "natural ", "monoH.FC"),[] [1543] [1544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24322--24322 []\T1/pcr/m/n/9 legend("topleft", paste("splinefun( \"", c("fmm", "monoH.CS"), "\" )", sep=\TS1/pcr/m/n/9 ''\T1/pcr/m/n/9 ),[] [1545] [1546] Underfull \hbox (badness 3240) in paragraph at lines 24429--24433 [][][]\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 [1547] [1548] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24557--24557 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1549] [1550] Underfull \hbox (badness 10000) in paragraph at lines 24667--24670 \T1/pcr/m/n/10 exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input)-exp(-exp(lKa)*input)) / Overfull \hbox (9.78043pt too wide) in paragraph at lines 24689--24689 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response and gradient[] [1551] [1552] [1553] Underfull \hbox (badness 2922) in paragraph at lines 24840--24845 []\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 [1554] Underfull \hbox (badness 2922) in paragraph at lines 24895--24900 []\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] [1556] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24990--24990 []\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 24992--24992 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1557] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25049--25049 []\T1/pcr/m/n/10 stat.anova(table, test = c("Chisq", "F", "Cp"), scale, df.sca le, n)[] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25558--25558 [] \T1/pcr/m/n/10 main = NULL, range.bars = TRUE, ..., col.range = "light gray")[] [1566] [1567] [1568] [1569] [1570] Underfull \hbox (badness 3396) in paragraph at lines 25856--25858 []\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 [1571] [1572] [1573] Underfull \hbox (badness 2237) in paragraph at lines 26028--26030 []\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 [1574] [1575] [1576] Underfull \hbox (badness 2591) in paragraph at lines 26185--26187 []\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 [1577] Underfull \hbox (badness 2237) in paragraph at lines 26231--26234 []\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 [1578] [1579] Underfull \hbox (badness 3407) in paragraph at lines 26409--26413 []\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) [1580] [1581] [1582] Underfull \hbox (badness 1337) in paragraph at lines 26542--26546 []\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 [1583] [1584] [1585] [1586] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26808--26808 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 26832--26835 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1587] [1588] [1589] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26958--26958 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1590] Underfull \hbox (badness 2205) in paragraph at lines 27041--27046 []\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 [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 10000) in paragraph at lines 27551--27555 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 tsp \T1/ptm/m/n/10 at-tribute was pre-vi-ou sly de-scribed here as \T1/pcr/m/n/10 c(start(x), end(x), [1600] Overfull \hbox (12.78088pt too wide) in paragraph at lines 27630--27630 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 27631--27631 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 1337) in paragraph at lines 28131--28135 []\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 [1610] [1611] [1612] [1613] Underfull \hbox (badness 1043) in paragraph at lines 28371--28374 []\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 -pweibull(t, a, b, lower = Overfull \hbox (4.38043pt too wide) in paragraph at lines 28398--28398 []\T1/pcr/m/n/9 all.equal(pweibull(x, 2.5, pi, lower.tail=FALSE, log.p=TRUE), -(x/pi)^2.5,[] [1614] [1615] [1616] Underfull \hbox (badness 1337) in paragraph at lines 28552--28556 []\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 [1617] [1618] [1619] [1620] [1621] [1622] [1623] Overfull \hbox (66.78088pt too wide) in paragraph at lines 28956--28956 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, na.action,[] [1624] [1625] [1626]) (./stats4-pkg.tex Chapter 9. [1627] [1628] [1629] Overfull \hbox (112.38031pt too wide) in paragraph at lines 227--227 [] \T1/pcr/m/n/9 if(ymax > 0 && xhalf > 0) -sum(stats::dpois(y, lambda=ymax /(1+x/xhalf), log=TRUE)) else NA[] [1630] Overfull \hbox (9.78043pt too wide) in paragraph at lines 242--242 []\T1/pcr/m/n/9 ## the lower bounds are really > 0, but we use >=0 to stress-t est profiling[] [1631] [1632] [1633]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.457 ... in Package 'stats4'}{show.Rdash.methods} [1634] Underfull \hbox (badness 10000) in paragraph at lines 490--493 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1635] [1636]) (./tcltk-pkg.tex Chapter 10. [1637] [1638] [1639] [1640] [1641] Overfull \hbox (36.7804pt too wide) in paragraph at lines 378--378 [] \T1/pcr/m/n/9 # Do some work to create a nice picture. Nothing will be displayed until...[] [1642] [1643] Overfull \hbox (30.78088pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/10 ## NB: some widgets also have a selection.clear command, henc e the "X".[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 548--548 []\T1/pcr/m/n/10 ## winfo actually has a large number of subcommands, but it\T S1/pcr/m/n/10 '\T1/pcr/m/n/10 s rarely[] Underfull \vbox (badness 10000) has occurred while \output is active [1644] Underfull \vbox (badness 10000) has occurred while \output is active [1645] Underfull \hbox (badness 1292) in paragraph at lines 641--648 []\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 [1646] [1647] [1648] [1649] Underfull \vbox (badness 10000) has occurred while \output is active [1650] [1651] [1652] [1653] [1654] [1655] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1345--1345 []\T1/pcr/m/n/10 tk_select.list(choices, preselect = NULL, multiple = FALSE, t itle = NULL)[] [1656] [1657]) (./tools-pkg.tex [1658] Chapter 11. [1659] Underfull \hbox (badness 1308) in paragraph at lines 80--95 []\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 types Underfull \hbox (badness 1742) in paragraph at lines 80--95 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as a rou-tine to pro-duce a sort Underfull \hbox (badness 1360) in paragraph at lines 80--95 \T1/ptm/m/n/10 key to sort the en-tries. The for-mer must be named \T1/pcr/m/n/ 10 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1660] Overfull \hbox (9.78043pt too wide) in paragraph at lines 129--129 []\T1/pcr/m/n/9 bibstyle("unsorted", sortKeys = function(refs) seq_along(refs) , .init=TRUE)[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 145--145 []\T1/pcr/m/n/10 buildVignettes(package, dir, lib.loc = NULL, quiet = TRUE, cl ean = TRUE)[] [1661] Underfull \hbox (badness 2644) in paragraph at lines 203--208 \T1/ptm/m/n/10 (there can be more than one name for a Uni-code point). The data are in the file Underfull \hbox (badness 10000) in paragraph at lines 211--212 [][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer / en / opentype / glyphlist . [1662] [1663] [1664] Underfull \vbox (badness 10000) has occurred while \output is active [1665] [1666] Overfull \hbox (0.78088pt too wide) in paragraph at lines 470--470 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1667] [1668] [1669] [1670] Underfull \hbox (badness 10000) in paragraph at lines 722--725 []\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 [1671] Overfull \hbox (36.78088pt too wide) in paragraph at lines 793--793 []\T1/pcr/m/n/10 dependsOnPkgs(pkgs, dependencies = c("Depends", "Imports", "L inkingTo"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 795--795 [] \T1/pcr/m/n/10 installed = installed.packages(lib.loc, fields = "Enhances"))[] Underfull \hbox (badness 7981) in paragraph at lines 802--805 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 802--805 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", [1672] [1673] [1674] [1675] [1676] Underfull \hbox (badness 10000) in paragraph at lines 1073--1078 []\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 1073--1078 \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 1073--1078 \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 [1677] [1678] [1679] [1680] [1681] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1346--1346 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1682] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1385--1385 []\T1/pcr/m/n/10 parseLatex(text, filename = deparse(substitute(text)), verbos e = FALSE,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1386--1386 [] \T1/pcr/m/n/10 verbatim = c("verbatim", "verbatim*", "Sinput", "S output"))[] [1683] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1466--1466 []\T1/pcr/m/n/10 parse_Rd(file, srcfile = NULL, encoding = "unknown", verbose = FALSE,[] [1684] [1685] [1686] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1646--1646 [] \T1/pcr/m/n/10 stages = "render", outputEncoding = "ASCII", fragmen t = FALSE, ...,[] [1687] Underfull \hbox (badness 1072) in paragraph at lines 1670--1672 []\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 [1688] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1792--1792 []\T1/pcr/m/n/9 browseURL(Rd2HTML(Rd, outfile, package="tools", stages=c("inst all", "render")))[] [1689] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1795--1795 []\T1/pcr/m/n/9 file.show(Rd2txt(Rd, outfile, package="tools", stages=c("insta ll", "render")))[] [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2382--2382 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Underfull \hbox (badness 2932) in paragraph at lines 2415--2421 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3758) in paragraph at lines 2695--2700 []\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 2695--2700 \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 [1705] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2734--2734 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Underfull \hbox (badness 1742) in paragraph at lines 2746--2758 \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 , [1706] Underfull \hbox (badness 3623) in paragraph at lines 2803--2806 []\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 [1707] [1708] [1709]) (./utils-pkg.tex [1710] Chapter 12. [1711] [1712] [1713] [1714] [1715] [1716] Overfull \hbox (24.78088pt too wide) in paragraph at lines 352--352 []\T1/pcr/m/n/10 available.packages(contriburl = contrib.url(getOption("repos" ), type),[] Underfull \hbox (badness 4505) in paragraph at lines 391--398 \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 [1717] Underfull \hbox (badness 1275) in paragraph at lines 439--445 []\T1/ptm/m/n/10 A ma-trix with one row per pack-age, row names the pack-age na mes and col-umn names Underfull \hbox (badness 2057) in paragraph at lines 439--445 \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 , \T1/pcr/m/n/10 "LinkingTo"\T1/p tm/m/n/10 , Underfull \hbox (badness 1603) in paragraph at lines 471--476 \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 471--476 \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 [1718] Overfull \hbox (6.78088pt too wide) in paragraph at lines 523--523 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL,[] [1719] [1720] [1721] Overfull \hbox (15.18042pt too wide) in paragraph at lines 712--712 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1722] [1723] Overfull \hbox (24.78088pt too wide) in paragraph at lines 825--825 []\T1/pcr/m/n/10 browseURL(url, browser = getOption("browser"), encodeIfNeeded = FALSE)[] [1724] [1725] [1726] [1727] Underfull \hbox (badness 1859) in paragraph at lines 1081--1090 []\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- [1728] [1729] [1730] [1731] [1732] [1733] Underfull \hbox (badness 1082) in paragraph at lines 1426--1430 [][][]\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; [1734] [1735] [1736] [1737] [1738] [1739] [1740] Underfull \hbox (badness 1430) in paragraph at lines 1837--1840 []\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 \T1/pcr/m/n/10 package = Overfull \hbox (15.18042pt too wide) in paragraph at lines 1878--1878 []\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 '[] [1741] Underfull \hbox (badness 2452) in paragraph at lines 1951--1954 []\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 [1742] [1743] [1744] [1745] [1746] [1747] Underfull \hbox (badness 1072) in paragraph at lines 2317--2323 []\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 2317--2323 \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 [1748] Underfull \hbox (badness 1057) in paragraph at lines 2343--2357 []\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 2343--2357 \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 2343--2357 \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 2358--2364 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1749] Underfull \hbox (badness 4660) in paragraph at lines 2416--2419 \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 [1750] [1751] [1752] Underfull \hbox (badness 1565) in paragraph at lines 2614--2618 []\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 [1753] Underfull \hbox (badness 3758) in paragraph at lines 2727--2734 []\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat -ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask=TRUE) [1754] [1755] [1756] [1757] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2914--2914 []\T1/pcr/m/n/10 findLineNum(srcfile, line, nameonly = TRUE, envir = parent.fr ame(),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2917--2917 []\T1/pcr/m/n/10 setBreakpoint(srcfile, line, nameonly = TRUE, envir = parent. frame(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2918--2918 [] \T1/pcr/m/n/10 lastenv, verbose = TRUE, tracer, print = FALSE, ...)[] [1758] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3006--3006 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1759]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.3077 ...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.3077 ...mat Unordered and Ordered Lists}{format} [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 10000) in paragraph at lines 3787--3791 []\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 Underfull \hbox (badness 1502) in paragraph at lines 3831--3836 []\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 3831--3836 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1772] [1773] [1774] Underfull \hbox (badness 10000) in paragraph at lines 3985--3994 []\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 3985--3994 \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 Underfull \hbox (badness 2717) in paragraph at lines 3985--3994 [][]\T1/pcr/m/n/10 make.packages.html[][][](temp = FALSE)\T1/ptm/m/n/10 . For l o-cal op-er-a-tion, the HTTP server will [1775] [1776] Underfull \hbox (badness 1590) in paragraph at lines 4125--4129 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 setClass[][][]\T1/ptm/m/n/10 , should be i n-stalled us-ing lazy-loading: use the field \T1/pcr/m/n/10 LazyLoad \T1/ptm/m/ n/10 in the [1777] Underfull \hbox (badness 4660) in paragraph at lines 4212--4215 \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 [1778] Underfull \hbox (badness 10000) in paragraph at lines 4239--4243 []\T1/ptm/m/n/10 Possible val-ues are \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 , [1779] Underfull \hbox (badness 10000) in paragraph at lines 4346--4351 [][][]\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 , [1780] Underfull \hbox (badness 5133) in paragraph at lines 4407--4411 []\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 4419--4422 []\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 [1781] [1782] [1783] [1784] [1785] Overfull \hbox (368.28088pt too wide) in paragraph at lines 4689--4690 [][][]$\T1/pcr/m/n/10 http : / / n4 . nabble . com / R-[]help-[]question-[]How- []can-[]we-[]enable-[]useRs-[]to-[]contribute-[]corrections-[]to-[]help-[]files -[]faster-[]tp1572568p1572868 . Overfull \hbox (24.78088pt too wide) in paragraph at lines 4710--4710 []\T1/pcr/m/n/10 make.packages.html(lib.loc = .libPaths(), temp = TRUE, verbos e = TRUE)[] [1786] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4770--4770 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE)[] [1787] [1788] [1789] Underfull \hbox (badness 10000) in paragraph at lines 4942--4944 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] Underfull \hbox (badness 10000) in paragraph at lines 5513--5515 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like \T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 5518--5523 []\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, [1799] [1800] Underfull \hbox (badness 10000) in paragraph at lines 5624--5627 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed", "not [1801] [1802] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5740--5740 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5741--5741 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1803] [1804] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5883--5883 [] \T1/pcr/m/n/9 comment = "S original, http://statwww.epfl.ch/davison /BMA/library.html"),[] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] [1813] [1814] Underfull \hbox (badness 5203) in paragraph at lines 6498--6501 []\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 [1815] Underfull \hbox (badness 1163) in paragraph at lines 6603--6606 []\T1/ptm/m/n/10 the to-ken that was (or, is to be) com-pleted, as set by the l ast call to [1816] Underfull \hbox (badness 1072) in paragraph at lines 6715--6723 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [1817] [1818] [1819] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6894--6894 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header= TRUE, tra nspose=TRUE)[] [1820] [1821] [1822] [1823] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7149--7149 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] [1824] Underfull \hbox (badness 1077) in paragraph at lines 7220--7223 []\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 [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 7797--7801 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1835] [1836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7915--7915 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0)[] [1837] [1838] [1839] [1840] Underfull \hbox (badness 6725) in paragraph at lines 8156--8165 \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 8156--8165 \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 8156--8165 \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 8156--8165 \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 [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8200--8200 []\T1/pcr/m/n/9 ## Search in R-devel archive and recent R-help (and store the query-string):[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8202--8202 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("S4", restrict = c("R-dev", "Rhelp10" , "Rhelp08"))[] [1842] Underfull \hbox (badness 10000) in paragraph at lines 8287--8289 [][][]$\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 / [1843] [1844] Underfull \hbox (badness 10000) in paragraph at lines 8406--8410 []\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 [1845] Underfull \hbox (badness 10000) in paragraph at lines 8437--8443 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1846] [1847] [1848] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8639--8639 []\T1/pcr/m/n/10 select.list(choices, preselect = NULL, multiple = FALSE, titl e = NULL,[] [1849] Underfull \hbox (badness 10000) in paragraph at lines 8728--8731 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. In re-cent ve r- Underfull \hbox (badness 10000) in paragraph at lines 8728--8731 \T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form [1850] Underfull \hbox (badness 10000) in paragraph at lines 8736--8739 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g Overfull \hbox (0.78088pt too wide) in paragraph at lines 8762--8762 []\T1/pcr/m/n/10 setRepositories(graphics = getOption("menu.graphics"), ind = NULL)[] Underfull \hbox (badness 10000) in paragraph at lines 8779--8783 \T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son al copy in [1851] Underfull \hbox (badness 2158) in paragraph at lines 8798--8801 []\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 [1852] [1853] [1854] [1855] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9027--9027 [] \T1/pcr/m/n/10 format(x, trim=TRUE, drop0trailing=TRU E, ...))[] Underfull \hbox (badness 5970) in paragraph at lines 9055--9058 []\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 9055--9058 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [1856] [1857] [1858] [1859] Underfull \hbox (badness 5504) in paragraph at lines 9296--9299 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 SweaveSyntax \T1/ptm/m/n/10 or a char-ac-ter string with its Underfull \hbox (badness 3635) in paragraph at lines 9296--9299 \T1/ptm/m/n/10 name. The de-fault in-stal-la-tion pro-vides \T1/pcr/m/n/10 Swea veSyntaxNoweb \T1/ptm/m/n/10 and Underfull \hbox (badness 1178) in paragraph at lines 9322--9334 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, a num-ber of hook func- tions can be ex-e-cuted. If [1860] [1861] [1862] [1863] Underfull \hbox (badness 10000) in paragraph at lines 9535--9538 [][][]$\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 : / / www . Underfull \hbox (badness 10000) in paragraph at lines 9535--9538 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 009695399 / utilities / pax . htm l # tag _ 04 _ 100 _ [1864] [1865] [1866] [1867] [1868] [1869] [1870] Underfull \hbox (badness 4660) in paragraph at lines 9973--9976 \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 (24.87935pt too wide) in paragraph at lines 9984--9988 []\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 . [1871] Underfull \hbox (badness 3557) in paragraph at lines 9990--9992 []\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 9993--9995 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 10023--10028 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 10000) in paragraph at lines 10044--10049 []\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 10052--10055 [][][]\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 , [1872] [1873] Underfull \hbox (badness 10000) in paragraph at lines 10140--10145 []\T1/ptm/m/n/10 Characters in a URL other than the En-glish al-phanu-meric cha r-ac-ters and [1874] [1875] [1876] [1877] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10357--10357 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ",[] Underfull \hbox (badness 1454) in paragraph at lines 10383--10387 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 10403--10406 []\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 [1878] [1879] Underfull \hbox (badness 3872) in paragraph at lines 10532--10534 []\T1/ptm/m/n/10 character string: the method to be used, an empty string in-di -cates [1880] [1881]) [1882] No file refman.ind. (./refman.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showMlist} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.standardGeneric} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Surv} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}< /usr/share/texmf-texlive/fonts/type1/urw/courier/ucrb8a.pfb> Output written on refman.pdf (1885 pages, 4547928 bytes). Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2009] (kpathsea + Thai support). Scanning input file refman.idx...............done (11412 entries accepted, 8 rejected). Sorting entries............................................................................................................................done (180010 comparisons). Generating output file refman.ind..............done (8596 lines written, 46 warnings). Output written in refman.ind. Transcript written in refman.ilg. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/bm.sty) (/usr/share/texmf-texlive/tex/latex/base/alltt.sty) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (../../share/texmf/tex/latex/upquote.sty (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))) NOT loading ae (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) NOT loading lmodern (/usr/share/texmf-texlive/tex/latex/graphics/color.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 332. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 332. ) (/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/base/makeidx.sty) Writing index file refman.idx (./refman.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./refman.out) (./refman.out) (/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-texlive/tex/latex/psnfss/ts1ptm.fd) [1{/var/l ib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./refman.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] (./base-pkg.tex Chapter 1. [1] Underfull \hbox (badness 2443) in paragraph at lines 71--77 []\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 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 2334) in paragraph at lines 71--77 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is Underfull \hbox (badness 3407) in paragraph at lines 71--77 \T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er- wise, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 1960) in paragraph at lines 77--85 []\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 . It Underfull \hbox (badness 1189) in paragraph at lines 77--85 \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, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 1661) in paragraph at lines 77--85 \T1/pcr/m/n/10 double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m/n /10 1.110223e-16\T1/ptm/m/n/10 . As [2] [3] [4] Underfull \hbox (badness 10000) in paragraph at lines 224--228 \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.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 261--264 [][][]\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, [5] Underfull \hbox (badness 2359) in paragraph at lines 305--308 []\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 [6] [7] [8] [9] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [10] [11] Overfull \hbox (0.78088pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE)[] [12] [13] [14] [15] Underfull \hbox (badness 1838) in paragraph at lines 933--936 []\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 [16] [17] [18] [19] [20] [21] [22] [23] Underfull \hbox (badness 2865) in paragraph at lines 1448--1451 []\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 [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1596--1598 []\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 [26] [27] Underfull \hbox (badness 10000) in paragraph at lines 1742--1744 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [28] [29] [30] [31] [32] [33] [34] [35] Underfull \hbox (badness 5878) in paragraph at lines 2233--2238 []\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 2233--2238 \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 [36] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 2432--2435 [39] Underfull \hbox (badness 10000) in paragraph at lines 2466--2468 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 forwardsolve(L, b) \T1/ptm/m/n/10 is just a wrap-per for \T1/pcr/m/n/10 backsolve(L, b, [40] [41] [42] Underfull \vbox (badness 3803) has occurred while \output is active [43] [44] [45] [46] [47] [48] Underfull \hbox (badness 10000) in paragraph at lines 3016--3018 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Underfull \hbox (badness 2521) in paragraph at lines 4046--4048 []\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 [66] [67] [68] [69] [70] Underfull \hbox (badness 1270) in paragraph at lines 4366--4374 []\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 \T1/pcr/m/n/10 c("first", [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2443) in paragraph at lines 4874--4881 []\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 : / / [79] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4904--4904 []\T1/pcr/m/n/9 z <- c(32:126, 160:255) # range of most 8-bit charsets, Latin- 1 in Unicode[] [80] [81] [82] [83] Underfull \hbox (badness 1635) in paragraph at lines 5180--5183 []\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 5184--5187 []\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 5201--5214 []\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 5215--5223 []\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 [84] [85] [86] [87] Underfull \hbox (badness 2158) in paragraph at lines 5424--5428 \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 [88] Underfull \hbox (badness 10000) in paragraph at lines 5506--5514 []\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 [89] [90] Underfull \hbox (badness 1067) in paragraph at lines 5698--5705 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [91] [92] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5803--5803 []\T1/pcr/m/n/9 ## fifo example -- may fail, e.g. on Cygwin, even with OS supp ort for fifos[] Underfull \vbox (badness 10000) has occurred while \output is active [93] [94] [95] [96] [97] [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6296--6298 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [101] [102] [103] [104] [105] [106] Underfull \hbox (badness 8132) in paragraph at lines 6666--6670 []\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 6666--6670 \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 [107] Underfull \hbox (badness 10000) in paragraph at lines 6685--6696 []\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 2875) in paragraph at lines 6685--6696 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional=TRUE)\T1/ptm/m/n/10 . As that i s a generic func-tion, meth-ods can be Overfull \hbox (4.63962pt too wide) in paragraph at lines 6717--6721 []\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") [108] [109] [110] [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 5802) in paragraph at lines 7298--7302 []\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 [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 7422--7426 \T1/pcr/m/n/10 trace("plot", browser, exit=browser, signature = c("track", [119] [120] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7550--7550 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO ! "); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 7567--7567 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] [121] [122] Underfull \hbox (badness 4254) in paragraph at lines 7697--7701 []\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 [123] [124] Underfull \hbox (badness 1603) in paragraph at lines 7844--7847 []\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 [125] Overfull \hbox (60.78088pt too wide) in paragraph at lines 7873--7873 []\T1/pcr/m/n/10 detach(name, pos = 2, unload = FALSE, character.only = FALSE, force = FALSE)[] [126] [127] [128] [129] [130] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8194--8194 []\T1/pcr/m/n/10 ## Group methods, notably for round(), signif(), floor(), cei ling(),[] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 2150) in paragraph at lines 8991--8994 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [143] Underfull \hbox (badness 5316) in paragraph at lines 9004--9012 \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 9013--9015 []\T1/pcr/m/n/10 duplicated(x, fromLast=TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than [144] [145] [146] Underfull \hbox (badness 10000) in paragraph at lines 9214--9217 []\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 [147] [148] [149] [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 5288) in paragraph at lines 9865--9867 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [156] Underfull \hbox (badness 3039) in paragraph at lines 9875--9878 []\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 Underfull \hbox (badness 10000) in paragraph at lines 9934--9936 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [157] [158] [159] Underfull \vbox (badness 3803) has occurred while \output is active [160] Underfull \hbox (badness 10000) in paragraph at lines 10159--10161 []\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 10342--10352 []\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 10342--10352 \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] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] Underfull \hbox (badness 2165) in paragraph at lines 11588--11590 []\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 \T1/pcr /m/n/10 fsep = [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 11791--11795 [][][]\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 , [186] Overfull \hbox (30.78088pt too wide) in paragraph at lines 11836--11836 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [187] Underfull \hbox (badness 10000) in paragraph at lines 11897--11900 [][][]\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 (0.78088pt too wide) in paragraph at lines 11918--11918 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE)[] [188] Underfull \hbox (badness 3965) in paragraph at lines 11944--11948 []\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] [191] [192] [193] [194] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12353--12353 [] \T1/pcr/m/n/10 decimal.mark = ".", zero.print = NULL, drop0trailing = FAL SE, ...)[] [195] Underfull \hbox (badness 1168) in paragraph at lines 12393--12397 []\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 12393--12397 \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 12479--12482 [][][]\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 , [197] [198] [199] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12647--12647 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA, ...)[] Underfull \hbox (badness 2790) in paragraph at lines 12653--12656 []\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 1024) in paragraph at lines 12684--12688 []\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 12750--12758 []\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] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] Underfull \hbox (badness 2418) in paragraph at lines 13701--13705 \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 13708--13711 []\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 [217] Underfull \hbox (badness 2326) in paragraph at lines 13737--13744 [][][]\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 , [218] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13837--13837 []\T1/pcr/m/n/9 ## Not run: ## for translation, those strings should appear in R-pkg.pot as[] [219] [220] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13978--13978 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE,[] [221] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13981--13981 []\T1/pcr/m/n/10 grepl(pattern, x, ignore.case = FALSE, perl = FALSE, fixed = FALSE,[] Underfull \hbox (badness 1867) in paragraph at lines 14000--14007 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] Underfull \hbox (badness 2285) in paragraph at lines 14871--14873 []\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 (24.78088pt too wide) in paragraph at lines 14901--14901 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE)[] [235] [236] [237] Underfull \hbox (badness 1072) in paragraph at lines 15084--15087 []\T1/ptm/m/n/10 Sometimes it is bet-ter to use a con-struc-tion such as \T1/pc r/m/n/10 (tmp <- yes; tmp[!test] <- [238] [239] [240] [241] Underfull \hbox (badness 10000) in paragraph at lines 15311--15313 []\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 [242] Underfull \hbox (badness 4217) in paragraph at lines 15395--15404 [][][]\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 15410--15426 [][][]\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 , [243] [244] [245] [246] [247] [248] [249] [250] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15912--15912 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [251] [252] [253] Underfull \hbox (badness 4739) in paragraph at lines 16035--16037 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [254] [255] [256] [257] [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16512--16514 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [262] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16559--16559 []\T1/pcr/m/n/9 vapply(i39, fivenum, c(Min.=0, "1st Qu."=0, Median=0, "3rd Qu. "=0, Max.=0))[] Underfull \hbox (badness 1975) in paragraph at lines 16575--16578 []\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 [263] [264] [265] [266] Underfull \hbox (badness 10000) in paragraph at lines 16835--16839 []\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 [267] [268] Underfull \hbox (badness 10000) in paragraph at lines 16990--16994 []\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 16990--16994 [][]\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 [269] Underfull \hbox (badness 1221) in paragraph at lines 17038--17043 []\T1/ptm/m/n/10 Normally \T1/pcr/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of loaded pack-ages, but \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 o r \T1/pcr/m/n/10 FALSE [270] Underfull \hbox (badness 10000) in paragraph at lines 17125--17131 [][][]\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 library.dynam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 data[][][]\T1/ptm/m/n/10 , [271] [272] Underfull \hbox (badness 10000) in paragraph at lines 17260--17264 []\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 [273] Underfull \hbox (badness 1264) in paragraph at lines 17309--17313 []\T1/phv/m/n/10 R \T1/ptm/m/n/10 is dis-tributed un-der the terms of the GNU G EN-ERAL PUB-LIC LI-CENSE Ver-sion 2, [274] [275] [276] [277] Underfull \hbox (badness 3343) in paragraph at lines 17523--17527 [][][]\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 17606--17606 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] [279] [280] Underfull \hbox (badness 6380) in paragraph at lines 17732--17737 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 10000) in paragraph at lines 17764--17767 []\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 , [281] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17832--17832 []\T1/pcr/m/n/9 Sys.setlocale("LC_COLLATE", "C") # turn off locale-specific sorting, usually[] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18697--18697 []\T1/pcr/m/n/9 ## Simple version: intersect <- function(x, y) y[match(x, y, nomatch = 0)][] [296] [297] Underfull \hbox (badness 1655) in paragraph at lines 18813--18817 []\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] [307] Underfull \hbox (badness 4366) in paragraph at lines 19405--19411 \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 . Overfull \hbox (60.78088pt too wide) in paragraph at lines 19444--19444 []\T1/pcr/m/n/10 R --min-vsize=vl --max-vsize=vu --min-nsize=nl --max-nsize=nu --max-ppsize=N[] [308] [309] [310] [311] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19694--19694 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19695--19695 [] \T1/pcr/m/n/10 sort = TRUE, suffixes = c(".x",".y"), incomparables = N ULL, ...)[] [312] [313] [314] [315] [316] [317] [318] [319] Underfull \hbox (badness 3849) in paragraph at lines 20216--20221 []\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 [320] [321] [322] [323] Underfull \hbox (badness 1609) in paragraph at lines 20439--20441 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of \T1/pcr/m/n/10 c("bytes", "chars", [324] [325] [326] [327] [328] [329] [330] [331] [332] Underfull \hbox (badness 10000) in paragraph at lines 21003--21009 []\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 21003--21009 \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] Underfull \hbox (badness 8189) in paragraph at lines 21188--21194 []\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 [][]mode [][][] [335] [336] [337] Underfull \hbox (badness 1694) in paragraph at lines 21371--21374 []\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] [341] Underfull \hbox (badness 1603) in paragraph at lines 21601--21603 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [342] Underfull \hbox (badness 1210) in paragraph at lines 21707--21716 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [343] [344] Underfull \hbox (badness 5475) in paragraph at lines 21802--21810 []\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 21819--21823 []\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 4048) in paragraph at lines 21835--21844 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue \T1/pcr/m/n/10 " [345] [346] Underfull \hbox (badness 3138) in paragraph at lines 22045--22051 []\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 3514) in paragraph at lines 22045--22051 \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- [347] Underfull \hbox (badness 10000) in paragraph at lines 22095--22102 []\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 22104--22111 []\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 2384) in paragraph at lines 22104--22111 \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 CRAN Underfull \hbox (badness 2837) in paragraph at lines 22104--22111 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke \T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 22104--22111 \T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran"; Underfull \hbox (badness 1881) in paragraph at lines 22117--22122 []\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] [352] Underfull \hbox (badness 10000) in paragraph at lines 22408--22411 []\T1/pcr/m/n/10 FUN = "*" \T1/ptm/m/n/10 is han-dled in-ter-nally as a spe-cia l case, \T1/ptm/m/it/10 via \T1/pcr/m/n/10 as.vector(X) %*% [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 23051--23055 []\T1/ptm/m/n/10 This func-tion is al-most never used: \T1/pcr/m/n/10 `name` \T 1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m/n/10 get[][][](name, [364] Underfull \hbox (badness 1796) in paragraph at lines 23114--23117 []\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] [368] [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 7415) in paragraph at lines 24177--24181 []\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 [382] [383] [384] [385] [386] Underfull \hbox (badness 1533) in paragraph at lines 24552--24555 []\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] [388] Underfull \hbox (badness 1337) in paragraph at lines 24649--24652 []\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., [389] Underfull \hbox (badness 1038) in paragraph at lines 24714--24724 []\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 [390] [391] [392] [393] [394] [395] [396] [397] Underfull \hbox (badness 4048) in paragraph at lines 25182--25187 []\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 25182--25187 \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 25182--25187 \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 , [398] [399] [400] [401] [402] [403] [404] [405] [406] [407] [408] Overfull \hbox (153.38951pt too wide) in paragraph at lines 25881--25883 []\T1/ptm/m/n/10 Punctuation char-ac-ters: `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr /m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/1 0 ` \T1/pcr/m/n/10 { | } ~\T1/ptm/m/n/10 '. Overfull \hbox (25.91963pt too wide) in paragraph at lines 25891--25893 []\T1/ptm/m/n/10 Hexadecimal dig-its: `\T1/pcr/m/n/10 0 1 2 3 4 5 6 7 8 9 A B C D E F a b c d e f\T1/ptm/m/n/10 '. [409] [410] [411] Underfull \hbox (badness 5417) in paragraph at lines 26101--26104 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 26105--26107 []\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 26108--26110 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / w ww . opengroup . org / onlinepubs / [412] [413] [414] [415] Underfull \hbox (badness 10000) in paragraph at lines 26387--26391 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] Underfull \hbox (badness 2302) in paragraph at lines 27340--27347 []\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 27340--27347 \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 2582) in paragraph at lines 27340--27347 \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, but Underfull \hbox (badness 4805) in paragraph at lines 27340--27347 \T1/ptm/m/n/10 in gen-eral it is not. (To scale by the stan-dard de-vi-a-tions with-out cen-ter-ing, use [431] [432] [433] Underfull \hbox (badness 1158) in paragraph at lines 27489--27494 []\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 27516--27520 []\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 27516--27520 \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- [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1803) in paragraph at lines 27904--27907 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length(along.with)\T1/ptm/m/n/10 . Underfull \hbox (badness 2809) in paragraph at lines 27908--27914 []\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 [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] Underfull \hbox (badness 4303) in paragraph at lines 28673--28676 []\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 [452] [453] [454] [455] [456] [457] [458] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29111--29111 []\T1/pcr/m/n/9 is.unsorted(x, strictly=TRUE) #-> TRUE : is not (and cannot be ) sorted strictly[] [459] [460] [461] [462] [463] [464] [465] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29565--29565 []\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)[] [466] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29580--29580 []\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 29929--29931 []\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 29989--29989 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known")[] [473] [474] Underfull \hbox (badness 6526) in paragraph at lines 30139--30149 []\T1/ptm/m/n/10 Then \T1/phv/m/n/10 R \T1/ptm/m/n/10 searches for the site-wid e startup pro-file un-less the com-mand line op-tion Underfull \hbox (badness 6110) in paragraph at lines 30175--30185 []\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 ' or Underfull \hbox (badness 2635) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the Underfull \hbox (badness 1112) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us- ing [475] Underfull \hbox (badness 7704) in paragraph at lines 30226--30231 \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, e.g. [476] [477] [478] [479] [480] [481] [482] [483] [484] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30818--30818 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [485] [486] [487] [488] [489] Overfull \hbox (6.78088pt too wide) in paragraph at lines 31070--31070 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31113--31113 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [490] [491] [492] [493] [494] [495] [496] [497] Underfull \hbox (badness 10000) in paragraph at lines 31564--31567 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 31611--31611 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision[] [498] [499] [500] [501] [502] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31902--31902 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a=, A=1, b=2:3, "Otherwise: last"),"\n")[] [503] [504] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32030--32030 []\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.[] [505] [506] [507] [508] Underfull \hbox (badness 4036) in paragraph at lines 32230--32233 []\T1/ptm/m/n/10 These set-tings are usu-ally con-trolled by the en-vi-ron-ment vari-ables \T1/pcr/m/n/10 LC_NUMERIC \T1/ptm/m/n/10 and [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 32354--32358 []\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 32369--32372 []\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] [514] [515] Underfull \hbox (badness 1082) in paragraph at lines 32644--32647 []\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] Underfull \hbox (badness 1038) in paragraph at lines 32816--32819 []\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 [518] [519] [520] [521] [522] [523] [524] Overfull \hbox (6.78088pt too wide) in paragraph at lines 33255--33255 []\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c ("no",[] [525] Underfull \hbox (badness 1270) in paragraph at lines 33273--33276 []\T1/ptm/m/n/10 levels to re-move from all fac-tors in \T1/pcr/m/n/10 ...\T1/p tm/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 33341--33344 []\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] [530] Underfull \hbox (badness 10000) in paragraph at lines 33573--33575 []\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 [531] Underfull \hbox (badness 10000) in paragraph at lines 33656--33659 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . [532] [533] Underfull \hbox (badness 5475) in paragraph at lines 33782--33786 [][][]\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 : / / [534] Underfull \hbox (badness 10000) in paragraph at lines 33844--33848 [][][]\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 : [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 4181) in paragraph at lines 34187--34191 []\T1/ptm/m/n/10 For most Unix-alikes use the Ol-son databases. The system-spec ific de-fault lo-ca-tion Underfull \hbox (badness 2495) in paragraph at lines 34187--34191 \T1/ptm/m/n/10 in the file sys-tem varies, e.g. `\T1/pcr/m/n/10 /usr/share/zone info\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 /usr/etc/zoneinfo\T1/ptm/m/n/10 ', Underfull \hbox (badness 3460) in paragraph at lines 34209--34211 [][][]$\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] [544] [545] Overfull \hbox (9.78043pt too wide) in paragraph at lines 34519--34519 []\T1/pcr/m/n/9 trace("f", quote(browser(skipCalls=4)), exit = quote(browser(s kipCalls=4)))[] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 1708) in paragraph at lines 34897--34905 []\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 34897--34905 \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 34906--34910 []\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-stead of \T1/pcr/m/n/10 tr y(expr, Underfull \hbox (badness 3977) in paragraph at lines 34906--34910 \T1/pcr/m/n/10 silent=TRUE)\T1/ptm/m/n/10 , some-thing like \T1/pcr/m/n/10 tryC atch(expr, error = function(e) e) \T1/ptm/m/n/10 (or Underfull \hbox (badness 4859) in paragraph at lines 34919--34924 [][][]\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 34978--34990 []\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 34978--34990 \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] [556] [557] [558] [559] [560] [561] [562] [563] Underfull \hbox (badness 1803) in paragraph at lines 35694--35697 []\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 35698--35705 []\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 [564] [565] Underfull \hbox (badness 3668) in paragraph at lines 35828--35830 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [566] [567] [568] [569] [570] Underfull \hbox (badness 6592) in paragraph at lines 36100--36105 []\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] [572] [573] Underfull \vbox (badness 3803) has occurred while \output is active [574] [575] [576] [577] [578] Underfull \hbox (badness 2846) in paragraph at lines 36608--36612 []\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 36635--36635 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 36656--36660 []\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]) (./datasets-pkg.tex Chapter 2. 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 [581] [582] [583] [584] [585] Underfull \vbox (badness 10000) has occurred while \output is active [586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 365--365 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \vbox (badness 10000) has occurred while \output is active [606] Underfull \hbox (badness 10000) in paragraph at lines 1490--1493 []\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 1490--1493 \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 [607] Underfull \vbox (badness 2368) has occurred while \output is active [608] Underfull \hbox (badness 1325) in paragraph at lines 1571--1576 []\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- [609] [610] [611] [612] [613] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1888--1888 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] [614] [615] [616] [617] [618] [619] [620] Overfull \vbox (17.60591pt too high) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \vbox (badness 10000) has occurred while \output is active [634] [635] Underfull \vbox (badness 1365) has occurred while \output is active [636] [637] [638] [639] [640] Underfull \hbox (badness 5175) in paragraph at lines 3452--3455 []\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 3452--3455 \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 . [641] [642] [643] Underfull \vbox (badness 10000) has occurred while \output is active [644] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3698--3698 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3727--3730 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] Overfull \vbox (18.9959pt too high) has occurred while \output is active [656] [657] [658]) (./grDevices-pkg.tex Chapter 3. [659] [660] [661] [662] [663] [664] Overfull \hbox (6.78088pt too wide) in paragraph at lines 367--367 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [665] [666] [667] [668] [669] [670] [671] [672] [673] Underfull \hbox (badness 5175) in paragraph at lines 898--900 []\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 [674] [675] Underfull \hbox (badness 10000) in paragraph at lines 1000--1002 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [676] [677] [678] [679] [680] [681] Underfull \hbox (badness 10000) in paragraph at lines 1424--1426 []\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, if [682] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1505--1505 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [683] Underfull \hbox (badness 1184) in paragraph at lines 1544--1557 []\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 1694) in paragraph at lines 1544--1557 \T1/pcr/m/n/10 "pbmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pgm"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "pgmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pgnm"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "pgnmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pnm"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "pnmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ppm"\T1/ptm/m/n/10 , Underfull \hbox (badness 6493) in paragraph at lines 1544--1557 \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/ptm/ m/n/10 , \T1/pcr/m/n/10 "psmono"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "psgray"\T1/ptm /m/n/10 , [684] [685] Underfull \hbox (badness 10000) in paragraph at lines 1650--1652 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [686] [687] [688] [689] Underfull \hbox (badness 2326) in paragraph at lines 1902--1912 \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 1902--1912 \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 1902--1912 \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 1902--1912 \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 [690] [691] Overfull \hbox (42.18039pt too wide) in paragraph at lines 2028--2028 []\T1/pcr/m/n/9 # This currently only works on the Windows and X11(type="Xlib" ) screen devices...[] [692] [693] [694] [695] Underfull \hbox (badness 10000) in paragraph at lines 2291--2292 [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] Underfull \hbox (badness 10000) in paragraph at lines 2888--2891 [][][]\T1/pcr/m/n/10 colors[][][] \T1/ptm/m/n/10 for the vec-tor of built-in na med col-ors; [][]\T1/pcr/m/n/10 hsv[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gr ay[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 rainbow[][][]\T1/ptm/m/n/10 , [706] [707] [708] [709] [710] [711] Underfull \hbox (badness 5939) in paragraph at lines 3331--3336 []\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 , [712] [713] [714] [715] [716] Underfull \vbox (badness 10000) has occurred while \output is active [717] [718] Underfull \vbox (badness 3803) has occurred while \output is active [719] [720] [721] [722] Underfull \hbox (badness 5077) in paragraph at lines 4011--4017 []\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 [723] [724] [725] Underfull \hbox (badness 1755) in paragraph at lines 4167--4169 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [726] [727] Underfull \hbox (badness 7344) in paragraph at lines 4319--4321 []\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 4330--4335 [][][]\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 [728] [729] Underfull \hbox (badness 2035) in paragraph at lines 4442--4451 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 3735) in paragraph at lines 4442--4451 \T1/ptm/m/n/10 vided: \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica- Underfull \hbox (badness 10000) in paragraph at lines 4442--4451 \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 ), Underfull \hbox (badness 4686) in paragraph at lines 4484--4490 \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 [730] Underfull \hbox (badness 10000) in paragraph at lines 4509--4517 []\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 4509--4517 \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 \hbox (badness 7344) in paragraph at lines 4528--4530 []\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 [731] [732] [733] [734] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4713--4713 []\T1/pcr/m/n/10 quartz(title, width, height, pointsize, family, fontsmooth, a ntialias,[] [735] Underfull \hbox (badness 10000) in paragraph at lines 4804--4806 []\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 [736] [737] [738] [739] [740] Underfull \hbox (badness 10000) in paragraph at lines 5111--5114 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [741] [742] [743] [744] [745] [746] [747] Underfull \hbox (badness 1189) in paragraph at lines 5478--5480 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [748] Underfull \hbox (badness 1132) in paragraph at lines 5546--5548 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and \T1/pcr/m/n/10 "-cronyx- Underfull \hbox (badness 2547) in paragraph at lines 5581--5587 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g. of \T1 /pcr/m/n/10 quote(pi)\T1/ptm/m/n/10 ) have been seen [749] [750] [751] [752] Underfull \hbox (badness 2065) in paragraph at lines 5814--5820 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/pcr/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , Underfull \hbox (badness 1360) in paragraph at lines 5814--5820 \T1/pcr/m/n/10 Narrow"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1 /ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 "Times "\T1/ptm/m/n/10 . Underfull \hbox (badness 1721) in paragraph at lines 5847--5850 []\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 / [753] [754] [755] Underfull \hbox (badness 1231) in paragraph at lines 6009--6011 []\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 [756] [757] [758]) (./graphics-pkg.tex Chapter 4. [759] [760] Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 []\T1/pcr/m/n/10 arrows(x0, y0, x1 = x0, y1 = y0, length = 0.25, angle = 30, c ode = 2,[] [761] Underfull \hbox (badness 2856) in paragraph at lines 175--178 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the point [762] Underfull \hbox (badness 1412) in paragraph at lines 283--288 []\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- [763] [764] [765] [766] Underfull \hbox (badness 2726) in paragraph at lines 462--468 []\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 [767] [768] [769] Underfull \hbox (badness 10000) in paragraph at lines 659--662 []\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 [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1233--1233 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [780] Underfull \hbox (badness 1024) in paragraph at lines 1278--1286 \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 Underfull \hbox (badness 3375) in paragraph at lines 1312--1314 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [781] [782] [783] [784] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1685--1691 [][][]\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 [787] [788] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1815--1815 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns,[] [789] [790] [791] [792] Underfull \hbox (badness 4859) in paragraph at lines 2003--2006 []\T1/ptm/m/n/10 labels and graph-i-cal pa-ram-e-ters can also be spec-i-fied a s ar-gu-ments. [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] Underfull \hbox (badness 1226) in paragraph at lines 2646--2650 \T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr /m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2753 []\T1/ptm/m/n/10 graphical pa-ram-e-ters, or ar-gu-ments to [][]\T1/pcr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [805] [806] [807] [808] Underfull \hbox (badness 1755) in paragraph at lines 2998--3002 []\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] [810] [811] [812] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3241--3241 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [813] [814] [815] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3413--3413 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [816] Underfull \vbox (badness 10000) has occurred while \output is active [817] [818] [819] [820] Underfull \hbox (badness 1867) in paragraph at lines 3723--3727 []\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 3886--3888 []\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] [828] [829] [830] [831] Underfull \hbox (badness 1264) in paragraph at lines 4387--4399 \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] [834] [835] [836] [837] [838] [839] [840] [841] [842] [843] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5259--5259 [] \T1/pcr/m/n/9 col = c("purple", "violetred1", "green3", "cornsilk", "cya n", "white"))[] [844] Underfull \hbox (badness 1052) in paragraph at lines 5313--5317 []\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., \T1/pcr/m/n/10 type = [845] [846] [847] [848] [849] [850] [851] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric vec tor ~ factor[] [852] [853] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5827--5827 [] \T1/pcr/m/n/10 axes = TRUE, labels = FALSE, add = FALSE, ann = TRUE, ...)[] [854] [855] [856] Underfull \hbox (badness 10000) in paragraph at lines 6058--6060 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [857] [858] Underfull \hbox (badness 1028) in paragraph at lines 6151--6153 []\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 [859] [860] Underfull \vbox (badness 3803) has occurred while \output is active [861] [862] Underfull \hbox (badness 10000) in paragraph at lines 6410--6412 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr [863] [864] Underfull \hbox (badness 2600) in paragraph at lines 6503--6505 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6574--6574 [] \T1/pcr/m/n/9 title="Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6583--6583 [] \T1/pcr/m/n/9 title="Overlapping rectangles, one clockwise, other anti-clockwise")[] [866] [867] [868] [869] [870] [871] [872] [873] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7100--7100 [] \T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), space = "Lab")[] [874] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7111--7111 [] \T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints=0 , add=TRUE))[] [875] [876] [877] [878] [879] [880] [881] [882] [883] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7618--7618 []\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 7619--7619 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [884] Underfull \hbox (badness 2080) in paragraph at lines 7721--7726 []\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 [885] Underfull \hbox (badness 1533) in paragraph at lines 7759--7763 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i]==1\T1/ptm/m/n/10 , a (slightly en -larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn. For [886] [887] [888] [889] [890] [891] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8121--8121 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 6691) in paragraph at lines 8147--8150 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) [892] Underfull \hbox (badness 1584) in paragraph at lines 8184--8190 []\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.8232 \HeaderA{units}{Graphical Units}{units} [894] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8290--8290 []\T1/pcr/m/n/10 xspline(x, y = NULL, shape = 0, open = TRUE, repEnds = TRUE, draw = TRUE,[] Underfull \hbox (badness 1205) in paragraph at lines 8297--8299 []\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] [897]) (./grid-pkg.tex [898] Chapter 5. Underfull \vbox (badness 10000) has occurred while \output is active [899] [900] [901] [902] [903] Underfull \hbox (badness 10000) in paragraph at lines 291--297 \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 291--297 \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 [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 888--888 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 890--890 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 892--892 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [914] [915] Underfull \hbox (badness 2781) in paragraph at lines 1037--1040 []\T1/ptm/m/n/10 Both func-tions cre-ate an ar-rows grob (a graph-i-cal ob-ject de-scrib-ing ar-rows), but only [916] [917] [918] [919] Underfull \hbox (badness 3219) in paragraph at lines 1212--1215 []\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 [920] [921] [922] [923] [924] [925] [926] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1652--1652 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [927] [928] Underfull \hbox (badness 2961) in paragraph at lines 1770--1775 []\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 , [929] [930] Underfull \hbox (badness 4479) in paragraph at lines 1858--1861 []\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] Underfull \hbox (badness 2894) in paragraph at lines 1924--1931 []\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 [932] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1969--1969 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [933] [934] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2126--2126 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [935] [936] [937] [938] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2361--2361 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [939] [940] [941] [942] [943] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2670--2670 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [944] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2709--2709 []\T1/pcr/m/n/10 moveToGrob(x = 0, y = 0, default.units = "npc", name = NULL, vp = NULL)[] [945] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2765--2765 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [946] [947] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2890--2890 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2897--2897 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [948] [949] [950] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3090--3090 [] \T1/pcr/m/n/9 title="Nested rectangles, outer clockwise, inn er anti-clockwise")[] [951] Overfull \hbox (58.38037pt too wide) in paragraph at lines 3105--3105 [] \T1/pcr/m/n/9 title="Overlapping rectangles, one clockwise, other anti-clockwise")[] [952] [953] [954] [955] [956] Underfull \hbox (badness 10000) in paragraph at lines 3390--3392 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 1067) in paragraph at lines 3787--3790 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 7256) in paragraph at lines 4026--4028 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] Underfull \hbox (badness 1867) in paragraph at lines 5325--5327 []\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 [991] Underfull \hbox (badness 10000) in paragraph at lines 5362--5368 [][][]\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 , [992] [993] [994] [995] [996] [997]) (./methods-pkg.tex [998] Chapter 6. [999] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459 []\T1/pcr/m/n/10 "namedList" # the alternative to "list" that preserves the na mes attribute[] [1005] [1006] [1007] Underfull \hbox (badness 1281) in paragraph at lines 654--663 []\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 [1008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 732--732 []\T1/pcr/m/n/9 setMethod("f", "B2", function(x) {x@b0 <- 111; c(x@b2, callNex tMethod())})[] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1302--1302 []\T1/pcr/m/n/9 ## the super- and subclasses of "standardGeneric" and "derived DefaultMethod"[] [1017] [1018] [1019] [1020] [1021] [1022] Overfull \hbox (198.78021pt too wide) in paragraph at lines 1714--1714 []\T1/pcr/m/n/9 stopifnot(identical(cc(letters, character(), cd1), paste(lette rs, character(), cd1))) # the "character" method[] Overfull \hbox (355.38004pt too wide) in paragraph at lines 1716--1716 []\T1/pcr/m/n/9 stopifnot(identical(cc(letters, character(), cd2), c(letters, character(), cd2))) # the default, because "vdate" doesn\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 t extend "character"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1718--1718 []\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 1720--1720 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 1726--1726 []\T1/pcr/m/n/9 setMethod("numMax", "numeric", function(...)max(...)) # won\TS 1/pcr/m/n/9 '\T1/pcr/m/n/9 t work for complex data[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 1727--1727 []\T1/pcr/m/n/9 setMethod("numMax", "Number", function(...) paste(...)) # shou ld not be selected w/o complex args[] [1023] Underfull \hbox (badness 10000) in paragraph at lines 1760--1762 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1024] [1025] Underfull \hbox (badness 10000) in paragraph at lines 1903--1908 []\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 [1026] [1027] [1028] [1029] [1030] Underfull \hbox (badness 10000) in paragraph at lines 2257--2261 []\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 [1031] [1032] [1033] Underfull \hbox (badness 3792) in paragraph at lines 2502--2505 []\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 [1034] Underfull \hbox (badness 1194) in paragraph at lines 2533--2537 []\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 [1035] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2589--2589 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1036] [1037] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2824--2824 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1038] [1039] [1040] [1041] [1042] [1043] Underfull \hbox (badness 1552) in paragraph at lines 3181--3183 []\T1/pcr/m/n/10 packageName \T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1044] [1045] [1046] [1047] Underfull \hbox (badness 10000) in paragraph at lines 3405--3409 []\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 [1048] Overfull \hbox (28.78088pt too wide) in paragraph at lines 3519--3528 [] [1049] [1050] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3610--3610 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1051] Underfull \hbox (badness 1394) in paragraph at lines 3681--3686 \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 [1052] [1053] [1054] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3943--3943 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3963--3963 []\T1/pcr/m/n/9 setClass("stringsDated", contains = "character", representatio n(stamp="POSIXt"))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 ## In contrast, a class that simply extends "factor" has no su ch ambiguities[] Underfull \vbox (badness 10000) has occurred while \output is active [1055] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3978--3978 []\T1/pcr/m/n/9 setClass("factorDated", contains = "factor", representation(st amp="POSIXt"))[] [1056] [1057] [1058] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4192--4192 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4193--4193 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1059] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4250--4250 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here)[] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 10000) in paragraph at lines 4722--4731 []\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 [1066] [1067] [1068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4915--4915 []\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 4944--4944 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier fails here)[] Underfull \vbox (badness 10000) has occurred while \output is active [1069] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4958--4958 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] [1070] [1071] Underfull \hbox (badness 10000) in paragraph at lines 5102--5104 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1072] [1073] [1074] [1075] Underfull \hbox (badness 1087) in paragraph at lines 5391--5396 []\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 [1076] [1077] [1078] [1079] [1080] [1081] Underfull \hbox (badness 1248) in paragraph at lines 5860--5864 []\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 5860--5864 \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 [1082] Underfull \hbox (badness 4291) in paragraph at lines 5918--5932 []\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 [1083] [1084] [1085] Underfull \vbox (badness 10000) has occurred while \output is active [1086] [1087]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6272 \aliasA{S4}{S3Part}{S4} [1088] [1089] [1090] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6500--6500 []\T1/pcr/m/n/9 ## two examples extending S3 class "lm", class "xlm" directly and "ylm" indirectly[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6512--6512 []\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 6517--6517 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c ("mlm", "lm")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6526--6526 []\T1/pcr/m/n/9 setClass("dataFrameD", representation(date = "Date"), contains = "data.frame")[] [1091]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.6546 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.6548 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.6549 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.6551 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.6552 \aliasA{Summary}{S4groupGeneric}{Summary} [1092] Underfull \hbox (badness 2050) in paragraph at lines 6612--6616 []\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 6625--6635 []\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 6625--6635 \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 , [1093] [1094] Underfull \hbox (badness 1694) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see [1095] Underfull \hbox (badness 10000) in paragraph at lines 6806--6809 []\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 [1096] [1097] Underfull \hbox (badness 2111) in paragraph at lines 6912--6919 []\T1/ptm/m/n/10 The slots in a class def-i-ni-tion will be the union of all th e slots spec-i-fied di-rectly by [1098] [1099] Underfull \vbox (badness 3803) has occurred while \output is active [1100] [1101] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7236--7236 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(),[] [1102] [1103] Underfull \hbox (badness 2277) in paragraph at lines 7367--7375 []\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 [1104] Underfull \hbox (badness 3128) in paragraph at lines 7408--7413 []\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 [1105] [1106] [1107] Underfull \hbox (badness 1755) in paragraph at lines 7622--7625 []\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the method. For [1108] [1109] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7765--7765 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li nk{setClass})[] [1110] [1111] [1112] [1113] [1114] Overfull \hbox (52.98038pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/9 ## two examples extending S3 class "lm", class "xlm" directly and "ylm" indirectly[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8170--8170 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date = "POSIXt"))[] [1115] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8178--8178 []\T1/pcr/m/n/9 someLetters <- stamped(sample(letters, 10), ISOdatetime(2008, 10, 15, 12, 0, 0))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8181--8181 []\T1/pcr/m/n/9 st # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m /n/9 s class, then calls the S3 print method.[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8192--8192 [] \T1/pcr/m/n/9 prototype(NA, tsp = rep(1,3))) # prototype to be a legal S3 time-series[] [1116] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8281--8281 []\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 8292--8292 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8894--8894 []\T1/pcr/m/n/9 ## if no other attached packages have methods for \TS1/pcr/m/ n/9 `\T1/pcr/m/n/9 +\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 or its group generic[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8895--8895 []\T1/pcr/m/n/9 ## functions, this returns a 16 by 2 matrix of selection patte rns (in R 2.9.0)[] [1126] Underfull \hbox (badness 10000) in paragraph at lines 8956--8958 []\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 8964--8968 []\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 8964--8968 \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 [1127] [1128] [1129] [1130]) (./splines-pkg.tex Chapter 7. 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] Overfull \hbox (20.58041pt too wide) in paragraph at lines 463--463 []\T1/pcr/m/n/9 ispl <- polySpline( interpSpline( weight ~ height, women, bSp line = TRUE ) )[] [1139] [1140] [1141] [1142] [1143] [1144] [1145]) (./stats-pkg.tex [1146] Chapter 8. [1147] 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 , [1148] [1149] [1150] [1151] [1152] [1153] Overfull \hbox (18.78088pt too wide) in paragraph at lines 425--425 [] \T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE)[] [1154] [1155] [1156] [1157] [1158] [1159] Underfull \hbox (badness 1024) in paragraph at lines 803--805 []\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 [1160] [1161] [1162] [1163] [1164] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1138--1138 [] \T1/pcr/m/n/10 c("Pillai", "Wilks", "Hotelling-Lawley", "Roy", "Sph erical"),[] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2566--2566 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(0), ma = numeric(0), lag.max = r, pacf = FALSE)[] [1188] [1189] [1190] [1191] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2802--2802 []\T1/pcr/m/n/9 legend(40,70, c("mean","median"), lty=1,col=c("blue","green"), bg="gray90")[] [1192] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2825--2825 []\T1/pcr/m/n/10 bw.ucv(x, nb = 1000, lower = 0.1 * hmax, upper = hmax, tol = 0.1 * lower)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2827--2827 []\T1/pcr/m/n/10 bw.bcv(x, nb = 1000, lower = 0.1 * hmax, upper = hmax, tol = 0.1 * lower)[] [1193] [1194] Underfull \hbox (badness 10000) in paragraph at lines 2991--2993 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1195] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3038--3038 []\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 3039--3039 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3627--3627 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0)[] [1205] [1206] [1207] [1208] [1209] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3911--3911 []\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 3912--3912 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1210] [1211] [1212] Underfull \hbox (badness 10000) in paragraph at lines 4070--4072 []\T1/ptm/m/n/10 the Pear-son resid-u-als, \T1/pcr/m/n/10 (observed - expected) / [1213] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4122--4122 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1214] [1215] [1216] [1217] Underfull \hbox (badness 3989) in paragraph at lines 4366--4373 []\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 = [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4929--4929 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] [1226] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4947--4947 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter"))[] Underfull \hbox (badness 10000) in paragraph at lines 4979--4981 []\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 , \T1/pcr/m/n/10 m <- [1227] [1228] [1229] Underfull \hbox (badness 1436) in paragraph at lines 5157--5162 []\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 5157--5162 \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 5157--5162 \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 , [1230] [1231] [1232] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5319--5319 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1233] [1234] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5484--5484 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE,[] [1235] [1236] [1237] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5664--5664 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL)[] [1238] [1239] [1240] [1241] [1242] [1243] Underfull \hbox (badness 5954) in paragraph at lines 5993--5995 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1244] Underfull \hbox (badness 2503) in paragraph at lines 6060--6062 []\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 6063--6065 []\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 [1245] [1246] [1247] [1248] [1249] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6354--6354 [] \T1/pcr/m/n/9 ylim = c(0, 1), xlab="", main="R\TS1/pcr/m/n/9 '\T1/pcr/m /n/9 s density() kernels with width = 1")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6363--6363 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1250] [1251] [1252] [1253] [1254] [1255] Underfull \hbox (badness 10000) in paragraph at lines 6730--6734 \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 [1256] Underfull \hbox (badness 6493) in paragraph at lines 6828--6831 []\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 [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] Underfull \hbox (badness 3780) in paragraph at lines 7360--7365 []\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 , ..., \T 1/pcr/m/n/10 x[t- [1266] [1267] [1268] [1269] [1270] Underfull \hbox (badness 1210) in paragraph at lines 7689--7691 []\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 [1271] [1272] [1273] [1274] [1275] [1276] [1277] Underfull \vbox (badness 3803) has occurred while \output is active [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8619--8619 [] \T1/pcr/m/n/9 satisfaction=c("VeryD", "LittleD", "ModerateS" , "VeryS")))[] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] Underfull \hbox (badness 2443) in paragraph at lines 9242--9248 [][][]\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); [1296] [1297] [1298] [1299] [1300] [1301] [1302] Underfull \hbox (badness 4518) in paragraph at lines 9684--9689 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1303] Underfull \hbox (badness 4132) in paragraph at lines 9723--9727 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1304] Underfull \hbox (badness 10000) in paragraph at lines 9826--9829 []\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 [1305] [1306] [1307] Underfull \hbox (badness 2142) in paragraph at lines 10025--10028 []\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 ^^@ [1308] [1309] Underfull \hbox (badness 1708) in paragraph at lines 10106--10109 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: Underfull \hbox (badness 10000) in paragraph at lines 10147--10153 [][][]\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, [1310] [1311] Underfull \hbox (badness 2635) in paragraph at lines 10315--10321 \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 [1312] [1313] [1314] Underfull \hbox (badness 1694) in paragraph at lines 10469--10472 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1315] [1316] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10598--10598 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 10611--10615 []\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 [1317] [1318] [1319] [1320] [1321] [1322] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10907--10907 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]),col=2:4), D EV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.10922 \aliasA{hat}{influence.measures}{hat} [1323] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10976--10976 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10988--10988 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 11034--11039 []\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- [1324] Underfull \hbox (badness 1052) in paragraph at lines 11045--11047 []\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 [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 4518) in paragraph at lines 12485--12490 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1349] [1350] [1351] Underfull \hbox (badness 10000) in paragraph at lines 12679--12683 []\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 , [1352] [1353] [1354] [1355] [1356] Underfull \hbox (badness 1163) in paragraph at lines 12997--13005 \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 , [1357] [1358] Underfull \hbox (badness 4518) in paragraph at lines 13107--13112 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1359] [1360] [1361] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13281--13281 []\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 13282--13282 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1362] Underfull \hbox (badness 10000) in paragraph at lines 13329--13332 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, \T1/pcr/m/n/10 plogis(x) == (1+ [1363] [1364] [1365] [1366] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13606--13606 []\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 13607--13607 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] Underfull \hbox (badness 2726) in paragraph at lines 14092--14095 []\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 , [1375] [1376] [1377] [1378] [1379] Underfull \vbox (badness 10000) has occurred while \output is active [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] Underfull \hbox (badness 1648) in paragraph at lines 14983--14985 []\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, [1390] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15061--15061 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a="contr.sum", b="c ontr.poly"))[] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15612--15612 []\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[] [1400] [1401] [1402] [1403] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15827--15827 []\T1/pcr/m/n/9 persp(x,size, dnb <- outer(x, size, function(x,s) dnbinom(x,s, prob= 0.4)),[] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] Underfull \vbox (badness 10000) has occurred while \output is active [1414] [1415] [1416] [1417] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16680--16680 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1418] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16727--16727 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1419] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16774--16774 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1420] [1421] [1422] [1423] [1424] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17076--17076 [] \T1/pcr/m/n/10 method = c("Nelder-Mead", "BFGS", "CG", "L-BFGS-B", "SA NN"),[] [1425] Underfull \hbox (badness 1248) in paragraph at lines 17182--17185 []\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 17195--17199 \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 [1426] Underfull \hbox (badness 2042) in paragraph at lines 17253--17255 []\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 [1427] [1428] Underfull \vbox (badness 10000) has occurred while \output is active [1429] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17382--17382 [] \T1/pcr/m/n/9 control = list(maxit=30000, temp=2000, trace=TRUE , REPORT=500))[] [1430] Underfull \hbox (badness 2564) in paragraph at lines 17457--17468 []\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 17457--17468 \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 [1431] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17516--17516 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1432] [1433] [1434] [1435] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17791--17791 [] \T1/pcr/m/n/10 alternative = c("two.sided", "less", "greater "), ...)[] Underfull \hbox (badness 1337) in paragraph at lines 17803--17806 []\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 [1436] [1437] [1438] [1439] [1440] [1441] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18119--18119 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1442] [1443] Overfull \hbox (42.78088pt too wide) in paragraph at lines 18207--18207 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s d ist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 18210--18210 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1444] [1445] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18325--18325 []\T1/pcr/m/n/9 plot(lm.SR <- lm(sr ~ pop15 + pop75 + dpi + ddpi, data = LifeC ycleSavings))[] [1446] [1447] [1448] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18512--18512 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 18522--18525 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1449] Underfull \hbox (badness 1107) in paragraph at lines 18580--18582 []\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 [1450] [1451] [1452] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18735--18735 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1453] [1454] [1455] Underfull \hbox (badness 2343) in paragraph at lines 18913--18915 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 6859) in paragraph at lines 19867--19874 [][][]\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 19877--19883 []\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 , [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20835--20835 [] \T1/pcr/m/n/10 cs.ind = 1L:k, tst.ind = k + 1L, zap.ind = integ er(0),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20838--20838 [] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == "Pr(",[] [1488] [1489] [1490] [1491] [1492] [1493] Underfull \hbox (badness 1337) in paragraph at lines 21160--21166 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 10000) in paragraph at lines 21904--21907 []\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 21904--21907 \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 [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] Underfull \hbox (badness 8094) in paragraph at lines 22480--22483 []\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 \T1/pcr/m/n/10 y[j] = [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] Underfull \hbox (badness 1412) in paragraph at lines 23298--23300 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1529] [1530] [1531] [1532] [1533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23657--23657 []\T1/pcr/m/n/9 (s2 <- smooth.spline(y18, control = list(trace=TRUE,tol=1e-6, low= -1.5)))[] [1534] [1535] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23795--23795 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail,[] [1536] [1537] [1538] [1539] [1540] [1541] [1542] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24170--24170 []\T1/pcr/m/n/10 splinefun(x, y = NULL, method = c("fmm", "periodic", "natural ", "monoH.FC"),[] [1543] [1544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24322--24322 []\T1/pcr/m/n/9 legend("topleft", paste("splinefun( \"", c("fmm", "monoH.CS"), "\" )", sep=\TS1/pcr/m/n/9 ''\T1/pcr/m/n/9 ),[] [1545] [1546] Underfull \hbox (badness 3240) in paragraph at lines 24429--24433 [][][]\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 [1547] [1548] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24557--24557 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1549] [1550] Underfull \hbox (badness 10000) in paragraph at lines 24667--24670 \T1/pcr/m/n/10 exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input)-exp(-exp(lKa)*input)) / Overfull \hbox (9.78043pt too wide) in paragraph at lines 24689--24689 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response and gradient[] [1551] [1552] [1553] Underfull \hbox (badness 2922) in paragraph at lines 24840--24845 []\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 [1554] Underfull \hbox (badness 2922) in paragraph at lines 24895--24900 []\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] [1556] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24990--24990 []\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 24992--24992 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1557] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25049--25049 []\T1/pcr/m/n/10 stat.anova(table, test = c("Chisq", "F", "Cp"), scale, df.sca le, n)[] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25558--25558 [] \T1/pcr/m/n/10 main = NULL, range.bars = TRUE, ..., col.range = "light gray")[] [1566] [1567] [1568] [1569] [1570] Underfull \hbox (badness 3396) in paragraph at lines 25856--25858 []\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 [1571] [1572] [1573] Underfull \hbox (badness 2237) in paragraph at lines 26028--26030 []\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 [1574] [1575] [1576] Underfull \hbox (badness 2591) in paragraph at lines 26185--26187 []\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 [1577] Underfull \hbox (badness 2237) in paragraph at lines 26231--26234 []\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 [1578] [1579] Underfull \hbox (badness 3407) in paragraph at lines 26409--26413 []\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) [1580] [1581] [1582] Underfull \hbox (badness 1337) in paragraph at lines 26542--26546 []\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 [1583] [1584] [1585] [1586] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26808--26808 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 26832--26835 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1587] [1588] [1589] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26958--26958 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1590] Underfull \hbox (badness 2205) in paragraph at lines 27041--27046 []\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 [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 10000) in paragraph at lines 27551--27555 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 tsp \T1/ptm/m/n/10 at-tribute was pre-vi-ou sly de-scribed here as \T1/pcr/m/n/10 c(start(x), end(x), [1600] Overfull \hbox (12.78088pt too wide) in paragraph at lines 27630--27630 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 27631--27631 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 1337) in paragraph at lines 28131--28135 []\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 [1610] [1611] [1612] [1613] Underfull \hbox (badness 1043) in paragraph at lines 28371--28374 []\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 -pweibull(t, a, b, lower = Overfull \hbox (4.38043pt too wide) in paragraph at lines 28398--28398 []\T1/pcr/m/n/9 all.equal(pweibull(x, 2.5, pi, lower.tail=FALSE, log.p=TRUE), -(x/pi)^2.5,[] [1614] [1615] [1616] Underfull \hbox (badness 1337) in paragraph at lines 28552--28556 []\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 [1617] [1618] [1619] [1620] [1621] [1622] [1623] Overfull \hbox (66.78088pt too wide) in paragraph at lines 28956--28956 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, na.action,[] [1624] [1625] [1626]) (./stats4-pkg.tex Chapter 9. [1627] [1628] [1629] Overfull \hbox (112.38031pt too wide) in paragraph at lines 227--227 [] \T1/pcr/m/n/9 if(ymax > 0 && xhalf > 0) -sum(stats::dpois(y, lambda=ymax /(1+x/xhalf), log=TRUE)) else NA[] [1630] Overfull \hbox (9.78043pt too wide) in paragraph at lines 242--242 []\T1/pcr/m/n/9 ## the lower bounds are really > 0, but we use >=0 to stress-t est profiling[] [1631] [1632] [1633]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.457 ... in Package 'stats4'}{show.Rdash.methods} [1634] Underfull \hbox (badness 10000) in paragraph at lines 490--493 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1635] [1636]) (./tcltk-pkg.tex Chapter 10. [1637] [1638] [1639] [1640] [1641] Overfull \hbox (36.7804pt too wide) in paragraph at lines 378--378 [] \T1/pcr/m/n/9 # Do some work to create a nice picture. Nothing will be displayed until...[] [1642] [1643] Overfull \hbox (30.78088pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/10 ## NB: some widgets also have a selection.clear command, henc e the "X".[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 548--548 []\T1/pcr/m/n/10 ## winfo actually has a large number of subcommands, but it\T S1/pcr/m/n/10 '\T1/pcr/m/n/10 s rarely[] Underfull \vbox (badness 10000) has occurred while \output is active [1644] Underfull \vbox (badness 10000) has occurred while \output is active [1645] Underfull \hbox (badness 1292) in paragraph at lines 641--648 []\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 [1646] [1647] [1648] [1649] Underfull \vbox (badness 10000) has occurred while \output is active [1650] [1651] [1652] [1653] [1654] [1655] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1345--1345 []\T1/pcr/m/n/10 tk_select.list(choices, preselect = NULL, multiple = FALSE, t itle = NULL)[] [1656] [1657]) (./tools-pkg.tex [1658] Chapter 11. [1659] Underfull \hbox (badness 1308) in paragraph at lines 80--95 []\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 types Underfull \hbox (badness 1742) in paragraph at lines 80--95 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as a rou-tine to pro-duce a sort Underfull \hbox (badness 1360) in paragraph at lines 80--95 \T1/ptm/m/n/10 key to sort the en-tries. The for-mer must be named \T1/pcr/m/n/ 10 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1660] Overfull \hbox (9.78043pt too wide) in paragraph at lines 129--129 []\T1/pcr/m/n/9 bibstyle("unsorted", sortKeys = function(refs) seq_along(refs) , .init=TRUE)[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 145--145 []\T1/pcr/m/n/10 buildVignettes(package, dir, lib.loc = NULL, quiet = TRUE, cl ean = TRUE)[] [1661] Underfull \hbox (badness 2644) in paragraph at lines 203--208 \T1/ptm/m/n/10 (there can be more than one name for a Uni-code point). The data are in the file Underfull \hbox (badness 10000) in paragraph at lines 211--212 [][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer / en / opentype / glyphlist . [1662] [1663] [1664] Underfull \vbox (badness 10000) has occurred while \output is active [1665] [1666] Overfull \hbox (0.78088pt too wide) in paragraph at lines 470--470 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1667] [1668] [1669] [1670] Underfull \hbox (badness 10000) in paragraph at lines 722--725 []\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 [1671] Overfull \hbox (36.78088pt too wide) in paragraph at lines 793--793 []\T1/pcr/m/n/10 dependsOnPkgs(pkgs, dependencies = c("Depends", "Imports", "L inkingTo"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 795--795 [] \T1/pcr/m/n/10 installed = installed.packages(lib.loc, fields = "Enhances"))[] Underfull \hbox (badness 7981) in paragraph at lines 802--805 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 802--805 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", [1672] [1673] [1674] [1675] [1676] Underfull \hbox (badness 10000) in paragraph at lines 1073--1078 []\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 1073--1078 \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 1073--1078 \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 [1677] [1678] [1679] [1680] [1681] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1346--1346 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1682] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1385--1385 []\T1/pcr/m/n/10 parseLatex(text, filename = deparse(substitute(text)), verbos e = FALSE,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1386--1386 [] \T1/pcr/m/n/10 verbatim = c("verbatim", "verbatim*", "Sinput", "S output"))[] [1683] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1466--1466 []\T1/pcr/m/n/10 parse_Rd(file, srcfile = NULL, encoding = "unknown", verbose = FALSE,[] [1684] [1685] [1686] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1646--1646 [] \T1/pcr/m/n/10 stages = "render", outputEncoding = "ASCII", fragmen t = FALSE, ...,[] [1687] Underfull \hbox (badness 1072) in paragraph at lines 1670--1672 []\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 [1688] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1792--1792 []\T1/pcr/m/n/9 browseURL(Rd2HTML(Rd, outfile, package="tools", stages=c("inst all", "render")))[] [1689] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1795--1795 []\T1/pcr/m/n/9 file.show(Rd2txt(Rd, outfile, package="tools", stages=c("insta ll", "render")))[] [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2382--2382 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Underfull \hbox (badness 2932) in paragraph at lines 2415--2421 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3758) in paragraph at lines 2695--2700 []\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 2695--2700 \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 [1705] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2734--2734 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Underfull \hbox (badness 1742) in paragraph at lines 2746--2758 \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 , [1706] Underfull \hbox (badness 3623) in paragraph at lines 2803--2806 []\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 [1707] [1708] [1709]) (./utils-pkg.tex [1710] Chapter 12. [1711] [1712] [1713] [1714] [1715] [1716] Overfull \hbox (24.78088pt too wide) in paragraph at lines 352--352 []\T1/pcr/m/n/10 available.packages(contriburl = contrib.url(getOption("repos" ), type),[] Underfull \hbox (badness 4505) in paragraph at lines 391--398 \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 [1717] Underfull \hbox (badness 1275) in paragraph at lines 439--445 []\T1/ptm/m/n/10 A ma-trix with one row per pack-age, row names the pack-age na mes and col-umn names Underfull \hbox (badness 2057) in paragraph at lines 439--445 \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 , \T1/pcr/m/n/10 "LinkingTo"\T1/p tm/m/n/10 , Underfull \hbox (badness 1603) in paragraph at lines 471--476 \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 471--476 \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 [1718] Overfull \hbox (6.78088pt too wide) in paragraph at lines 523--523 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL,[] [1719] [1720] [1721] Overfull \hbox (15.18042pt too wide) in paragraph at lines 712--712 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1722] [1723] Overfull \hbox (24.78088pt too wide) in paragraph at lines 825--825 []\T1/pcr/m/n/10 browseURL(url, browser = getOption("browser"), encodeIfNeeded = FALSE)[] [1724] [1725] [1726] [1727] Underfull \hbox (badness 1859) in paragraph at lines 1081--1090 []\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- [1728] [1729] [1730] [1731] [1732] [1733] Underfull \hbox (badness 1082) in paragraph at lines 1426--1430 [][][]\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; [1734] [1735] [1736] [1737] [1738] [1739] [1740] Underfull \hbox (badness 1430) in paragraph at lines 1837--1840 []\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 \T1/pcr/m/n/10 package = Overfull \hbox (15.18042pt too wide) in paragraph at lines 1878--1878 []\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 '[] [1741] Underfull \hbox (badness 2452) in paragraph at lines 1951--1954 []\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 [1742] [1743] [1744] [1745] [1746] [1747] Underfull \hbox (badness 1072) in paragraph at lines 2317--2323 []\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 2317--2323 \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 [1748] Underfull \hbox (badness 1057) in paragraph at lines 2343--2357 []\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 2343--2357 \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 2343--2357 \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 2358--2364 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1749] Underfull \hbox (badness 4660) in paragraph at lines 2416--2419 \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 [1750] [1751] [1752] Underfull \hbox (badness 1565) in paragraph at lines 2614--2618 []\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 [1753] Underfull \hbox (badness 3758) in paragraph at lines 2727--2734 []\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat -ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask=TRUE) [1754] [1755] [1756] [1757] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2914--2914 []\T1/pcr/m/n/10 findLineNum(srcfile, line, nameonly = TRUE, envir = parent.fr ame(),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2917--2917 []\T1/pcr/m/n/10 setBreakpoint(srcfile, line, nameonly = TRUE, envir = parent. frame(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2918--2918 [] \T1/pcr/m/n/10 lastenv, verbose = TRUE, tracer, print = FALSE, ...)[] [1758] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3006--3006 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1759]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.3077 ...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.3077 ...mat Unordered and Ordered Lists}{format} [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 10000) in paragraph at lines 3787--3791 []\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 Underfull \hbox (badness 1502) in paragraph at lines 3831--3836 []\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 3831--3836 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1772] [1773] [1774] Underfull \hbox (badness 10000) in paragraph at lines 3985--3994 []\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 3985--3994 \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 Underfull \hbox (badness 2717) in paragraph at lines 3985--3994 [][]\T1/pcr/m/n/10 make.packages.html[][][](temp = FALSE)\T1/ptm/m/n/10 . For l o-cal op-er-a-tion, the HTTP server will [1775] [1776] Underfull \hbox (badness 1590) in paragraph at lines 4125--4129 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 setClass[][][]\T1/ptm/m/n/10 , should be i n-stalled us-ing lazy-loading: use the field \T1/pcr/m/n/10 LazyLoad \T1/ptm/m/ n/10 in the [1777] Underfull \hbox (badness 4660) in paragraph at lines 4212--4215 \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 [1778] Underfull \hbox (badness 10000) in paragraph at lines 4239--4243 []\T1/ptm/m/n/10 Possible val-ues are \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 , [1779] Underfull \hbox (badness 10000) in paragraph at lines 4346--4351 [][][]\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 , [1780] Underfull \hbox (badness 5133) in paragraph at lines 4407--4411 []\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 4419--4422 []\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 [1781] [1782] [1783] [1784] [1785] Overfull \hbox (368.28088pt too wide) in paragraph at lines 4689--4690 [][][]$\T1/pcr/m/n/10 http : / / n4 . nabble . com / R-[]help-[]question-[]How- []can-[]we-[]enable-[]useRs-[]to-[]contribute-[]corrections-[]to-[]help-[]files -[]faster-[]tp1572568p1572868 . Overfull \hbox (24.78088pt too wide) in paragraph at lines 4710--4710 []\T1/pcr/m/n/10 make.packages.html(lib.loc = .libPaths(), temp = TRUE, verbos e = TRUE)[] [1786] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4770--4770 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE)[] [1787] [1788] [1789] Underfull \hbox (badness 10000) in paragraph at lines 4942--4944 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] Underfull \hbox (badness 10000) in paragraph at lines 5513--5515 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like \T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 5518--5523 []\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, [1799] [1800] Underfull \hbox (badness 10000) in paragraph at lines 5624--5627 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed", "not [1801] [1802] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5740--5740 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5741--5741 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1803] [1804] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5883--5883 [] \T1/pcr/m/n/9 comment = "S original, http://statwww.epfl.ch/davison /BMA/library.html"),[] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] [1813] [1814] Underfull \hbox (badness 5203) in paragraph at lines 6498--6501 []\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 [1815] Underfull \hbox (badness 1163) in paragraph at lines 6603--6606 []\T1/ptm/m/n/10 the to-ken that was (or, is to be) com-pleted, as set by the l ast call to [1816] Underfull \hbox (badness 1072) in paragraph at lines 6715--6723 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [1817] [1818] [1819] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6894--6894 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header= TRUE, tra nspose=TRUE)[] [1820] [1821] [1822] [1823] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7149--7149 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] [1824] Underfull \hbox (badness 1077) in paragraph at lines 7220--7223 []\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 [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 7797--7801 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1835] [1836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7915--7915 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0)[] [1837] [1838] [1839] [1840] Underfull \hbox (badness 6725) in paragraph at lines 8156--8165 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 8156--8165 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 8156--8165 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 8156--8165 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8200--8200 []\T1/pcr/m/n/9 ## Search in R-devel archive and recent R-help (and store the query-string):[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8202--8202 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("S4", restrict = c("R-dev", "Rhelp10" , "Rhelp08"))[] [1842] Underfull \hbox (badness 10000) in paragraph at lines 8287--8289 [][][]$\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 / [1843] [1844] Underfull \hbox (badness 10000) in paragraph at lines 8406--8410 []\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 [1845] Underfull \hbox (badness 10000) in paragraph at lines 8437--8443 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1846] [1847] [1848] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8639--8639 []\T1/pcr/m/n/10 select.list(choices, preselect = NULL, multiple = FALSE, titl e = NULL,[] [1849] Underfull \hbox (badness 10000) in paragraph at lines 8728--8731 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. In re-cent ve r- Underfull \hbox (badness 10000) in paragraph at lines 8728--8731 \T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form [1850] Underfull \hbox (badness 10000) in paragraph at lines 8736--8739 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g Overfull \hbox (0.78088pt too wide) in paragraph at lines 8762--8762 []\T1/pcr/m/n/10 setRepositories(graphics = getOption("menu.graphics"), ind = NULL)[] Underfull \hbox (badness 10000) in paragraph at lines 8779--8783 \T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son al copy in [1851] Underfull \hbox (badness 2158) in paragraph at lines 8798--8801 []\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 [1852] [1853] [1854] [1855] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9027--9027 [] \T1/pcr/m/n/10 format(x, trim=TRUE, drop0trailing=TRU E, ...))[] Underfull \hbox (badness 5970) in paragraph at lines 9055--9058 []\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 9055--9058 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [1856] [1857] [1858] [1859] Underfull \hbox (badness 5504) in paragraph at lines 9296--9299 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 SweaveSyntax \T1/ptm/m/n/10 or a char-ac-ter string with its Underfull \hbox (badness 3635) in paragraph at lines 9296--9299 \T1/ptm/m/n/10 name. The de-fault in-stal-la-tion pro-vides \T1/pcr/m/n/10 Swea veSyntaxNoweb \T1/ptm/m/n/10 and Underfull \hbox (badness 1178) in paragraph at lines 9322--9334 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, a num-ber of hook func- tions can be ex-e-cuted. If [1860] [1861] [1862] [1863] Underfull \hbox (badness 10000) in paragraph at lines 9535--9538 [][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ fo rmat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / www . Underfull \hbox (badness 10000) in paragraph at lines 9535--9538 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 009695399 / utilities / pax . htm l # tag _ 04 _ 100 _ [1864] [1865] [1866] [1867] [1868] [1869] [1870] Underfull \hbox (badness 4660) in paragraph at lines 9973--9976 \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 (24.87935pt too wide) in paragraph at lines 9984--9988 []\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 . [1871] Underfull \hbox (badness 3557) in paragraph at lines 9990--9992 []\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 9993--9995 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 10023--10028 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 10000) in paragraph at lines 10044--10049 []\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 10052--10055 [][][]\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 , [1872] [1873] Underfull \hbox (badness 10000) in paragraph at lines 10140--10145 []\T1/ptm/m/n/10 Characters in a URL other than the En-glish al-phanu-meric cha r-ac-ters and [1874] [1875] [1876] [1877] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10357--10357 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ",[] Underfull \hbox (badness 1454) in paragraph at lines 10383--10387 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 10403--10406 []\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 [1878] [1879] Underfull \hbox (badness 3872) in paragraph at lines 10532--10534 []\T1/ptm/m/n/10 character string: the method to be used, an empty string in-di -cates [1880] [1881]) [1882] (./refman.ind [1883] [1884] [1885] [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] Overfull \hbox (32.8567pt too wide) in paragraph at lines 2538--2540 []\T1/pcr/m/n/10 aspell_write_personal_dictionary_file [1906] [1907] [1908] [1909] [1910] [1911] Overfull \hbox (20.8567pt too wide) in paragraph at lines 3358--3360 []\T1/pcr/m/n/10 derivedDefaultMethodWithTrace-class [1912] [1913] [1914] [1915] [1916] [1917] [1918] Overfull \hbox (20.8567pt too wide) in paragraph at lines 4268--4270 []\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class [1919] Underfull \vbox (badness 2035) has occurred while \output is active [1920] [1921] [1922] [1923] [1924] [1925] [1926] Overfull \hbox (8.8567pt too wide) in paragraph at lines 5400--5402 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (26.8567pt too wide) in paragraph at lines 5486--5488 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method [1927] Underfull \vbox (badness 1642) has occurred while \output is active [1928] [1929] [1930] Overfull \hbox (4.01662pt too wide) in paragraph at lines 6068--6070 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [1931] Overfull \hbox (4.01662pt too wide) in paragraph at lines 6112--6114 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [1932] [1933] [1934] Underfull \vbox (badness 1226) has occurred while \output is active [1935] [1936] [1937] Overfull \hbox (26.8567pt too wide) in paragraph at lines 7078--7080 []\T1/pcr/m/n/10 show,genericFunctionWithTrace-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7082--7084 []\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method [1938] Overfull \hbox (20.8567pt too wide) in paragraph at lines 7086--7088 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7092--7094 []\T1/pcr/m/n/10 show,refClassRepresentation-method [1939] [1940] Underfull \vbox (badness 1019) has occurred while \output is active [1941] [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949]) (./refman.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showMlist} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.standardGeneric} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Surv} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}< /usr/share/texmf-texlive/fonts/type1/urw/courier/ucrb8a.pfb> Output written on refman.pdf (1978 pages, 5000315 bytes). Transcript written on refman.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/bm.sty) (/usr/share/texmf-texlive/tex/latex/base/alltt.sty) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (../../share/texmf/tex/latex/upquote.sty (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))) NOT loading ae (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) NOT loading lmodern (/usr/share/texmf-texlive/tex/latex/graphics/color.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 332. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 332. ) (/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/base/makeidx.sty) Writing index file refman.idx (./refman.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./refman.out) (./refman.out) (/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-texlive/tex/latex/psnfss/ts1ptm.fd) [1{/var/l ib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./refman.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] (./base-pkg.tex Chapter 1. [1] Underfull \hbox (badness 2443) in paragraph at lines 71--77 []\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 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 2334) in paragraph at lines 71--77 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is Underfull \hbox (badness 3407) in paragraph at lines 71--77 \T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er- wise, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 1960) in paragraph at lines 77--85 []\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 . It Underfull \hbox (badness 1189) in paragraph at lines 77--85 \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, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 1661) in paragraph at lines 77--85 \T1/pcr/m/n/10 double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m/n /10 1.110223e-16\T1/ptm/m/n/10 . As [2] [3] [4] Underfull \hbox (badness 10000) in paragraph at lines 224--228 \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.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 261--264 [][][]\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, [5] Underfull \hbox (badness 2359) in paragraph at lines 305--308 []\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 [6] [7] [8] [9] (/usr/share/texmf-texlive/tex/latex/psnfss/ts1pcr.fd) [10] [11] Overfull \hbox (0.78088pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE)[] [12] [13] [14] [15] Underfull \hbox (badness 1838) in paragraph at lines 933--936 []\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 [16] [17] [18] [19] [20] [21] [22] [23] Underfull \hbox (badness 2865) in paragraph at lines 1448--1451 []\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 [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1596--1598 []\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 [26] [27] Underfull \hbox (badness 10000) in paragraph at lines 1742--1744 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [28] [29] [30] [31] [32] [33] [34] [35] Underfull \hbox (badness 5878) in paragraph at lines 2233--2238 []\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 2233--2238 \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 [36] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 2432--2435 [39] Underfull \hbox (badness 10000) in paragraph at lines 2466--2468 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 forwardsolve(L, b) \T1/ptm/m/n/10 is just a wrap-per for \T1/pcr/m/n/10 backsolve(L, b, [40] [41] [42] Underfull \vbox (badness 3803) has occurred while \output is active [43] [44] [45] [46] [47] [48] Underfull \hbox (badness 10000) in paragraph at lines 3016--3018 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Underfull \hbox (badness 2521) in paragraph at lines 4046--4048 []\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 [66] [67] [68] [69] [70] Underfull \hbox (badness 1270) in paragraph at lines 4366--4374 []\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 \T1/pcr/m/n/10 c("first", [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2443) in paragraph at lines 4874--4881 []\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 : / / [79] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4904--4904 []\T1/pcr/m/n/9 z <- c(32:126, 160:255) # range of most 8-bit charsets, Latin- 1 in Unicode[] [80] [81] [82] [83] Underfull \hbox (badness 1635) in paragraph at lines 5180--5183 []\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 5184--5187 []\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 5201--5214 []\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 5215--5223 []\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 [84] [85] [86] [87] Underfull \hbox (badness 2158) in paragraph at lines 5424--5428 \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 [88] Underfull \hbox (badness 10000) in paragraph at lines 5506--5514 []\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 [89] [90] Underfull \hbox (badness 1067) in paragraph at lines 5698--5705 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [91] [92] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5803--5803 []\T1/pcr/m/n/9 ## fifo example -- may fail, e.g. on Cygwin, even with OS supp ort for fifos[] Underfull \vbox (badness 10000) has occurred while \output is active [93] [94] [95] [96] [97] [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6296--6298 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [101] [102] [103] [104] [105] [106] Underfull \hbox (badness 8132) in paragraph at lines 6666--6670 []\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 6666--6670 \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 [107] Underfull \hbox (badness 10000) in paragraph at lines 6685--6696 []\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 2875) in paragraph at lines 6685--6696 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional=TRUE)\T1/ptm/m/n/10 . As that i s a generic func-tion, meth-ods can be Overfull \hbox (4.63962pt too wide) in paragraph at lines 6717--6721 []\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") [108] [109] [110] [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 5802) in paragraph at lines 7298--7302 []\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 [117] [118] Underfull \hbox (badness 10000) in paragraph at lines 7422--7426 \T1/pcr/m/n/10 trace("plot", browser, exit=browser, signature = c("track", [119] [120] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7550--7550 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(1+2, "y", {cat(" HO ! "); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 7567--7567 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] [121] [122] Underfull \hbox (badness 4254) in paragraph at lines 7697--7701 []\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 [123] [124] Underfull \hbox (badness 1603) in paragraph at lines 7844--7847 []\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 [125] Overfull \hbox (60.78088pt too wide) in paragraph at lines 7873--7873 []\T1/pcr/m/n/10 detach(name, pos = 2, unload = FALSE, character.only = FALSE, force = FALSE)[] [126] [127] [128] [129] [130] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8194--8194 []\T1/pcr/m/n/10 ## Group methods, notably for round(), signif(), floor(), cei ling(),[] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 2150) in paragraph at lines 8991--8994 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [143] Underfull \hbox (badness 5316) in paragraph at lines 9004--9012 \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 9013--9015 []\T1/pcr/m/n/10 duplicated(x, fromLast=TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than [144] [145] [146] Underfull \hbox (badness 10000) in paragraph at lines 9214--9217 []\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 [147] [148] [149] [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 5288) in paragraph at lines 9865--9867 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [156] Underfull \hbox (badness 3039) in paragraph at lines 9875--9878 []\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 Underfull \hbox (badness 10000) in paragraph at lines 9934--9936 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [157] [158] [159] Underfull \vbox (badness 3803) has occurred while \output is active [160] Underfull \hbox (badness 10000) in paragraph at lines 10159--10161 []\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 10342--10352 []\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 10342--10352 \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] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] Underfull \hbox (badness 2165) in paragraph at lines 11588--11590 []\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 \T1/pcr /m/n/10 fsep = [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 11791--11795 [][][]\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 , [186] Overfull \hbox (30.78088pt too wide) in paragraph at lines 11836--11836 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [187] Underfull \hbox (badness 10000) in paragraph at lines 11897--11900 [][][]\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 (0.78088pt too wide) in paragraph at lines 11918--11918 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE)[] [188] Underfull \hbox (badness 3965) in paragraph at lines 11944--11948 []\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] [191] [192] [193] [194] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12353--12353 [] \T1/pcr/m/n/10 decimal.mark = ".", zero.print = NULL, drop0trailing = FAL SE, ...)[] [195] Underfull \hbox (badness 1168) in paragraph at lines 12393--12397 []\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 12393--12397 \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 12479--12482 [][][]\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 , [197] [198] [199] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12647--12647 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA, ...)[] Underfull \hbox (badness 2790) in paragraph at lines 12653--12656 []\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 1024) in paragraph at lines 12684--12688 []\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 12750--12758 []\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] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] Underfull \hbox (badness 2418) in paragraph at lines 13701--13705 \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 13708--13711 []\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 [217] Underfull \hbox (badness 2326) in paragraph at lines 13737--13744 [][][]\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 , [218] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13837--13837 []\T1/pcr/m/n/9 ## Not run: ## for translation, those strings should appear in R-pkg.pot as[] [219] [220] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13978--13978 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE,[] [221] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13981--13981 []\T1/pcr/m/n/10 grepl(pattern, x, ignore.case = FALSE, perl = FALSE, fixed = FALSE,[] Underfull \hbox (badness 1867) in paragraph at lines 14000--14007 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] Underfull \hbox (badness 2285) in paragraph at lines 14871--14873 []\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 (24.78088pt too wide) in paragraph at lines 14901--14901 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE)[] [235] [236] [237] Underfull \hbox (badness 1072) in paragraph at lines 15084--15087 []\T1/ptm/m/n/10 Sometimes it is bet-ter to use a con-struc-tion such as \T1/pc r/m/n/10 (tmp <- yes; tmp[!test] <- [238] [239] [240] [241] Underfull \hbox (badness 10000) in paragraph at lines 15311--15313 []\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 [242] Underfull \hbox (badness 4217) in paragraph at lines 15395--15404 [][][]\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 15410--15426 [][][]\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 , [243] [244] [245] [246] [247] [248] [249] [250] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15912--15912 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [251] [252] [253] Underfull \hbox (badness 4739) in paragraph at lines 16035--16037 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [254] [255] [256] [257] [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16512--16514 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [262] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16559--16559 []\T1/pcr/m/n/9 vapply(i39, fivenum, c(Min.=0, "1st Qu."=0, Median=0, "3rd Qu. "=0, Max.=0))[] Underfull \hbox (badness 1975) in paragraph at lines 16575--16578 []\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 [263] [264] [265] [266] Underfull \hbox (badness 10000) in paragraph at lines 16835--16839 []\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 [267] [268] Underfull \hbox (badness 10000) in paragraph at lines 16990--16994 []\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 16990--16994 [][]\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 [269] Underfull \hbox (badness 1221) in paragraph at lines 17038--17043 []\T1/ptm/m/n/10 Normally \T1/pcr/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of loaded pack-ages, but \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 o r \T1/pcr/m/n/10 FALSE [270] Underfull \hbox (badness 10000) in paragraph at lines 17125--17131 [][][]\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 library.dynam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 data[][][]\T1/ptm/m/n/10 , [271] [272] Underfull \hbox (badness 10000) in paragraph at lines 17260--17264 []\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 [273] Underfull \hbox (badness 1264) in paragraph at lines 17309--17313 []\T1/phv/m/n/10 R \T1/ptm/m/n/10 is dis-tributed un-der the terms of the GNU G EN-ERAL PUB-LIC LI-CENSE Ver-sion 2, [274] [275] [276] [277] Underfull \hbox (badness 3343) in paragraph at lines 17523--17527 [][][]\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 17606--17606 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] [279] [280] Underfull \hbox (badness 6380) in paragraph at lines 17732--17737 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 10000) in paragraph at lines 17764--17767 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/pcr/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only \T1/pcr/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "LC _CTYPE"\T1/ptm/m/n/10 , [281] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17832--17832 []\T1/pcr/m/n/9 Sys.setlocale("LC_COLLATE", "C") # turn off locale-specific sorting, usually[] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18697--18697 []\T1/pcr/m/n/9 ## Simple version: intersect <- function(x, y) y[match(x, y, nomatch = 0)][] [296] [297] Underfull \hbox (badness 1655) in paragraph at lines 18813--18817 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] Underfull \hbox (badness 4366) in paragraph at lines 19405--19411 \T1/pcr/m/n/10 www . bzip . org/$[][]\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 . Overfull \hbox (60.78088pt too wide) in paragraph at lines 19444--19444 []\T1/pcr/m/n/10 R --min-vsize=vl --max-vsize=vu --min-nsize=nl --max-nsize=nu --max-ppsize=N[] [308] [309] [310] [311] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19694--19694 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19695--19695 [] \T1/pcr/m/n/10 sort = TRUE, suffixes = c(".x",".y"), incomparables = N ULL, ...)[] [312] [313] [314] [315] [316] [317] [318] [319] Underfull \hbox (badness 3849) in paragraph at lines 20216--20221 []\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 [320] [321] [322] [323] Underfull \hbox (badness 1609) in paragraph at lines 20439--20441 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of \T1/pcr/m/n/10 c("bytes", "chars", [324] [325] [326] [327] [328] [329] [330] [331] [332] Underfull \hbox (badness 10000) in paragraph at lines 21003--21009 []\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 21003--21009 \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] Underfull \hbox (badness 8189) in paragraph at lines 21188--21194 []\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 [][]mode [][][] [335] [336] [337] Underfull \hbox (badness 1694) in paragraph at lines 21371--21374 []\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] [341] Underfull \hbox (badness 1603) in paragraph at lines 21601--21603 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [342] Underfull \hbox (badness 1210) in paragraph at lines 21707--21716 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [343] [344] Underfull \hbox (badness 5475) in paragraph at lines 21802--21810 []\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 21819--21823 []\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 4048) in paragraph at lines 21835--21844 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue \T1/pcr/m/n/10 " [345] [346] Underfull \hbox (badness 3138) in paragraph at lines 22045--22051 []\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 3514) in paragraph at lines 22045--22051 \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- [347] Underfull \hbox (badness 10000) in paragraph at lines 22095--22102 []\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 22104--22111 []\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 2384) in paragraph at lines 22104--22111 \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 CRAN Underfull \hbox (badness 2837) in paragraph at lines 22104--22111 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke \T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 22104--22111 \T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran"; Underfull \hbox (badness 1881) in paragraph at lines 22117--22122 []\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] [352] Underfull \hbox (badness 10000) in paragraph at lines 22408--22411 []\T1/pcr/m/n/10 FUN = "*" \T1/ptm/m/n/10 is han-dled in-ter-nally as a spe-cia l case, \T1/ptm/m/it/10 via \T1/pcr/m/n/10 as.vector(X) %*% [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 23051--23055 []\T1/ptm/m/n/10 This func-tion is al-most never used: \T1/pcr/m/n/10 `name` \T 1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m/n/10 get[][][](name, [364] Underfull \hbox (badness 1796) in paragraph at lines 23114--23117 []\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] [368] [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 7415) in paragraph at lines 24177--24181 []\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 [382] [383] [384] [385] [386] Underfull \hbox (badness 1533) in paragraph at lines 24552--24555 []\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] [388] Underfull \hbox (badness 1337) in paragraph at lines 24649--24652 []\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., [389] Underfull \hbox (badness 1038) in paragraph at lines 24714--24724 []\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 [390] [391] [392] [393] [394] [395] [396] [397] Underfull \hbox (badness 4048) in paragraph at lines 25182--25187 []\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 25182--25187 \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 25182--25187 \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 , [398] [399] [400] [401] [402] [403] [404] [405] [406] [407] [408] Overfull \hbox (153.38951pt too wide) in paragraph at lines 25881--25883 []\T1/ptm/m/n/10 Punctuation char-ac-ters: `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr /m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/1 0 ` \T1/pcr/m/n/10 { | } ~\T1/ptm/m/n/10 '. Overfull \hbox (25.91963pt too wide) in paragraph at lines 25891--25893 []\T1/ptm/m/n/10 Hexadecimal dig-its: `\T1/pcr/m/n/10 0 1 2 3 4 5 6 7 8 9 A B C D E F a b c d e f\T1/ptm/m/n/10 '. [409] [410] [411] Underfull \hbox (badness 5417) in paragraph at lines 26101--26104 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 26105--26107 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 26108--26110 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / w ww . opengroup . org / onlinepubs / [412] [413] [414] [415] Underfull \hbox (badness 10000) in paragraph at lines 26387--26391 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] Underfull \hbox (badness 2302) in paragraph at lines 27340--27347 []\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 27340--27347 \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 2582) in paragraph at lines 27340--27347 \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, but Underfull \hbox (badness 4805) in paragraph at lines 27340--27347 \T1/ptm/m/n/10 in gen-eral it is not. (To scale by the stan-dard de-vi-a-tions with-out cen-ter-ing, use [431] [432] [433] Underfull \hbox (badness 1158) in paragraph at lines 27489--27494 []\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 27516--27520 []\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 27516--27520 \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- [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1803) in paragraph at lines 27904--27907 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length(along.with)\T1/ptm/m/n/10 . Underfull \hbox (badness 2809) in paragraph at lines 27908--27914 []\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 [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] Underfull \hbox (badness 4303) in paragraph at lines 28673--28676 []\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 [452] [453] [454] [455] [456] [457] [458] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29111--29111 []\T1/pcr/m/n/9 is.unsorted(x, strictly=TRUE) #-> TRUE : is not (and cannot be ) sorted strictly[] [459] [460] [461] [462] [463] [464] [465] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29565--29565 []\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)[] [466] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29580--29580 []\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 29929--29931 []\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 29989--29989 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known")[] [473] [474] Underfull \hbox (badness 6526) in paragraph at lines 30139--30149 []\T1/ptm/m/n/10 Then \T1/phv/m/n/10 R \T1/ptm/m/n/10 searches for the site-wid e startup pro-file un-less the com-mand line op-tion Underfull \hbox (badness 6110) in paragraph at lines 30175--30185 []\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 ' or Underfull \hbox (badness 2635) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the Underfull \hbox (badness 1112) in paragraph at lines 30175--30185 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us- ing [475] Underfull \hbox (badness 7704) in paragraph at lines 30226--30231 \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, e.g. [476] [477] [478] [479] [480] [481] [482] [483] [484] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30818--30818 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [485] [486] [487] [488] [489] Overfull \hbox (6.78088pt too wide) in paragraph at lines 31070--31070 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31113--31113 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [490] [491] [492] [493] [494] [495] [496] [497] Underfull \hbox (badness 10000) in paragraph at lines 31564--31567 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 31611--31611 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision[] [498] [499] [500] [501] [502] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31902--31902 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a=, A=1, b=2:3, "Otherwise: last"),"\n")[] [503] [504] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32030--32030 []\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.[] [505] [506] [507] [508] Underfull \hbox (badness 4036) in paragraph at lines 32230--32233 []\T1/ptm/m/n/10 These set-tings are usu-ally con-trolled by the en-vi-ron-ment vari-ables \T1/pcr/m/n/10 LC_NUMERIC \T1/ptm/m/n/10 and [509] [510] Underfull \hbox (badness 10000) in paragraph at lines 32354--32358 []\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 32369--32372 []\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] [514] [515] Underfull \hbox (badness 1082) in paragraph at lines 32644--32647 []\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] Underfull \hbox (badness 1038) in paragraph at lines 32816--32819 []\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 [518] [519] [520] [521] [522] [523] [524] Overfull \hbox (6.78088pt too wide) in paragraph at lines 33255--33255 []\T1/pcr/m/n/10 table(..., exclude = if (useNA == "no") c(NA, NaN), useNA = c ("no",[] [525] Underfull \hbox (badness 1270) in paragraph at lines 33273--33276 []\T1/ptm/m/n/10 levels to re-move from all fac-tors in \T1/pcr/m/n/10 ...\T1/p tm/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 33341--33344 []\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] [530] Underfull \hbox (badness 10000) in paragraph at lines 33573--33575 []\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 [531] Underfull \hbox (badness 10000) in paragraph at lines 33656--33659 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . [532] [533] Underfull \hbox (badness 5475) in paragraph at lines 33782--33786 [][][]\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 \ [][]$\T1/pcr/m/n/10 http : / / [534] Underfull \hbox (badness 10000) in paragraph at lines 33844--33848 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 http : [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 4181) in paragraph at lines 34187--34191 []\T1/ptm/m/n/10 For most Unix-alikes use the Ol-son databases. The system-spec ific de-fault lo-ca-tion Underfull \hbox (badness 2495) in paragraph at lines 34187--34191 \T1/ptm/m/n/10 in the file sys-tem varies, e.g. `\T1/pcr/m/n/10 /usr/share/zone info\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 /usr/etc/zoneinfo\T1/ptm/m/n/10 ', Underfull \hbox (badness 3460) in paragraph at lines 34209--34211 [][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Time _ zone$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / www . twinsun . com / [541] [542] [543] [544] [545] Overfull \hbox (9.78043pt too wide) in paragraph at lines 34519--34519 []\T1/pcr/m/n/9 trace("f", quote(browser(skipCalls=4)), exit = quote(browser(s kipCalls=4)))[] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 1708) in paragraph at lines 34897--34905 []\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 34897--34905 \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 34906--34910 []\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-stead of \T1/pcr/m/n/10 tr y(expr, Underfull \hbox (badness 3977) in paragraph at lines 34906--34910 \T1/pcr/m/n/10 silent=TRUE)\T1/ptm/m/n/10 , some-thing like \T1/pcr/m/n/10 tryC atch(expr, error = function(e) e) \T1/ptm/m/n/10 (or Underfull \hbox (badness 4859) in paragraph at lines 34919--34924 [][][]\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 34978--34990 []\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 34978--34990 \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] [556] [557] [558] [559] [560] [561] [562] [563] Underfull \hbox (badness 1803) in paragraph at lines 35694--35697 []\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 35698--35705 []\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 [564] [565] Underfull \hbox (badness 3668) in paragraph at lines 35828--35830 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [566] [567] [568] [569] [570] Underfull \hbox (badness 6592) in paragraph at lines 36100--36105 []\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] [572] [573] Underfull \vbox (badness 3803) has occurred while \output is active [574] [575] [576] [577] [578] Underfull \hbox (badness 2846) in paragraph at lines 36608--36612 []\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 36635--36635 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 36656--36660 []\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]) (./datasets-pkg.tex Chapter 2. 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 [581] [582] [583] [584] [585] Underfull \vbox (badness 10000) has occurred while \output is active [586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 365--365 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \vbox (badness 10000) has occurred while \output is active [606] Underfull \hbox (badness 10000) in paragraph at lines 1490--1493 []\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 1490--1493 \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 [607] Underfull \vbox (badness 2368) has occurred while \output is active [608] Underfull \hbox (badness 1325) in paragraph at lines 1571--1576 []\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- [609] [610] [611] [612] [613] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1888--1888 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] [614] [615] [616] [617] [618] [619] [620] Overfull \vbox (17.60591pt too high) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \vbox (badness 10000) has occurred while \output is active [634] [635] Underfull \vbox (badness 1365) has occurred while \output is active [636] [637] [638] [639] [640] Underfull \hbox (badness 5175) in paragraph at lines 3452--3455 []\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 3452--3455 \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 . [641] [642] [643] Underfull \vbox (badness 10000) has occurred while \output is active [644] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3698--3698 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3727--3730 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655] Overfull \vbox (18.9959pt too high) has occurred while \output is active [656] [657] [658]) (./grDevices-pkg.tex Chapter 3. [659] [660] [661] [662] [663] [664] Overfull \hbox (6.78088pt too wide) in paragraph at lines 367--367 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [665] [666] [667] [668] [669] [670] [671] [672] [673] Underfull \hbox (badness 5175) in paragraph at lines 898--900 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [674] [675] Underfull \hbox (badness 10000) in paragraph at lines 1000--1002 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [676] [677] [678] [679] [680] [681] Underfull \hbox (badness 10000) in paragraph at lines 1424--1426 []\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, if [682] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1505--1505 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [683] Underfull \hbox (badness 1184) in paragraph at lines 1544--1557 []\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 1694) in paragraph at lines 1544--1557 \T1/pcr/m/n/10 "pbmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pgm"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "pgmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pgnm"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "pgnmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "pnm"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "pnmraw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ppm"\T1/ptm/m/n/10 , Underfull \hbox (badness 6493) in paragraph at lines 1544--1557 \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/ptm/ m/n/10 , \T1/pcr/m/n/10 "psmono"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "psgray"\T1/ptm /m/n/10 , [684] [685] Underfull \hbox (badness 10000) in paragraph at lines 1650--1652 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [686] [687] [688] [689] Underfull \hbox (badness 2326) in paragraph at lines 1902--1912 \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 1902--1912 \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 1902--1912 \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 1902--1912 \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 [690] [691] Overfull \hbox (42.18039pt too wide) in paragraph at lines 2028--2028 []\T1/pcr/m/n/9 # This currently only works on the Windows and X11(type="Xlib" ) screen devices...[] [692] [693] [694] [695] Underfull \hbox (badness 10000) in paragraph at lines 2291--2292 [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] Underfull \hbox (badness 10000) in paragraph at lines 2888--2891 [][][]\T1/pcr/m/n/10 colors[][][] \T1/ptm/m/n/10 for the vec-tor of built-in na med col-ors; [][]\T1/pcr/m/n/10 hsv[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gr ay[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 rainbow[][][]\T1/ptm/m/n/10 , [706] [707] [708] [709] [710] [711] Underfull \hbox (badness 5939) in paragraph at lines 3331--3336 []\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 , [712] [713] [714] [715] [716] Underfull \vbox (badness 10000) has occurred while \output is active [717] [718] Underfull \vbox (badness 3803) has occurred while \output is active [719] [720] [721] [722] Underfull \hbox (badness 5077) in paragraph at lines 4011--4017 []\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 [723] [724] [725] Underfull \hbox (badness 1755) in paragraph at lines 4167--4169 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [726] [727] Underfull \hbox (badness 7344) in paragraph at lines 4319--4321 []\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 4330--4335 [][][]\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 [728] [729] Underfull \hbox (badness 2035) in paragraph at lines 4442--4451 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 3735) in paragraph at lines 4442--4451 \T1/ptm/m/n/10 vided: \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica- Underfull \hbox (badness 10000) in paragraph at lines 4442--4451 \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 ), Underfull \hbox (badness 4686) in paragraph at lines 4484--4490 \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 [730] Underfull \hbox (badness 10000) in paragraph at lines 4509--4517 []\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 4509--4517 \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 \hbox (badness 7344) in paragraph at lines 4528--4530 []\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 [731] [732] [733] [734] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4713--4713 []\T1/pcr/m/n/10 quartz(title, width, height, pointsize, family, fontsmooth, a ntialias,[] [735] Underfull \hbox (badness 10000) in paragraph at lines 4804--4806 []\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 [736] [737] [738] [739] [740] Underfull \hbox (badness 10000) in paragraph at lines 5111--5114 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [741] [742] [743] [744] [745] [746] [747] Underfull \hbox (badness 1189) in paragraph at lines 5478--5480 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [748] Underfull \hbox (badness 1132) in paragraph at lines 5546--5548 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and \T1/pcr/m/n/10 "-cronyx- Underfull \hbox (badness 2547) in paragraph at lines 5581--5587 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g. of \T1 /pcr/m/n/10 quote(pi)\T1/ptm/m/n/10 ) have been seen [749] [750] [751] [752] Underfull \hbox (badness 2065) in paragraph at lines 5814--5820 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/pcr/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , Underfull \hbox (badness 1360) in paragraph at lines 5814--5820 \T1/pcr/m/n/10 Narrow"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1 /ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 "Times "\T1/ptm/m/n/10 . Underfull \hbox (badness 1721) in paragraph at lines 5847--5850 []\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 / [753] [754] [755] Underfull \hbox (badness 1231) in paragraph at lines 6009--6011 []\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 [756] [757] [758]) (./graphics-pkg.tex Chapter 4. [759] [760] Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 []\T1/pcr/m/n/10 arrows(x0, y0, x1 = x0, y1 = y0, length = 0.25, angle = 30, c ode = 2,[] [761] Underfull \hbox (badness 2856) in paragraph at lines 175--178 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the point [762] Underfull \hbox (badness 1412) in paragraph at lines 283--288 []\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- [763] [764] [765] [766] Underfull \hbox (badness 2726) in paragraph at lines 462--468 []\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 [767] [768] [769] Underfull \hbox (badness 10000) in paragraph at lines 659--662 []\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 [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1233--1233 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [780] Underfull \hbox (badness 1024) in paragraph at lines 1278--1286 \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 Underfull \hbox (badness 3375) in paragraph at lines 1312--1314 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [781] [782] [783] [784] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1685--1691 [][][]\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 [787] [788] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1815--1815 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns,[] [789] [790] [791] [792] Underfull \hbox (badness 4859) in paragraph at lines 2003--2006 []\T1/ptm/m/n/10 labels and graph-i-cal pa-ram-e-ters can also be spec-i-fied a s ar-gu-ments. [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] Underfull \hbox (badness 1226) in paragraph at lines 2646--2650 \T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr /m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2753 []\T1/ptm/m/n/10 graphical pa-ram-e-ters, or ar-gu-ments to [][]\T1/pcr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [805] [806] [807] [808] Underfull \hbox (badness 1755) in paragraph at lines 2998--3002 []\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] [810] [811] [812] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3241--3241 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [813] [814] [815] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3413--3413 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [816] Underfull \vbox (badness 10000) has occurred while \output is active [817] [818] [819] [820] Underfull \hbox (badness 1867) in paragraph at lines 3723--3727 []\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 3886--3888 []\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] [828] [829] [830] [831] Underfull \hbox (badness 1264) in paragraph at lines 4387--4399 \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] [834] [835] [836] [837] [838] [839] [840] [841] [842] [843] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5259--5259 [] \T1/pcr/m/n/9 col = c("purple", "violetred1", "green3", "cornsilk", "cya n", "white"))[] [844] Underfull \hbox (badness 1052) in paragraph at lines 5313--5317 []\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., \T1/pcr/m/n/10 type = [845] [846] [847] [848] [849] [850] [851] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric vec tor ~ factor[] [852] [853] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5827--5827 [] \T1/pcr/m/n/10 axes = TRUE, labels = FALSE, add = FALSE, ann = TRUE, ...)[] [854] [855] [856] Underfull \hbox (badness 10000) in paragraph at lines 6058--6060 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [857] [858] Underfull \hbox (badness 1028) in paragraph at lines 6151--6153 []\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 [859] [860] Underfull \vbox (badness 3803) has occurred while \output is active [861] [862] Underfull \hbox (badness 10000) in paragraph at lines 6410--6412 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr [863] [864] Underfull \hbox (badness 2600) in paragraph at lines 6503--6505 []\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] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6574--6574 [] \T1/pcr/m/n/9 title="Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6583--6583 [] \T1/pcr/m/n/9 title="Overlapping rectangles, one clockwise, other anti-clockwise")[] [866] [867] [868] [869] [870] [871] [872] [873] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7100--7100 [] \T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), space = "Lab")[] [874] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7111--7111 [] \T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints=0 , add=TRUE))[] [875] [876] [877] [878] [879] [880] [881] [882] [883] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7618--7618 []\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 7619--7619 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [884] Underfull \hbox (badness 2080) in paragraph at lines 7721--7726 []\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 [885] Underfull \hbox (badness 1533) in paragraph at lines 7759--7763 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i]==1\T1/ptm/m/n/10 , a (slightly en -larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn. For [886] [887] [888] [889] [890] [891] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8121--8121 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 6691) in paragraph at lines 8147--8150 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) [892] Underfull \hbox (badness 1584) in paragraph at lines 8184--8190 []\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.8232 \HeaderA{units}{Graphical Units}{units} [894] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8290--8290 []\T1/pcr/m/n/10 xspline(x, y = NULL, shape = 0, open = TRUE, repEnds = TRUE, draw = TRUE,[] Underfull \hbox (badness 1205) in paragraph at lines 8297--8299 []\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] [897]) (./grid-pkg.tex [898] Chapter 5. Underfull \vbox (badness 10000) has occurred while \output is active [899] [900] [901] [902] [903] Underfull \hbox (badness 10000) in paragraph at lines 291--297 \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 291--297 \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 [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 888--888 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 890--890 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 892--892 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [914] [915] Underfull \hbox (badness 2781) in paragraph at lines 1037--1040 []\T1/ptm/m/n/10 Both func-tions cre-ate an ar-rows grob (a graph-i-cal ob-ject de-scrib-ing ar-rows), but only [916] [917] [918] [919] Underfull \hbox (badness 3219) in paragraph at lines 1212--1215 []\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 [920] [921] [922] [923] [924] [925] [926] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1652--1652 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [927] [928] Underfull \hbox (badness 2961) in paragraph at lines 1770--1775 []\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 , [929] [930] Underfull \hbox (badness 4479) in paragraph at lines 1858--1861 []\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] Underfull \hbox (badness 2894) in paragraph at lines 1924--1931 []\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 [932] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1969--1969 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [933] [934] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2126--2126 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [935] [936] [937] [938] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2361--2361 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [939] [940] [941] [942] [943] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2670--2670 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [944] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2709--2709 []\T1/pcr/m/n/10 moveToGrob(x = 0, y = 0, default.units = "npc", name = NULL, vp = NULL)[] [945] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2765--2765 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [946] [947] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2890--2890 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2897--2897 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [948] [949] [950] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3090--3090 [] \T1/pcr/m/n/9 title="Nested rectangles, outer clockwise, inn er anti-clockwise")[] [951] Overfull \hbox (58.38037pt too wide) in paragraph at lines 3105--3105 [] \T1/pcr/m/n/9 title="Overlapping rectangles, one clockwise, other anti-clockwise")[] [952] [953] [954] [955] [956] Underfull \hbox (badness 10000) in paragraph at lines 3390--3392 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 1067) in paragraph at lines 3787--3790 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 7256) in paragraph at lines 4026--4028 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] Underfull \hbox (badness 1867) in paragraph at lines 5325--5327 []\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 [991] Underfull \hbox (badness 10000) in paragraph at lines 5362--5368 [][][]\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 , [992] [993] [994] [995] [996] [997]) (./methods-pkg.tex [998] Chapter 6. [999] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (48.78088pt too wide) in paragraph at lines 459--459 []\T1/pcr/m/n/10 "namedList" # the alternative to "list" that preserves the na mes attribute[] [1005] [1006] [1007] Underfull \hbox (badness 1281) in paragraph at lines 654--663 []\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 [1008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 732--732 []\T1/pcr/m/n/9 setMethod("f", "B2", function(x) {x@b0 <- 111; c(x@b2, callNex tMethod())})[] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1302--1302 []\T1/pcr/m/n/9 ## the super- and subclasses of "standardGeneric" and "derived DefaultMethod"[] [1017] [1018] [1019] [1020] [1021] [1022] Overfull \hbox (198.78021pt too wide) in paragraph at lines 1714--1714 []\T1/pcr/m/n/9 stopifnot(identical(cc(letters, character(), cd1), paste(lette rs, character(), cd1))) # the "character" method[] Overfull \hbox (355.38004pt too wide) in paragraph at lines 1716--1716 []\T1/pcr/m/n/9 stopifnot(identical(cc(letters, character(), cd2), c(letters, character(), cd2))) # the default, because "vdate" doesn\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 t extend "character"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1718--1718 []\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 1720--1720 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 1726--1726 []\T1/pcr/m/n/9 setMethod("numMax", "numeric", function(...)max(...)) # won\TS 1/pcr/m/n/9 '\T1/pcr/m/n/9 t work for complex data[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 1727--1727 []\T1/pcr/m/n/9 setMethod("numMax", "Number", function(...) paste(...)) # shou ld not be selected w/o complex args[] [1023] Underfull \hbox (badness 10000) in paragraph at lines 1760--1762 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1024] [1025] Underfull \hbox (badness 10000) in paragraph at lines 1903--1908 []\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 [1026] [1027] [1028] [1029] [1030] Underfull \hbox (badness 10000) in paragraph at lines 2257--2261 []\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 [1031] [1032] [1033] Underfull \hbox (badness 3792) in paragraph at lines 2502--2505 []\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 [1034] Underfull \hbox (badness 1194) in paragraph at lines 2533--2537 []\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 [1035] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2589--2589 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1036] [1037] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2824--2824 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1038] [1039] [1040] [1041] [1042] [1043] Underfull \hbox (badness 1552) in paragraph at lines 3181--3183 []\T1/pcr/m/n/10 packageName \T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1044] [1045] [1046] [1047] Underfull \hbox (badness 10000) in paragraph at lines 3405--3409 []\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 [1048] Overfull \hbox (28.78088pt too wide) in paragraph at lines 3519--3528 [] [1049] [1050] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3610--3610 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1051] Underfull \hbox (badness 1394) in paragraph at lines 3681--3686 \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 [1052] [1053] [1054] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3943--3943 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3963--3963 []\T1/pcr/m/n/9 setClass("stringsDated", contains = "character", representatio n(stamp="POSIXt"))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 ## In contrast, a class that simply extends "factor" has no su ch ambiguities[] Underfull \vbox (badness 10000) has occurred while \output is active [1055] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3978--3978 []\T1/pcr/m/n/9 setClass("factorDated", contains = "factor", representation(st amp="POSIXt"))[] [1056] [1057] [1058] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4192--4192 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4193--4193 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1059] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4250--4250 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here)[] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 10000) in paragraph at lines 4722--4731 []\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 [1066] [1067] [1068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4915--4915 []\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 4944--4944 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), 1:10)) # (version 2.9.0 or earlier fails here)[] Underfull \vbox (badness 10000) has occurred while \output is active [1069] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4958--4958 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] [1070] [1071] Underfull \hbox (badness 10000) in paragraph at lines 5102--5104 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1072] [1073] [1074] [1075] Underfull \hbox (badness 1087) in paragraph at lines 5391--5396 []\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 [1076] [1077] [1078] [1079] [1080] [1081] Underfull \hbox (badness 1248) in paragraph at lines 5860--5864 []\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 5860--5864 \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 [1082] Underfull \hbox (badness 4291) in paragraph at lines 5918--5932 []\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 [1083] [1084] [1085] Underfull \vbox (badness 10000) has occurred while \output is active [1086] [1087]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6272 \aliasA{S4}{S3Part}{S4} [1088] [1089] [1090] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6500--6500 []\T1/pcr/m/n/9 ## two examples extending S3 class "lm", class "xlm" directly and "ylm" indirectly[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6512--6512 []\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 6517--6517 []\T1/pcr/m/n/9 ##similar classes to "xlm" and "ylm", but extending S3 class c ("mlm", "lm")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6526--6526 []\T1/pcr/m/n/9 setClass("dataFrameD", representation(date = "Date"), contains = "data.frame")[] [1091]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.6546 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.6548 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.6549 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.6551 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.6552 \aliasA{Summary}{S4groupGeneric}{Summary} [1092] Underfull \hbox (badness 2050) in paragraph at lines 6612--6616 []\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 6625--6635 []\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 6625--6635 \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 , [1093] [1094] Underfull \hbox (badness 1694) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see [1095] Underfull \hbox (badness 10000) in paragraph at lines 6806--6809 []\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 [1096] [1097] Underfull \hbox (badness 2111) in paragraph at lines 6912--6919 []\T1/ptm/m/n/10 The slots in a class def-i-ni-tion will be the union of all th e slots spec-i-fied di-rectly by [1098] [1099] Underfull \vbox (badness 3803) has occurred while \output is active [1100] [1101] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7236--7236 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(),[] [1102] [1103] Underfull \hbox (badness 2277) in paragraph at lines 7367--7375 []\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 [1104] Underfull \hbox (badness 3128) in paragraph at lines 7408--7413 []\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 [1105] [1106] [1107] Underfull \hbox (badness 1755) in paragraph at lines 7622--7625 []\T1/ptm/m/n/10 the en-vi-ron-ment in which to store the def-i-ni-tion of the method. For [1108] [1109] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7765--7765 []\T1/pcr/m/n/9 ## methods for plotting track objects (see the example for \li nk{setClass})[] [1110] [1111] [1112] [1113] [1114] Overfull \hbox (52.98038pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/9 ## two examples extending S3 class "lm", class "xlm" directly and "ylm" indirectly[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8170--8170 []\T1/pcr/m/n/9 setClass("stamped4", contains = "vector", representation(date = "POSIXt"))[] [1115] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8178--8178 []\T1/pcr/m/n/9 someLetters <- stamped(sample(letters, 10), ISOdatetime(2008, 10, 15, 12, 0, 0))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8181--8181 []\T1/pcr/m/n/9 st # show() method prints the object\TS1/pcr/m/n/9 '\T1/pcr/m /n/9 s class, then calls the S3 print method.[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8192--8192 [] \T1/pcr/m/n/9 prototype(NA, tsp = rep(1,3))) # prototype to be a legal S3 time-series[] [1116] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8281--8281 []\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 8292--8292 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8894--8894 []\T1/pcr/m/n/9 ## if no other attached packages have methods for \TS1/pcr/m/ n/9 `\T1/pcr/m/n/9 +\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 or its group generic[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8895--8895 []\T1/pcr/m/n/9 ## functions, this returns a 16 by 2 matrix of selection patte rns (in R 2.9.0)[] [1126] Underfull \hbox (badness 10000) in paragraph at lines 8956--8958 []\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 8964--8968 []\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 8964--8968 \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 [1127] [1128] [1129] [1130]) (./splines-pkg.tex Chapter 7. 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] Overfull \hbox (20.58041pt too wide) in paragraph at lines 463--463 []\T1/pcr/m/n/9 ispl <- polySpline( interpSpline( weight ~ height, women, bSp line = TRUE ) )[] [1139] [1140] [1141] [1142] [1143] [1144] [1145]) (./stats-pkg.tex [1146] Chapter 8. [1147] 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 , [1148] [1149] [1150] [1151] [1152] [1153] Overfull \hbox (18.78088pt too wide) in paragraph at lines 425--425 [] \T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE)[] [1154] [1155] [1156] [1157] [1158] [1159] Underfull \hbox (badness 1024) in paragraph at lines 803--805 []\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 [1160] [1161] [1162] [1163] [1164] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1138--1138 [] \T1/pcr/m/n/10 c("Pillai", "Wilks", "Hotelling-Lawley", "Roy", "Sph erical"),[] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2566--2566 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(0), ma = numeric(0), lag.max = r, pacf = FALSE)[] [1188] [1189] [1190] [1191] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2802--2802 []\T1/pcr/m/n/9 legend(40,70, c("mean","median"), lty=1,col=c("blue","green"), bg="gray90")[] [1192] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2825--2825 []\T1/pcr/m/n/10 bw.ucv(x, nb = 1000, lower = 0.1 * hmax, upper = hmax, tol = 0.1 * lower)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2827--2827 []\T1/pcr/m/n/10 bw.bcv(x, nb = 1000, lower = 0.1 * hmax, upper = hmax, tol = 0.1 * lower)[] [1193] [1194] Underfull \hbox (badness 10000) in paragraph at lines 2991--2993 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1195] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3038--3038 []\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 3039--3039 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3627--3627 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0)[] [1205] [1206] [1207] [1208] [1209] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3911--3911 []\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 3912--3912 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1210] [1211] [1212] Underfull \hbox (badness 10000) in paragraph at lines 4070--4072 []\T1/ptm/m/n/10 the Pear-son resid-u-als, \T1/pcr/m/n/10 (observed - expected) / [1213] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4122--4122 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1214] [1215] [1216] [1217] Underfull \hbox (badness 3989) in paragraph at lines 4366--4373 []\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 = [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4929--4929 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] [1226] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4947--4947 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter"))[] Underfull \hbox (badness 10000) in paragraph at lines 4979--4981 []\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 , \T1/pcr/m/n/10 m <- [1227] [1228] [1229] Underfull \hbox (badness 1436) in paragraph at lines 5157--5162 []\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 5157--5162 \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 5157--5162 \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 , [1230] [1231] [1232] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5319--5319 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1233] [1234] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5484--5484 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE,[] [1235] [1236] [1237] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5664--5664 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL)[] [1238] [1239] [1240] [1241] [1242] [1243] Underfull \hbox (badness 5954) in paragraph at lines 5993--5995 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1244] Underfull \hbox (badness 2503) in paragraph at lines 6060--6062 []\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 6063--6065 []\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 [1245] [1246] [1247] [1248] [1249] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6354--6354 [] \T1/pcr/m/n/9 ylim = c(0, 1), xlab="", main="R\TS1/pcr/m/n/9 '\T1/pcr/m /n/9 s density() kernels with width = 1")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6363--6363 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1250] [1251] [1252] [1253] [1254] [1255] Underfull \hbox (badness 10000) in paragraph at lines 6730--6734 \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 [1256] Underfull \hbox (badness 6493) in paragraph at lines 6828--6831 []\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 [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] Underfull \hbox (badness 3780) in paragraph at lines 7360--7365 []\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 , ..., \T 1/pcr/m/n/10 x[t- [1266] [1267] [1268] [1269] [1270] Underfull \hbox (badness 1210) in paragraph at lines 7689--7691 []\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 [1271] [1272] [1273] [1274] [1275] [1276] [1277] Underfull \vbox (badness 3803) has occurred while \output is active [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8619--8619 [] \T1/pcr/m/n/9 satisfaction=c("VeryD", "LittleD", "ModerateS" , "VeryS")))[] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] Underfull \hbox (badness 2443) in paragraph at lines 9242--9248 [][][]\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); [1296] [1297] [1298] [1299] [1300] [1301] [1302] Underfull \hbox (badness 4518) in paragraph at lines 9684--9689 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1303] Underfull \hbox (badness 4132) in paragraph at lines 9723--9727 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1304] Underfull \hbox (badness 10000) in paragraph at lines 9826--9829 []\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 [1305] [1306] [1307] Underfull \hbox (badness 2142) in paragraph at lines 10025--10028 []\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 ^^@ [1308] [1309] Underfull \hbox (badness 1708) in paragraph at lines 10106--10109 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: Underfull \hbox (badness 10000) in paragraph at lines 10147--10153 [][][]\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, [1310] [1311] Underfull \hbox (badness 2635) in paragraph at lines 10315--10321 \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 [1312] [1313] [1314] Underfull \hbox (badness 1694) in paragraph at lines 10469--10472 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1315] [1316] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10598--10598 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 10611--10615 []\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 [1317] [1318] [1319] [1320] [1321] [1322] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10907--10907 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]),col=2:4), D EV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.10922 \aliasA{hat}{influence.measures}{hat} [1323] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10976--10976 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10988--10988 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 11034--11039 []\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- [1324] Underfull \hbox (badness 1052) in paragraph at lines 11045--11047 []\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 [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 4518) in paragraph at lines 12485--12490 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1349] [1350] [1351] Underfull \hbox (badness 10000) in paragraph at lines 12679--12683 []\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 , [1352] [1353] [1354] [1355] [1356] Underfull \hbox (badness 1163) in paragraph at lines 12997--13005 \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 , [1357] [1358] Underfull \hbox (badness 4518) in paragraph at lines 13107--13112 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1359] [1360] [1361] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13281--13281 []\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 13282--13282 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1362] Underfull \hbox (badness 10000) in paragraph at lines 13329--13332 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, \T1/pcr/m/n/10 plogis(x) == (1+ [1363] [1364] [1365] [1366] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13606--13606 []\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 13607--13607 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] Underfull \hbox (badness 2726) in paragraph at lines 14092--14095 []\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 , [1375] [1376] [1377] [1378] [1379] Underfull \vbox (badness 10000) has occurred while \output is active [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] Underfull \hbox (badness 1648) in paragraph at lines 14983--14985 []\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, [1390] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15061--15061 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a="contr.sum", b="c ontr.poly"))[] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15612--15612 []\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[] [1400] [1401] [1402] [1403] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15827--15827 []\T1/pcr/m/n/9 persp(x,size, dnb <- outer(x, size, function(x,s) dnbinom(x,s, prob= 0.4)),[] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] Underfull \vbox (badness 10000) has occurred while \output is active [1414] [1415] [1416] [1417] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16680--16680 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1418] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16727--16727 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1419] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16774--16774 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1420] [1421] [1422] [1423] [1424] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17076--17076 [] \T1/pcr/m/n/10 method = c("Nelder-Mead", "BFGS", "CG", "L-BFGS-B", "SA NN"),[] [1425] Underfull \hbox (badness 1248) in paragraph at lines 17182--17185 []\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 17195--17199 \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 [1426] Underfull \hbox (badness 2042) in paragraph at lines 17253--17255 []\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 [1427] [1428] Underfull \vbox (badness 10000) has occurred while \output is active [1429] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17382--17382 [] \T1/pcr/m/n/9 control = list(maxit=30000, temp=2000, trace=TRUE , REPORT=500))[] [1430] Underfull \hbox (badness 2564) in paragraph at lines 17457--17468 []\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 17457--17468 \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 [1431] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17516--17516 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1432] [1433] [1434] [1435] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17791--17791 [] \T1/pcr/m/n/10 alternative = c("two.sided", "less", "greater "), ...)[] Underfull \hbox (badness 1337) in paragraph at lines 17803--17806 []\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 [1436] [1437] [1438] [1439] [1440] [1441] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18119--18119 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1442] [1443] Overfull \hbox (42.78088pt too wide) in paragraph at lines 18207--18207 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s d ist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 18210--18210 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1444] [1445] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18325--18325 []\T1/pcr/m/n/9 plot(lm.SR <- lm(sr ~ pop15 + pop75 + dpi + ddpi, data = LifeC ycleSavings))[] [1446] [1447] [1448] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18512--18512 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 18522--18525 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1449] Underfull \hbox (badness 1107) in paragraph at lines 18580--18582 []\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 [1450] [1451] [1452] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18735--18735 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1453] [1454] [1455] Underfull \hbox (badness 2343) in paragraph at lines 18913--18915 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 6859) in paragraph at lines 19867--19874 [][][]\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 19877--19883 []\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 , [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20835--20835 [] \T1/pcr/m/n/10 cs.ind = 1L:k, tst.ind = k + 1L, zap.ind = integ er(0),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20838--20838 [] \T1/pcr/m/n/10 substr(colnames(x)[nc], 1L, 3L) == "Pr(",[] [1488] [1489] [1490] [1491] [1492] [1493] Underfull \hbox (badness 1337) in paragraph at lines 21160--21166 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 10000) in paragraph at lines 21904--21907 []\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 21904--21907 \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 [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] Underfull \hbox (badness 8094) in paragraph at lines 22480--22483 []\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 \T1/pcr/m/n/10 y[j] = [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] Underfull \hbox (badness 1412) in paragraph at lines 23298--23300 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1529] [1530] [1531] [1532] [1533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23657--23657 []\T1/pcr/m/n/9 (s2 <- smooth.spline(y18, control = list(trace=TRUE,tol=1e-6, low= -1.5)))[] [1534] [1535] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23795--23795 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail,[] [1536] [1537] [1538] [1539] [1540] [1541] [1542] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24170--24170 []\T1/pcr/m/n/10 splinefun(x, y = NULL, method = c("fmm", "periodic", "natural ", "monoH.FC"),[] [1543] [1544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24322--24322 []\T1/pcr/m/n/9 legend("topleft", paste("splinefun( \"", c("fmm", "monoH.CS"), "\" )", sep=\TS1/pcr/m/n/9 ''\T1/pcr/m/n/9 ),[] [1545] [1546] Underfull \hbox (badness 3240) in paragraph at lines 24429--24433 [][][]\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 [1547] [1548] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24557--24557 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1549] [1550] Underfull \hbox (badness 10000) in paragraph at lines 24667--24670 \T1/pcr/m/n/10 exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input)-exp(-exp(lKa)*input)) / Overfull \hbox (9.78043pt too wide) in paragraph at lines 24689--24689 []\T1/pcr/m/n/9 SSfol(Theoph.1$Dose, Theoph.1$Time, lKe, lKa, lCl) # response and gradient[] [1551] [1552] [1553] Underfull \hbox (badness 2922) in paragraph at lines 24840--24845 []\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 [1554] Underfull \hbox (badness 2922) in paragraph at lines 24895--24900 []\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] [1556] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24990--24990 []\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 24992--24992 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1557] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25049--25049 []\T1/pcr/m/n/10 stat.anova(table, test = c("Chisq", "F", "Cp"), scale, df.sca le, n)[] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25558--25558 [] \T1/pcr/m/n/10 main = NULL, range.bars = TRUE, ..., col.range = "light gray")[] [1566] [1567] [1568] [1569] [1570] Underfull \hbox (badness 3396) in paragraph at lines 25856--25858 []\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 [1571] [1572] [1573] Underfull \hbox (badness 2237) in paragraph at lines 26028--26030 []\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 [1574] [1575] [1576] Underfull \hbox (badness 2591) in paragraph at lines 26185--26187 []\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 [1577] Underfull \hbox (badness 2237) in paragraph at lines 26231--26234 []\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 [1578] [1579] Underfull \hbox (badness 3407) in paragraph at lines 26409--26413 []\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) [1580] [1581] [1582] Underfull \hbox (badness 1337) in paragraph at lines 26542--26546 []\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 [1583] [1584] [1585] [1586] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26808--26808 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 26832--26835 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1587] [1588] [1589] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26958--26958 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1590] Underfull \hbox (badness 2205) in paragraph at lines 27041--27046 []\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 [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 10000) in paragraph at lines 27551--27555 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 tsp \T1/ptm/m/n/10 at-tribute was pre-vi-ou sly de-scribed here as \T1/pcr/m/n/10 c(start(x), end(x), [1600] Overfull \hbox (12.78088pt too wide) in paragraph at lines 27630--27630 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 27631--27631 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 1337) in paragraph at lines 28131--28135 []\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 [1610] [1611] [1612] [1613] Underfull \hbox (badness 1043) in paragraph at lines 28371--28374 []\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 -pweibull(t, a, b, lower = Overfull \hbox (4.38043pt too wide) in paragraph at lines 28398--28398 []\T1/pcr/m/n/9 all.equal(pweibull(x, 2.5, pi, lower.tail=FALSE, log.p=TRUE), -(x/pi)^2.5,[] [1614] [1615] [1616] Underfull \hbox (badness 1337) in paragraph at lines 28552--28556 []\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 [1617] [1618] [1619] [1620] [1621] [1622] [1623] Overfull \hbox (66.78088pt too wide) in paragraph at lines 28956--28956 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, na.action,[] [1624] [1625] [1626]) (./stats4-pkg.tex Chapter 9. [1627] [1628] [1629] Overfull \hbox (112.38031pt too wide) in paragraph at lines 227--227 [] \T1/pcr/m/n/9 if(ymax > 0 && xhalf > 0) -sum(stats::dpois(y, lambda=ymax /(1+x/xhalf), log=TRUE)) else NA[] [1630] Overfull \hbox (9.78043pt too wide) in paragraph at lines 242--242 []\T1/pcr/m/n/9 ## the lower bounds are really > 0, but we use >=0 to stress-t est profiling[] [1631] [1632] [1633]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.457 ... in Package 'stats4'}{show.Rdash.methods} [1634] Underfull \hbox (badness 10000) in paragraph at lines 490--493 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1635] [1636]) (./tcltk-pkg.tex Chapter 10. [1637] [1638] [1639] [1640] [1641] Overfull \hbox (36.7804pt too wide) in paragraph at lines 378--378 [] \T1/pcr/m/n/9 # Do some work to create a nice picture. Nothing will be displayed until...[] [1642] [1643] Overfull \hbox (30.78088pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/10 ## NB: some widgets also have a selection.clear command, henc e the "X".[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 548--548 []\T1/pcr/m/n/10 ## winfo actually has a large number of subcommands, but it\T S1/pcr/m/n/10 '\T1/pcr/m/n/10 s rarely[] Underfull \vbox (badness 10000) has occurred while \output is active [1644] Underfull \vbox (badness 10000) has occurred while \output is active [1645] Underfull \hbox (badness 1292) in paragraph at lines 641--648 []\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 [1646] [1647] [1648] [1649] Underfull \vbox (badness 10000) has occurred while \output is active [1650] [1651] [1652] [1653] [1654] [1655] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1345--1345 []\T1/pcr/m/n/10 tk_select.list(choices, preselect = NULL, multiple = FALSE, t itle = NULL)[] [1656] [1657]) (./tools-pkg.tex [1658] Chapter 11. [1659] Underfull \hbox (badness 1308) in paragraph at lines 80--95 []\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 types Underfull \hbox (badness 1742) in paragraph at lines 80--95 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as a rou-tine to pro-duce a sort Underfull \hbox (badness 1360) in paragraph at lines 80--95 \T1/ptm/m/n/10 key to sort the en-tries. The for-mer must be named \T1/pcr/m/n/ 10 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1660] Overfull \hbox (9.78043pt too wide) in paragraph at lines 129--129 []\T1/pcr/m/n/9 bibstyle("unsorted", sortKeys = function(refs) seq_along(refs) , .init=TRUE)[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 145--145 []\T1/pcr/m/n/10 buildVignettes(package, dir, lib.loc = NULL, quiet = TRUE, cl ean = TRUE)[] [1661] Underfull \hbox (badness 2644) in paragraph at lines 203--208 \T1/ptm/m/n/10 (there can be more than one name for a Uni-code point). The data are in the file Underfull \hbox (badness 10000) in paragraph at lines 211--212 [][][]$\T1/pcr/m/n/10 http : / / partners . adobe . com / public / developer / en / opentype / glyphlist . [1662] [1663] [1664] Underfull \vbox (badness 10000) has occurred while \output is active [1665] [1666] Overfull \hbox (0.78088pt too wide) in paragraph at lines 470--470 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1667] [1668] [1669] [1670] Underfull \hbox (badness 10000) in paragraph at lines 722--725 []\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 [1671] Overfull \hbox (36.78088pt too wide) in paragraph at lines 793--793 []\T1/pcr/m/n/10 dependsOnPkgs(pkgs, dependencies = c("Depends", "Imports", "L inkingTo"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 795--795 [] \T1/pcr/m/n/10 installed = installed.packages(lib.loc, fields = "Enhances"))[] Underfull \hbox (badness 7981) in paragraph at lines 802--805 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 802--805 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", [1672] [1673] [1674] [1675] [1676] Underfull \hbox (badness 10000) in paragraph at lines 1073--1078 []\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 1073--1078 \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 1073--1078 \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 [1677] [1678] [1679] [1680] [1681] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1346--1346 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1682] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1385--1385 []\T1/pcr/m/n/10 parseLatex(text, filename = deparse(substitute(text)), verbos e = FALSE,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1386--1386 [] \T1/pcr/m/n/10 verbatim = c("verbatim", "verbatim*", "Sinput", "S output"))[] [1683] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1466--1466 []\T1/pcr/m/n/10 parse_Rd(file, srcfile = NULL, encoding = "unknown", verbose = FALSE,[] [1684] [1685] [1686] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1646--1646 [] \T1/pcr/m/n/10 stages = "render", outputEncoding = "ASCII", fragmen t = FALSE, ...,[] [1687] Underfull \hbox (badness 1072) in paragraph at lines 1670--1672 []\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 [1688] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1792--1792 []\T1/pcr/m/n/9 browseURL(Rd2HTML(Rd, outfile, package="tools", stages=c("inst all", "render")))[] [1689] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1795--1795 []\T1/pcr/m/n/9 file.show(Rd2txt(Rd, outfile, package="tools", stages=c("insta ll", "render")))[] [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2382--2382 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Underfull \hbox (badness 2932) in paragraph at lines 2415--2421 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3758) in paragraph at lines 2695--2700 []\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 2695--2700 \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 [1705] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2734--2734 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Underfull \hbox (badness 1742) in paragraph at lines 2746--2758 \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 , [1706] Underfull \hbox (badness 3623) in paragraph at lines 2803--2806 []\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 [1707] [1708] [1709]) (./utils-pkg.tex [1710] Chapter 12. [1711] [1712] [1713] [1714] [1715] [1716] Overfull \hbox (24.78088pt too wide) in paragraph at lines 352--352 []\T1/pcr/m/n/10 available.packages(contriburl = contrib.url(getOption("repos" ), type),[] Underfull \hbox (badness 4505) in paragraph at lines 391--398 \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 [1717] Underfull \hbox (badness 1275) in paragraph at lines 439--445 []\T1/ptm/m/n/10 A ma-trix with one row per pack-age, row names the pack-age na mes and col-umn names Underfull \hbox (badness 2057) in paragraph at lines 439--445 \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 , \T1/pcr/m/n/10 "LinkingTo"\T1/p tm/m/n/10 , Underfull \hbox (badness 1603) in paragraph at lines 471--476 \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 471--476 \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 [1718] Overfull \hbox (6.78088pt too wide) in paragraph at lines 523--523 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL,[] [1719] [1720] [1721] Overfull \hbox (15.18042pt too wide) in paragraph at lines 712--712 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1722] [1723] Overfull \hbox (24.78088pt too wide) in paragraph at lines 825--825 []\T1/pcr/m/n/10 browseURL(url, browser = getOption("browser"), encodeIfNeeded = FALSE)[] [1724] [1725] [1726] [1727] Underfull \hbox (badness 1859) in paragraph at lines 1081--1090 []\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- [1728] [1729] [1730] [1731] [1732] [1733] Underfull \hbox (badness 1082) in paragraph at lines 1426--1430 [][][]\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; [1734] [1735] [1736] [1737] [1738] [1739] [1740] Underfull \hbox (badness 1430) in paragraph at lines 1837--1840 []\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 \T1/pcr/m/n/10 package = Overfull \hbox (15.18042pt too wide) in paragraph at lines 1878--1878 []\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 '[] [1741] Underfull \hbox (badness 2452) in paragraph at lines 1951--1954 []\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 [1742] [1743] [1744] [1745] [1746] [1747] Underfull \hbox (badness 1072) in paragraph at lines 2317--2323 []\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 2317--2323 \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 [1748] Underfull \hbox (badness 1057) in paragraph at lines 2343--2357 []\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 2343--2357 \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 2343--2357 \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 2358--2364 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1749] Underfull \hbox (badness 4660) in paragraph at lines 2416--2419 \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 [1750] [1751] [1752] Underfull \hbox (badness 1565) in paragraph at lines 2614--2618 []\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 [1753] Underfull \hbox (badness 3758) in paragraph at lines 2727--2734 []\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat -ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask=TRUE) [1754] [1755] [1756] [1757] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2914--2914 []\T1/pcr/m/n/10 findLineNum(srcfile, line, nameonly = TRUE, envir = parent.fr ame(),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2917--2917 []\T1/pcr/m/n/10 setBreakpoint(srcfile, line, nameonly = TRUE, envir = parent. frame(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2918--2918 [] \T1/pcr/m/n/10 lastenv, verbose = TRUE, tracer, print = FALSE, ...)[] [1758] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3006--3006 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1759]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.3077 ...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.3077 ...mat Unordered and Ordered Lists}{format} [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 10000) in paragraph at lines 3787--3791 []\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 Underfull \hbox (badness 1502) in paragraph at lines 3831--3836 []\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 3831--3836 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1772] [1773] [1774] Underfull \hbox (badness 10000) in paragraph at lines 3985--3994 []\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 3985--3994 \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 Underfull \hbox (badness 2717) in paragraph at lines 3985--3994 [][]\T1/pcr/m/n/10 make.packages.html[][][](temp = FALSE)\T1/ptm/m/n/10 . For l o-cal op-er-a-tion, the HTTP server will [1775] [1776] Underfull \hbox (badness 1590) in paragraph at lines 4125--4129 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 setClass[][][]\T1/ptm/m/n/10 , should be i n-stalled us-ing lazy-loading: use the field \T1/pcr/m/n/10 LazyLoad \T1/ptm/m/ n/10 in the [1777] Underfull \hbox (badness 4660) in paragraph at lines 4212--4215 \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 [1778] Underfull \hbox (badness 10000) in paragraph at lines 4239--4243 []\T1/ptm/m/n/10 Possible val-ues are \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "mac.binary"\T1/ptm/m/n/10 , [1779] Underfull \hbox (badness 10000) in paragraph at lines 4346--4351 [][][]\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 , [1780] Underfull \hbox (badness 5133) in paragraph at lines 4407--4411 []\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 4419--4422 []\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 [1781] [1782] [1783] [1784] [1785] Overfull \hbox (368.28088pt too wide) in paragraph at lines 4689--4690 [][][]$\T1/pcr/m/n/10 http : / / n4 . nabble . com / R-[]help-[]question-[]How- []can-[]we-[]enable-[]useRs-[]to-[]contribute-[]corrections-[]to-[]help-[]files -[]faster-[]tp1572568p1572868 . Overfull \hbox (24.78088pt too wide) in paragraph at lines 4710--4710 []\T1/pcr/m/n/10 make.packages.html(lib.loc = .libPaths(), temp = TRUE, verbos e = TRUE)[] [1786] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4770--4770 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE)[] [1787] [1788] [1789] Underfull \hbox (badness 10000) in paragraph at lines 4942--4944 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] Underfull \hbox (badness 10000) in paragraph at lines 5513--5515 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like \T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 5518--5523 []\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, [1799] [1800] Underfull \hbox (badness 10000) in paragraph at lines 5624--5627 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed", "not [1801] [1802] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5740--5740 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5741--5741 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1803] [1804] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5883--5883 [] \T1/pcr/m/n/9 comment = "S original, http://statwww.epfl.ch/davison /BMA/library.html"),[] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] [1813] [1814] Underfull \hbox (badness 5203) in paragraph at lines 6498--6501 []\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 [1815] Underfull \hbox (badness 1163) in paragraph at lines 6603--6606 []\T1/ptm/m/n/10 the to-ken that was (or, is to be) com-pleted, as set by the l ast call to [1816] Underfull \hbox (badness 1072) in paragraph at lines 6715--6723 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [1817] [1818] [1819] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6894--6894 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header= TRUE, tra nspose=TRUE)[] [1820] [1821] [1822] [1823] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7149--7149 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] [1824] Underfull \hbox (badness 1077) in paragraph at lines 7220--7223 []\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 [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 7797--7801 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1835] [1836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7915--7915 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0)[] [1837] [1838] [1839] [1840] Underfull \hbox (badness 6725) in paragraph at lines 8156--8165 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 8156--8165 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 8156--8165 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 8156--8165 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8200--8200 []\T1/pcr/m/n/9 ## Search in R-devel archive and recent R-help (and store the query-string):[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8202--8202 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("S4", restrict = c("R-dev", "Rhelp10" , "Rhelp08"))[] [1842] Underfull \hbox (badness 10000) in paragraph at lines 8287--8289 [][][]$\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 / [1843] [1844] Underfull \hbox (badness 10000) in paragraph at lines 8406--8410 []\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 [1845] Underfull \hbox (badness 10000) in paragraph at lines 8437--8443 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1846] [1847] [1848] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8639--8639 []\T1/pcr/m/n/10 select.list(choices, preselect = NULL, multiple = FALSE, titl e = NULL,[] [1849] Underfull \hbox (badness 10000) in paragraph at lines 8728--8731 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form. In re-cent ve r- Underfull \hbox (badness 10000) in paragraph at lines 8728--8731 \T1/ptm/m/n/10 sions where sub-architectures are in use this is of the form [1850] Underfull \hbox (badness 10000) in paragraph at lines 8736--8739 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g Overfull \hbox (0.78088pt too wide) in paragraph at lines 8762--8762 []\T1/pcr/m/n/10 setRepositories(graphics = getOption("menu.graphics"), ind = NULL)[] Underfull \hbox (badness 10000) in paragraph at lines 8779--8783 \T1/ptm/m/n/10 That file can be edited for a site, or a user can have a per-son al copy in [1851] Underfull \hbox (badness 2158) in paragraph at lines 8798--8801 []\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 [1852] [1853] [1854] [1855] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9027--9027 [] \T1/pcr/m/n/10 format(x, trim=TRUE, drop0trailing=TRU E, ...))[] Underfull \hbox (badness 5970) in paragraph at lines 9055--9058 []\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 9055--9058 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [1856] [1857] [1858] [1859] Underfull \hbox (badness 5504) in paragraph at lines 9296--9299 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 SweaveSyntax \T1/ptm/m/n/10 or a char-ac-ter string with its Underfull \hbox (badness 3635) in paragraph at lines 9296--9299 \T1/ptm/m/n/10 name. The de-fault in-stal-la-tion pro-vides \T1/pcr/m/n/10 Swea veSyntaxNoweb \T1/ptm/m/n/10 and Underfull \hbox (badness 1178) in paragraph at lines 9322--9334 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, a num-ber of hook func- tions can be ex-e-cuted. If [1860] [1861] [1862] [1863] Underfull \hbox (badness 10000) in paragraph at lines 9535--9538 [][][]$\T1/pcr/m/n/10 http : / / en . wikipedia . org / wiki / Tar _ (file _ fo rmat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / www . Underfull \hbox (badness 10000) in paragraph at lines 9535--9538 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 009695399 / utilities / pax . htm l # tag _ 04 _ 100 _ [1864] [1865] [1866] [1867] [1868] [1869] [1870] Underfull \hbox (badness 4660) in paragraph at lines 9973--9976 \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 (24.87935pt too wide) in paragraph at lines 9984--9988 []\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 . [1871] Underfull \hbox (badness 3557) in paragraph at lines 9990--9992 []\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 9993--9995 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 10023--10028 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 10000) in paragraph at lines 10044--10049 []\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 10052--10055 [][][]\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 , [1872] [1873] Underfull \hbox (badness 10000) in paragraph at lines 10140--10145 []\T1/ptm/m/n/10 Characters in a URL other than the En-glish al-phanu-meric cha r-ac-ters and [1874] [1875] [1876] [1877] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10357--10357 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ",[] Underfull \hbox (badness 1454) in paragraph at lines 10383--10387 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 10403--10406 []\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 [1878] [1879] Underfull \hbox (badness 3872) in paragraph at lines 10532--10534 []\T1/ptm/m/n/10 character string: the method to be used, an empty string in-di -cates [1880] [1881]) [1882] (./refman.ind [1883] [1884] [1885] [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] Overfull \hbox (32.8567pt too wide) in paragraph at lines 2538--2540 []\T1/pcr/m/n/10 aspell_write_personal_dictionary_file [1906] [1907] [1908] [1909] [1910] [1911] Overfull \hbox (20.8567pt too wide) in paragraph at lines 3358--3360 []\T1/pcr/m/n/10 derivedDefaultMethodWithTrace-class [1912] [1913] [1914] [1915] [1916] [1917] [1918] Overfull \hbox (20.8567pt too wide) in paragraph at lines 4268--4270 []\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class [1919] Underfull \vbox (badness 2035) has occurred while \output is active [1920] [1921] [1922] [1923] [1924] [1925] [1926] Overfull \hbox (8.8567pt too wide) in paragraph at lines 5400--5402 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (26.8567pt too wide) in paragraph at lines 5486--5488 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method [1927] Underfull \vbox (badness 1642) has occurred while \output is active [1928] [1929] [1930] Overfull \hbox (4.01662pt too wide) in paragraph at lines 6068--6070 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [1931] Overfull \hbox (4.01662pt too wide) in paragraph at lines 6112--6114 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [1932] [1933] [1934] Underfull \vbox (badness 1226) has occurred while \output is active [1935] [1936] [1937] Overfull \hbox (26.8567pt too wide) in paragraph at lines 7078--7080 []\T1/pcr/m/n/10 show,genericFunctionWithTrace-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7082--7084 []\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method [1938] Overfull \hbox (20.8567pt too wide) in paragraph at lines 7086--7088 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7092--7094 []\T1/pcr/m/n/10 show,refClassRepresentation-method [1939] [1940] Underfull \vbox (badness 1019) has occurred while \output is active [1941] [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949]) (./refman.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re placed by a fixed one pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showMlist} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.standardGeneric} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Surv} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}< /usr/share/texmf-texlive/fonts/type1/urw/courier/ucrb8a.pfb> Output written on refman.pdf (1978 pages, 5000134 bytes). Transcript written on refman.log. /bin/bash: line 0: test: too many arguments TEXINPUTS=".:$TEXINPUTS" /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. Chapter 2 [1] [2] [3] [4] [5] Underfull \hbox (badness 3158) in paragraph at lines 571--584 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of [6] Underfull \hbox (badness 10000) in paragraph at lines 681--684 []@textrm John M. Cham-bers (2008), ``Soft-ware for Data Anal-y-sis: Pro- Underfull \hbox (badness 8132) in paragraph at lines 681--684 @textrm gram-ming with R''. Springer, New York, ISBN 978-0-387-75935-7, Underfull \hbox (badness 10000) in paragraph at lines 689--692 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 689--692 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 2846) in paragraph at lines 708--711 []@textrm William N. Ven-ables and Brian D. Rip-ley (2002), ``Mod-ern Ap-plied Underfull \hbox (badness 10000) in paragraph at lines 708--711 @textrm Statis-tics with S'' (4th edi-tion). Springer, ISBN 0-387-95457-0, [7] [8] [9] [10] Chapter 3 [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (5.53629pt too wide) in paragraph at lines 1618--1621 []@textrm See also [][]@texttt http://en.wikipedia.org/wiki/R_programming_langu age#Commercialized_ Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] Underfull \hbox (badness 4217) in paragraph at lines 3303--3314 @texttt doku.php?id=tips:graphics-base:2yaxes[][][] @textrm for more in-for-ma- tion, in-clud-ing strong Chapter 8 [41] Chapter 9 [42] [43] [44] Chapter 10 [45] [46] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (48 pages, 398601 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4] [5] Underfull \hbox (badness 3158) in paragraph at lines 571--584 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of [6] Underfull \hbox (badness 10000) in paragraph at lines 681--684 []@textrm John M. Cham-bers (2008), ``Soft-ware for Data Anal-y-sis: Pro- Underfull \hbox (badness 8132) in paragraph at lines 681--684 @textrm gram-ming with R''. Springer, New York, ISBN 978-0-387-75935-7, Underfull \hbox (badness 10000) in paragraph at lines 689--692 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 689--692 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 2846) in paragraph at lines 708--711 []@textrm William N. Ven-ables and Brian D. Rip-ley (2002), ``Mod-ern Ap-plied Underfull \hbox (badness 10000) in paragraph at lines 708--711 @textrm Statis-tics with S'' (4th edi-tion). Springer, ISBN 0-387-95457-0, [7] [8] [9] [10] Chapter 3 [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (5.53629pt too wide) in paragraph at lines 1618--1621 []@textrm See also [][]@texttt http://en.wikipedia.org/wiki/R_programming_langu age#Commercialized_ Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] Underfull \hbox (badness 4217) in paragraph at lines 3303--3314 @texttt doku.php?id=tips:graphics-base:2yaxes[][][] @textrm for more in-for-ma- tion, in-clud-ing strong Chapter 8 [41] Chapter 9 [42] [43] [44] Chapter 10 [45] [46] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (50 pages, 448696 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 Chapter 2 [1] [2] [3] [4] [5] Underfull \hbox (badness 3158) in paragraph at lines 571--584 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of [6] Underfull \hbox (badness 10000) in paragraph at lines 681--684 []@textrm John M. Cham-bers (2008), ``Soft-ware for Data Anal-y-sis: Pro- Underfull \hbox (badness 8132) in paragraph at lines 681--684 @textrm gram-ming with R''. Springer, New York, ISBN 978-0-387-75935-7, Underfull \hbox (badness 10000) in paragraph at lines 689--692 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 689--692 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 2846) in paragraph at lines 708--711 []@textrm William N. Ven-ables and Brian D. Rip-ley (2002), ``Mod-ern Ap-plied Underfull \hbox (badness 10000) in paragraph at lines 708--711 @textrm Statis-tics with S'' (4th edi-tion). Springer, ISBN 0-387-95457-0, [7] [8] [9] [10] Chapter 3 [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (5.53629pt too wide) in paragraph at lines 1618--1621 []@textrm See also [][]@texttt http://en.wikipedia.org/wiki/R_programming_langu age#Commercialized_ Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] Underfull \hbox (badness 4217) in paragraph at lines 3303--3314 @texttt doku.php?id=tips:graphics-base:2yaxes[][][] @textrm for more in-for-ma- tion, in-clud-ing strong Chapter 8 [41] Chapter 9 [42] [43] [44] Chapter 10 [45] [46] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (50 pages, 448696 bytes). Transcript written on R-FAQ.log. /bin/bash: line 0: test: too many arguments TEXINPUTS=".:$TEXINPUTS" /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 [1] Overfull \hbox (5.09695pt too wide) in paragraph at lines 187--192 @textsl x.y.0 @textrm re-lease are avail-able from `@texttt https://svn.r-proje ct.org/R/branches/R-@textttsl x@texttt -@textttsl y@texttt -branch/[]@textrm '[ ] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] Underfull \hbox (badness 2103) in paragraph at lines 589--596 @textrm head-ers are not in-stalled into a sub-di-rec-tory you prob-a-bly want some-thing like [6] [7] Underfull \hbox (badness 2762) in paragraph at lines 736--746 @textrm be the last in-stalled, but architecture-specific ver-sions will be ava il-able in e.g. Underfull \hbox (badness 3965) in paragraph at lines 756--768 @textrm the ap-pro-pri-ate `@texttt bin[]@textrm '[] di-rec-tory, `@textttsl R_ HOME@texttt /bin/i386[]@textrm '[] or `@textttsl R_HOME@texttt /bin/x64[]@textr m '[]. For [8] [9] Chapter 3 [10] Underfull \hbox (badness 2970) in paragraph at lines 990--994 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [11] Underfull \hbox (badness 10000) in paragraph at lines 1023--1030 []@textrm You need @texttt libpng[]@textrm , @texttt jpeg[] @textrm and @textt t libtiff[] @textrm sources (avail-able, e.g., from Overfull \hbox (7.19868pt too wide) in paragraph at lines 1023--1030 [][]@texttt http://www.libpng.org/[][][]@textrm , [][]@texttt http://www.ijg.o rg[][][] @textrm and [][]@texttt ftp://ftp.remotesensing.org/ [12] Underfull \hbox (badness 10000) in paragraph at lines 1118--1122 []@textrm Running @texttt make[] @textrm in `@textttsl R_HOME@texttt /src/gnuwi n32/bitmap[]@textrm '[] or @texttt make bitmapdll[] @textrm in Underfull \hbox (badness 10000) in paragraph at lines 1118--1122 @textrm `@textttsl R_HOME@texttt /src/gnuwin32[]@textrm '[] should build `@text tt Rbitmap.dll[]@textrm '[] and in-stall it un-der [13] [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1444--1448 []@textrm For com-pat-i-bil-ity with the @reducedrm CRAN @textrm dis-tri-bu-tio n you may need to spec-ify Chapter 5 [17] Chapter 6 [18] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1531--1531 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1753--1755 []@textrm Some notes on port-ing pack-ages to 64-bit Win-dows can be found at [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1832--1836 []@textrm where there is a non-empty `@texttt configure.win[]@textrm '[] scrip t, or a file Underfull \hbox (badness 10000) in paragraph at lines 1832--1836 @textrm `@texttt src/Makefile.win[]@textrm '[] (with some ex-cep-tions where t he pack-age is Underfull \hbox (badness 8132) in paragraph at lines 1832--1836 @textrm known to have an architecture-independent `@texttt configure.win[]@tex trm '[], or if [23] Overfull \hbox (51.96864pt too wide) in paragraph at lines 1990--1990 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkgname@texttt .log @textttsl pkg- [24] Overfull \hbox (50.70126pt too wide) in paragraph at lines 2010--2010 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkgname@texttt .log @textttsl pkg- Overfull \hbox (44.95258pt too wide) in paragraph at lines 2011--2011 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkgname@texttt .log @textttsl pkg- Chapter 7 [25] Underfull \hbox (badness 2393) in paragraph at lines 2081--2088 @texttt en.wikipedia.org/wiki/ISO_3166[][][]@textrm ). Some-times the com-bi-n a-tion of lan-guage Underfull \hbox (badness 2050) in paragraph at lines 2114--2120 []@textrm Modern Linux uses the XPG lo-cale spec-i-fi-ca-tions which have the f orm `@texttt en_GB[]@textrm '[], Underfull \hbox (badness 8170) in paragraph at lines 2124--2128 @textrm found at [][]@texttt http://msdn.microsoft.com/library/default.asp?url= /library/en-us/ [26] [27] Chapter 8 [28] Chapter 9 [29] [30] [31] [32] Appendix A [33] [34] [35] Underfull \hbox (badness 3098) in paragraph at lines 2719--2723 []@textrm A few code de-vel-op-ers may want Perl ver-sion 5.8.0 or later, avail -able via Underfull \hbox (badness 2951) in paragraph at lines 2728--2734 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and also @texttt embedFonts()[] @textrm use ghost-script [36] Underfull \hbox (badness 2302) in paragraph at lines 2777--2783 @textrm JVM, which are stored in en-vi-ron-ment vari-able []@texttt R_JAVA_LD_L IBRARY_PATH[] @textrm in file [37] [38] Underfull \hbox (badness 2197) in paragraph at lines 2989--2994 []@textrm svn up For In-tel pro-ces-sors un-der Linux, there is In-tel's Math K er-nel Li-brary Overfull \hbox (43.6852pt too wide) in paragraph at lines 3012--3012 []@texttt MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_sequential -lmkl_lapack - lmkl_core"[] [39] [40] Overfull \hbox (27.70651pt too wide) in paragraph at lines 3111--3111 []@texttt ln -s /opt/acml4.4.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] Appendix B [41] [42] [43] Underfull \hbox (badness 3428) in paragraph at lines 3363--3376 @textrm `@texttt -L/usr/local/lib64[]@textrm '[] on most 64-bit Linux OSes) and `@texttt -I/usr/local/include[]@textrm '[] Underfull \hbox (badness 10000) in paragraph at lines 3377--3388 @textrm `@texttt '-Bdirect,--hash-style=both,-Wl,-O1'[]@textrm '[] is rec-om-me nded at [][]@texttt http://lwn.net/ [44] [45] Underfull \hbox (badness 3701) in paragraph at lines 3601--3605 []@textrm To com-pile a pro-fil-ing ver-sion of R, one might for ex-am-ple want to use [46] Appendix C [47] [48] Underfull \hbox (badness 3029) in paragraph at lines 3771--3775 @textrm is ap-pro-pri-ate since most (but not all) soft-ware in-stalls its 64-b it li-braries in [49] [50] [51] [52] Overfull \hbox (2.58777pt too wide) in paragraph at lines 4051--4054 []@textrm A large se-lec-tion of Open Source soft-ware can be in-stalled from [ ][]@texttt http://www.opencsw.org[][][] [53] Overfull \hbox (53.87451pt too wide) in paragraph at lines 4187--4187 [][][][][]@smalltt http://www.sun.com/download/index.jsp?cat=Application%20Deve lopment&tab=3&subcat=Development%20Tools[][][]| [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4291--4317 @textrm ([][]@texttt http://www-03.ibm.com/systems/power/software/aix/linux/[][ ][]@textrm ) and [][]@texttt http://www. Underfull \hbox (badness 3735) in paragraph at lines 4291--4317 @textrm ([][]@texttt http://www.icu-project.org/download/[][][]@textrm ), which of-fers pre-compiled bi-na-ries for [56] [57] Underfull \hbox (badness 2486) in paragraph at lines 4446--4454 []@textrm It seems that @texttt gcc[] @textrm 3.4.x and later on `@texttt ix86[ ]@textrm '[] Linux de-feat at-tempts by the Appendix D [58] [59] Underfull \hbox (badness 2119) in paragraph at lines 4644--4647 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [60] Underfull \hbox (badness 5203) in paragraph at lines 4713--4723 []@textrm The toolchain we use is tech-ni-cally a cross-compiler: the tools run un- Underfull \hbox (badness 3128) in paragraph at lines 4713--4723 @textrm der 32-bit Win-dows but pro-duce code to run un-der 64-bit Win-dows.$[] $ This Underfull \hbox (badness 10000) in paragraph at lines 4713--4723 @textrm is based on files from [][]@texttt http://sourceforge.net/projects/ming w-w64/files/ Underfull \hbox (badness 10000) in paragraph at lines 4713--4723 @texttt Toolchains%20targetting%20Win64/Automated%20Builds/[][][] @textrm and h as a name like [61] (Function and variable index) [62] (Concept index) [63] (Environment variable index) [64] [65] ) (see the transcript file for additional information) Output written on R-admin.pdf (68 pages, 452069 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-admin.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-admin.toc [-1] [-2]) [-3] (./R-admin.toc) (./R-admin.toc) Chapter 1 [1] Overfull \hbox (5.09695pt too wide) in paragraph at lines 187--192 @textsl x.y.0 @textrm re-lease are avail-able from `@texttt https://svn.r-proje ct.org/R/branches/R-@textttsl x@texttt -@textttsl y@texttt -branch/[]@textrm '[ ] Chapter 2 [2] [3] [4] [5] Underfull \hbox (badness 2103) in paragraph at lines 589--596 @textrm head-ers are not in-stalled into a sub-di-rec-tory you prob-a-bly want some-thing like [6] [7] Underfull \hbox (badness 2762) in paragraph at lines 736--746 @textrm be the last in-stalled, but architecture-specific ver-sions will be ava il-able in e.g. Underfull \hbox (badness 3965) in paragraph at lines 756--768 @textrm the ap-pro-pri-ate `@texttt bin[]@textrm '[] di-rec-tory, `@textttsl R_ HOME@texttt /bin/i386[]@textrm '[] or `@textttsl R_HOME@texttt /bin/x64[]@textr m '[]. For [8] [9] Chapter 3 [10] Underfull \hbox (badness 2970) in paragraph at lines 990--994 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [11] Underfull \hbox (badness 10000) in paragraph at lines 1023--1030 []@textrm You need @texttt libpng[]@textrm , @texttt jpeg[] @textrm and @textt t libtiff[] @textrm sources (avail-able, e.g., from Overfull \hbox (7.19868pt too wide) in paragraph at lines 1023--1030 [][]@texttt http://www.libpng.org/[][][]@textrm , [][]@texttt http://www.ijg.o rg[][][] @textrm and [][]@texttt ftp://ftp.remotesensing.org/ [12] Underfull \hbox (badness 10000) in paragraph at lines 1118--1122 []@textrm Running @texttt make[] @textrm in `@textttsl R_HOME@texttt /src/gnuwi n32/bitmap[]@textrm '[] or @texttt make bitmapdll[] @textrm in Underfull \hbox (badness 10000) in paragraph at lines 1118--1122 @textrm `@textttsl R_HOME@texttt /src/gnuwin32[]@textrm '[] should build `@text tt Rbitmap.dll[]@textrm '[] and in-stall it un-der [13] [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1444--1448 []@textrm For com-pat-i-bil-ity with the @reducedrm CRAN @textrm dis-tri-bu-tio n you may need to spec-ify Chapter 5 [17] Chapter 6 [18] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1531--1531 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1753--1755 []@textrm Some notes on port-ing pack-ages to 64-bit Win-dows can be found at [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1832--1836 []@textrm where there is a non-empty `@texttt configure.win[]@textrm '[] scrip t, or a file Underfull \hbox (badness 10000) in paragraph at lines 1832--1836 @textrm `@texttt src/Makefile.win[]@textrm '[] (with some ex-cep-tions where t he pack-age is Underfull \hbox (badness 8132) in paragraph at lines 1832--1836 @textrm known to have an architecture-independent `@texttt configure.win[]@tex trm '[], or if [23] Overfull \hbox (51.96864pt too wide) in paragraph at lines 1990--1990 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkgname@texttt .log @textttsl pkg- [24] Overfull \hbox (50.70126pt too wide) in paragraph at lines 2010--2010 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkgname@texttt .log @textttsl pkg- Overfull \hbox (44.95258pt too wide) in paragraph at lines 2011--2011 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkgname@texttt .log @textttsl pkg- Chapter 7 [25] Underfull \hbox (badness 2393) in paragraph at lines 2081--2088 @texttt en.wikipedia.org/wiki/ISO_3166[][][]@textrm ). Some-times the com-bi-n a-tion of lan-guage Underfull \hbox (badness 2050) in paragraph at lines 2114--2120 []@textrm Modern Linux uses the XPG lo-cale spec-i-fi-ca-tions which have the f orm `@texttt en_GB[]@textrm '[], Underfull \hbox (badness 8170) in paragraph at lines 2124--2128 @textrm found at [][]@texttt http://msdn.microsoft.com/library/default.asp?url= /library/en-us/ [26] [27] Chapter 8 [28] Chapter 9 [29] [30] [31] [32] Appendix A [33] [34] [35] Underfull \hbox (badness 3098) in paragraph at lines 2719--2723 []@textrm A few code de-vel-op-ers may want Perl ver-sion 5.8.0 or later, avail -able via Underfull \hbox (badness 2951) in paragraph at lines 2728--2734 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and also @texttt embedFonts()[] @textrm use ghost-script [36] Underfull \hbox (badness 2302) in paragraph at lines 2777--2783 @textrm JVM, which are stored in en-vi-ron-ment vari-able []@texttt R_JAVA_LD_L IBRARY_PATH[] @textrm in file [37] [38] Underfull \hbox (badness 2197) in paragraph at lines 2989--2994 []@textrm svn up For In-tel pro-ces-sors un-der Linux, there is In-tel's Math K er-nel Li-brary Overfull \hbox (43.6852pt too wide) in paragraph at lines 3012--3012 []@texttt MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_sequential -lmkl_lapack - lmkl_core"[] [39] [40] Overfull \hbox (27.70651pt too wide) in paragraph at lines 3111--3111 []@texttt ln -s /opt/acml4.4.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] Appendix B [41] [42] [43] Underfull \hbox (badness 3428) in paragraph at lines 3363--3376 @textrm `@texttt -L/usr/local/lib64[]@textrm '[] on most 64-bit Linux OSes) and `@texttt -I/usr/local/include[]@textrm '[] Underfull \hbox (badness 10000) in paragraph at lines 3377--3388 @textrm `@texttt '-Bdirect,--hash-style=both,-Wl,-O1'[]@textrm '[] is rec-om-me nded at [][]@texttt http://lwn.net/ [44] [45] Underfull \hbox (badness 3701) in paragraph at lines 3601--3605 []@textrm To com-pile a pro-fil-ing ver-sion of R, one might for ex-am-ple want to use [46] Appendix C [47] [48] Underfull \hbox (badness 3029) in paragraph at lines 3771--3775 @textrm is ap-pro-pri-ate since most (but not all) soft-ware in-stalls its 64-b it li-braries in [49] [50] [51] [52] Overfull \hbox (2.58777pt too wide) in paragraph at lines 4051--4054 []@textrm A large se-lec-tion of Open Source soft-ware can be in-stalled from [ ][]@texttt http://www.opencsw.org[][][] [53] Overfull \hbox (53.87451pt too wide) in paragraph at lines 4187--4187 [][][][][]@smalltt http://www.sun.com/download/index.jsp?cat=Application%20Deve lopment&tab=3&subcat=Development%20Tools[][][]| [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4291--4317 @textrm ([][]@texttt http://www-03.ibm.com/systems/power/software/aix/linux/[][ ][]@textrm ) and [][]@texttt http://www. Underfull \hbox (badness 3735) in paragraph at lines 4291--4317 @textrm ([][]@texttt http://www.icu-project.org/download/[][][]@textrm ), which of-fers pre-compiled bi-na-ries for [56] [57] Underfull \hbox (badness 2486) in paragraph at lines 4446--4454 []@textrm It seems that @texttt gcc[] @textrm 3.4.x and later on `@texttt ix86[ ]@textrm '[] Linux de-feat at-tempts by the Appendix D [58] [59] Underfull \hbox (badness 2119) in paragraph at lines 4644--4647 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [60] Underfull \hbox (badness 5203) in paragraph at lines 4713--4723 []@textrm The toolchain we use is tech-ni-cally a cross-compiler: the tools run un- Underfull \hbox (badness 3128) in paragraph at lines 4713--4723 @textrm der 32-bit Win-dows but pro-duce code to run un-der 64-bit Win-dows.$[] $ This Underfull \hbox (badness 10000) in paragraph at lines 4713--4723 @textrm is based on files from [][]@texttt http://sourceforge.net/projects/ming w-w64/files/ Underfull \hbox (badness 10000) in paragraph at lines 4713--4723 @texttt Toolchains%20targetting%20Win64/Automated%20Builds/[][][] @textrm and h as a name like [61] (Function and variable index) [62] (./R-admin.vrs) (Concept index) [63] (./R-admin.cps) (Environment variable index) [64] (./R-admin.ens) [65] ) (see the transcript file for additional information) Output written on R-admin.pdf (70 pages, 547066 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-admin.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-admin.toc [-1] [-2]) [-3] (./R-admin.toc) (./R-admin.toc) Chapter 1 [1] Overfull \hbox (5.09695pt too wide) in paragraph at lines 187--192 @textsl x.y.0 @textrm re-lease are avail-able from `@texttt https://svn.r-proje ct.org/R/branches/R-@textttsl x@texttt -@textttsl y@texttt -branch/[]@textrm '[ ] Chapter 2 [2] [3] [4] [5] Underfull \hbox (badness 2103) in paragraph at lines 589--596 @textrm head-ers are not in-stalled into a sub-di-rec-tory you prob-a-bly want some-thing like [6] [7] Underfull \hbox (badness 2762) in paragraph at lines 736--746 @textrm be the last in-stalled, but architecture-specific ver-sions will be ava il-able in e.g. Underfull \hbox (badness 3965) in paragraph at lines 756--768 @textrm the ap-pro-pri-ate `@texttt bin[]@textrm '[] di-rec-tory, `@textttsl R_ HOME@texttt /bin/i386[]@textrm '[] or `@textttsl R_HOME@texttt /bin/x64[]@textr m '[]. For [8] [9] Chapter 3 [10] Underfull \hbox (badness 2970) in paragraph at lines 990--994 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [11] Underfull \hbox (badness 10000) in paragraph at lines 1023--1030 []@textrm You need @texttt libpng[]@textrm , @texttt jpeg[] @textrm and @textt t libtiff[] @textrm sources (avail-able, e.g., from Overfull \hbox (7.19868pt too wide) in paragraph at lines 1023--1030 [][]@texttt http://www.libpng.org/[][][]@textrm , [][]@texttt http://www.ijg.o rg[][][] @textrm and [][]@texttt ftp://ftp.remotesensing.org/ [12] Underfull \hbox (badness 10000) in paragraph at lines 1118--1122 []@textrm Running @texttt make[] @textrm in `@textttsl R_HOME@texttt /src/gnuwi n32/bitmap[]@textrm '[] or @texttt make bitmapdll[] @textrm in Underfull \hbox (badness 10000) in paragraph at lines 1118--1122 @textrm `@textttsl R_HOME@texttt /src/gnuwin32[]@textrm '[] should build `@text tt Rbitmap.dll[]@textrm '[] and in-stall it un-der [13] [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1444--1448 []@textrm For com-pat-i-bil-ity with the @reducedrm CRAN @textrm dis-tri-bu-tio n you may need to spec-ify Chapter 5 [17] Chapter 6 [18] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1531--1531 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1753--1755 []@textrm Some notes on port-ing pack-ages to 64-bit Win-dows can be found at [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1832--1836 []@textrm where there is a non-empty `@texttt configure.win[]@textrm '[] scrip t, or a file Underfull \hbox (badness 10000) in paragraph at lines 1832--1836 @textrm `@texttt src/Makefile.win[]@textrm '[] (with some ex-cep-tions where t he pack-age is Underfull \hbox (badness 8132) in paragraph at lines 1832--1836 @textrm known to have an architecture-independent `@texttt configure.win[]@tex trm '[], or if [23] Overfull \hbox (51.96864pt too wide) in paragraph at lines 1990--1990 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkgname@texttt .log @textttsl pkg- [24] Overfull \hbox (50.70126pt too wide) in paragraph at lines 2010--2010 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkgname@texttt .log @textttsl pkg- Overfull \hbox (44.95258pt too wide) in paragraph at lines 2011--2011 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkgname@texttt .log @textttsl pkg- Chapter 7 [25] Underfull \hbox (badness 2393) in paragraph at lines 2081--2088 @texttt en.wikipedia.org/wiki/ISO_3166[][][]@textrm ). Some-times the com-bi-n a-tion of lan-guage Underfull \hbox (badness 2050) in paragraph at lines 2114--2120 []@textrm Modern Linux uses the XPG lo-cale spec-i-fi-ca-tions which have the f orm `@texttt en_GB[]@textrm '[], Underfull \hbox (badness 8170) in paragraph at lines 2124--2128 @textrm found at [][]@texttt http://msdn.microsoft.com/library/default.asp?url= /library/en-us/ [26] [27] Chapter 8 [28] Chapter 9 [29] [30] [31] [32] Appendix A [33] [34] [35] Underfull \hbox (badness 3098) in paragraph at lines 2719--2723 []@textrm A few code de-vel-op-ers may want Perl ver-sion 5.8.0 or later, avail -able via Underfull \hbox (badness 2951) in paragraph at lines 2728--2734 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and also @texttt embedFonts()[] @textrm use ghost-script [36] Underfull \hbox (badness 2302) in paragraph at lines 2777--2783 @textrm JVM, which are stored in en-vi-ron-ment vari-able []@texttt R_JAVA_LD_L IBRARY_PATH[] @textrm in file [37] [38] Underfull \hbox (badness 2197) in paragraph at lines 2989--2994 []@textrm svn up For In-tel pro-ces-sors un-der Linux, there is In-tel's Math K er-nel Li-brary Overfull \hbox (43.6852pt too wide) in paragraph at lines 3012--3012 []@texttt MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_sequential -lmkl_lapack - lmkl_core"[] [39] [40] Overfull \hbox (27.70651pt too wide) in paragraph at lines 3111--3111 []@texttt ln -s /opt/acml4.4.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] Appendix B [41] [42] [43] Underfull \hbox (badness 3428) in paragraph at lines 3363--3376 @textrm `@texttt -L/usr/local/lib64[]@textrm '[] on most 64-bit Linux OSes) and `@texttt -I/usr/local/include[]@textrm '[] Underfull \hbox (badness 10000) in paragraph at lines 3377--3388 @textrm `@texttt '-Bdirect,--hash-style=both,-Wl,-O1'[]@textrm '[] is rec-om-me nded at [][]@texttt http://lwn.net/ [44] [45] Underfull \hbox (badness 3701) in paragraph at lines 3601--3605 []@textrm To com-pile a pro-fil-ing ver-sion of R, one might for ex-am-ple want to use [46] Appendix C [47] [48] Underfull \hbox (badness 3029) in paragraph at lines 3771--3775 @textrm is ap-pro-pri-ate since most (but not all) soft-ware in-stalls its 64-b it li-braries in [49] [50] [51] [52] Overfull \hbox (2.58777pt too wide) in paragraph at lines 4051--4054 []@textrm A large se-lec-tion of Open Source soft-ware can be in-stalled from [ ][]@texttt http://www.opencsw.org[][][] [53] Overfull \hbox (53.87451pt too wide) in paragraph at lines 4187--4187 [][][][][]@smalltt http://www.sun.com/download/index.jsp?cat=Application%20Deve lopment&tab=3&subcat=Development%20Tools[][][]| [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4291--4317 @textrm ([][]@texttt http://www-03.ibm.com/systems/power/software/aix/linux/[][ ][]@textrm ) and [][]@texttt http://www. Underfull \hbox (badness 3735) in paragraph at lines 4291--4317 @textrm ([][]@texttt http://www.icu-project.org/download/[][][]@textrm ), which of-fers pre-compiled bi-na-ries for [56] [57] Underfull \hbox (badness 2486) in paragraph at lines 4446--4454 []@textrm It seems that @texttt gcc[] @textrm 3.4.x and later on `@texttt ix86[ ]@textrm '[] Linux de-feat at-tempts by the Appendix D [58] [59] Underfull \hbox (badness 2119) in paragraph at lines 4644--4647 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [60] Underfull \hbox (badness 5203) in paragraph at lines 4713--4723 []@textrm The toolchain we use is tech-ni-cally a cross-compiler: the tools run un- Underfull \hbox (badness 3128) in paragraph at lines 4713--4723 @textrm der 32-bit Win-dows but pro-duce code to run un-der 64-bit Win-dows.$[] $ This Underfull \hbox (badness 10000) in paragraph at lines 4713--4723 @textrm is based on files from [][]@texttt http://sourceforge.net/projects/ming w-w64/files/ Underfull \hbox (badness 10000) in paragraph at lines 4713--4723 @texttt Toolchains%20targetting%20Win64/Automated%20Builds/[][][] @textrm and h as a name like [61] (Function and variable index) [62] (./R-admin.vrs) (Concept index) [63] (./R-admin.cps) (Environment variable index) [64] (./R-admin.ens) [65] ) (see the transcript file for additional information) Output written on R-admin.pdf (70 pages, 547066 bytes). Transcript written on R-admin.log. /bin/bash: line 0: test: too many arguments TEXINPUTS=".:$TEXINPUTS" /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Overfull \hbox (8.53186pt too wide) in paragraph at lines 96--96 @textbf dataframes2xls| Overfull \hbox (2.70708pt too wide) in paragraph at lines 107--107 @textbf RPostgreSQL| Overfull \hbox (2.49414pt too wide) in paragraph at lines 113--113 @textbf xlsReadWrite| Chapter 1 [1] Cross reference values unknown; you must run TeX again. [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14] [15] [16] [17] Overfull \hbox (9.3377pt too wide) in paragraph at lines 1359--1363 []@textrm On Mac OS X the Ac-tual Tech-nolo-gies ([][]@texttt http://www.actual technologies.com/product_ [18] [19] Chapter 5 [20] Underfull \hbox (badness 10000) in paragraph at lines 1619--1624 @textrm HDF5 (Hi-er-ar-chi-cal Data For-mat, see [][]@texttt http://hdf.ncsa.ui uc.edu/HDF5/[][][]@textrm ) Underfull \hbox (badness 10000) in paragraph at lines 1619--1624 @textrm and to UCAR's netCDF data files (net-work Com-mon Data Form, see Chapter 6 [21] [22] [23] [24] [25] Chapter 7 [26] Underfull \hbox (badness 2538) in paragraph at lines 2104--2111 @textrm ap-pli-ca-tions to call meth-ods, or op-er-a-tions, in server ob-jects run-ning in other [27] Chapter 8 [28] Underfull \hbox (badness 4739) in paragraph at lines 2159--2168 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such Underfull \hbox (badness 10000) in paragraph at lines 2159--2168 @textrm am-ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[] [][]@textrm ) and OpenOf-fice Appendix A [29] (Function and variable index) [30] (Concept index) [31] [32] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 286139 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-data.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) Overfull \hbox (8.53186pt too wide) in paragraph at lines 96--96 @textbf dataframes2xls| Overfull \hbox (2.70708pt too wide) in paragraph at lines 107--107 @textbf RPostgreSQL| Overfull \hbox (2.49414pt too wide) in paragraph at lines 113--113 @textbf xlsReadWrite| Chapter 1 [1] [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14] [15] [16] [17] Overfull \hbox (9.3377pt too wide) in paragraph at lines 1359--1363 []@textrm On Mac OS X the Ac-tual Tech-nolo-gies ([][]@texttt http://www.actual technologies.com/product_ [18] [19] Chapter 5 [20] Underfull \hbox (badness 10000) in paragraph at lines 1619--1624 @textrm HDF5 (Hi-er-ar-chi-cal Data For-mat, see [][]@texttt http://hdf.ncsa.ui uc.edu/HDF5/[][][]@textrm ) Underfull \hbox (badness 10000) in paragraph at lines 1619--1624 @textrm and to UCAR's netCDF data files (net-work Com-mon Data Form, see Chapter 6 [21] [22] [23] [24] [25] Chapter 7 [26] Underfull \hbox (badness 2538) in paragraph at lines 2104--2111 @textrm ap-pli-ca-tions to call meth-ods, or op-er-a-tions, in server ob-jects run-ning in other [27] Chapter 8 [28] Underfull \hbox (badness 4739) in paragraph at lines 2159--2168 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such Underfull \hbox (badness 10000) in paragraph at lines 2159--2168 @textrm am-ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[] [][]@textrm ) and OpenOf-fice Appendix A [29] (Function and variable index) [30] (./R-data.vrs [31]) (Concept index) [32] (./R-data.cps) [33] ) (see the transcript file for additional information) Output written on R-data.pdf (37 pages, 365005 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-data.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) Overfull \hbox (8.53186pt too wide) in paragraph at lines 96--96 @textbf dataframes2xls| Overfull \hbox (2.70708pt too wide) in paragraph at lines 107--107 @textbf RPostgreSQL| Overfull \hbox (2.49414pt too wide) in paragraph at lines 113--113 @textbf xlsReadWrite| Chapter 1 [1] [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14] [15] [16] [17] Overfull \hbox (9.3377pt too wide) in paragraph at lines 1359--1363 []@textrm On Mac OS X the Ac-tual Tech-nolo-gies ([][]@texttt http://www.actual technologies.com/product_ [18] [19] Chapter 5 [20] Underfull \hbox (badness 10000) in paragraph at lines 1619--1624 @textrm HDF5 (Hi-er-ar-chi-cal Data For-mat, see [][]@texttt http://hdf.ncsa.ui uc.edu/HDF5/[][][]@textrm ) Underfull \hbox (badness 10000) in paragraph at lines 1619--1624 @textrm and to UCAR's netCDF data files (net-work Com-mon Data Form, see Chapter 6 [21] [22] [23] [24] [25] Chapter 7 [26] Underfull \hbox (badness 2538) in paragraph at lines 2104--2111 @textrm ap-pli-ca-tions to call meth-ods, or op-er-a-tions, in server ob-jects run-ning in other [27] Chapter 8 [28] Underfull \hbox (badness 4739) in paragraph at lines 2159--2168 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such Underfull \hbox (badness 10000) in paragraph at lines 2159--2168 @textrm am-ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[] [][]@textrm ) and OpenOf-fice Appendix A [29] (Function and variable index) [30] (./R-data.vrs [31]) (Concept index) [32] (./R-data.cps) [33] ) (see the transcript file for additional information) Output written on R-data.pdf (37 pages, 365002 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-data.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc) (Acknowledgements) Overfull \hbox (8.53186pt too wide) in paragraph at lines 96--96 @textbf dataframes2xls| Overfull \hbox (2.70708pt too wide) in paragraph at lines 107--107 @textbf RPostgreSQL| Overfull \hbox (2.49414pt too wide) in paragraph at lines 113--113 @textbf xlsReadWrite| Chapter 1 [1] [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14] [15] [16] [17] Overfull \hbox (9.3377pt too wide) in paragraph at lines 1359--1363 []@textrm On Mac OS X the Ac-tual Tech-nolo-gies ([][]@texttt http://www.actual technologies.com/product_ [18] [19] Chapter 5 [20] Underfull \hbox (badness 10000) in paragraph at lines 1619--1624 @textrm HDF5 (Hi-er-ar-chi-cal Data For-mat, see [][]@texttt http://hdf.ncsa.ui uc.edu/HDF5/[][][]@textrm ) Underfull \hbox (badness 10000) in paragraph at lines 1619--1624 @textrm and to UCAR's netCDF data files (net-work Com-mon Data Form, see Chapter 6 [21] [22] [23] [24] [25] Chapter 7 [26] Underfull \hbox (badness 2538) in paragraph at lines 2104--2111 @textrm ap-pli-ca-tions to call meth-ods, or op-er-a-tions, in server ob-jects run-ning in other [27] Chapter 8 [28] Underfull \hbox (badness 4739) in paragraph at lines 2159--2168 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such Underfull \hbox (badness 10000) in paragraph at lines 2159--2168 @textrm am-ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[] [][]@textrm ) and OpenOf-fice Appendix A [29] (Function and variable index) [30] (./R-data.vrs [31]) (Concept index) [32] (./R-data.cps) [33] ) (see the transcript file for additional information) Output written on R-data.pdf (37 pages, 365002 bytes). Transcript written on R-data.log. /bin/bash: line 0: test: too many arguments TEXINPUTS=".:$TEXINPUTS" /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Cross reference values unknown; you must run TeX again. [2] Underfull \hbox (badness 3049) in paragraph at lines 267--276 [][]@texttt http://www.debian.org/doc/debian-policy/ch-controlfields.html[][][] @textrm : R does not [3] Underfull \hbox (badness 3826) in paragraph at lines 304--321 []@textrm The names of ab-bre-vi-a-tions of free or open source soft-ware (FOS S, e.g., Underfull \hbox (badness 2608) in paragraph at lines 304--321 @textrm soft-ware (see [][]@texttt http://www.opensource.org/licenses/bsd-lice nse.php[][][]@textrm ) li-censes [4] [5] Underfull \hbox (badness 6741) in paragraph at lines 442--446 []@textrm Packages whose name space only is needed to load the pack-age us-ing Underfull \hbox (badness 3118) in paragraph at lines 446--450 []@textrm Packages that need to be at-tached to suc-cess-fully load the pack-a ge us-ing [6] Underfull \hbox (badness 4543) in paragraph at lines 546--556 []@textrm Finally, an `@texttt Language[]@textrm '[] field can be used to in-di -cate if the pack-age doc- Underfull \hbox (badness 8038) in paragraph at lines 546--556 @textrm u-men-ta-tion is not in En-glish: this should be a comma-separated list of Underfull \hbox (badness 10000) in paragraph at lines 546--556 @textrm stan-dard (not pri-vate use or grand-fa-thered) IETF lan-guage tags as cur- Underfull \hbox (badness 7012) in paragraph at lines 546--556 @textrm rently de-fined by RFC 5646 ([][]@texttt http://tools.ietf.org/html/rfc 5646[][][]@textrm , see also [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (16.92342pt too wide) in paragraph at lines 1359--1359 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [18] Overfull \hbox (8.1238pt too wide) in paragraph at lines 1444--1446 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as `@smalltt ~/.R/check.Renviron.i386[]@smallrm '[] [19] [20] Underfull \hbox (badness 3919) in paragraph at lines 1583--1589 @textrm de-fined$@textsy i$ @textrm [Writ-ing R doc-u-men-ta-tion files], page $@textsy h$@textrm un-de-fined$@textsy i$[][]@textrm , for in-for-ma-tion Underfull \hbox (badness 2662) in paragraph at lines 1583--1589 @textrm `@texttt tests/Examples/@textttsl pkg@texttt -Ex.Rout.save[]@textrm '[ ], the out-put of run-ning the ex-am-ples is [21] Underfull \hbox (badness 3291) in paragraph at lines 1634--1647 []@textbf Multiple sub-architectures: @textrm On sys-tems which sup-port mul-t i-ple sub- [22] [23] [24] Underfull \hbox (badness 2951) in paragraph at lines 1845--1849 []@textrm Read through the PDF man-ual that was pro-duced by @texttt R CMD che ck[] @textrm at Underfull \hbox (badness 7576) in paragraph at lines 1879--1889 []@textrm Note also that for run-ning L[]T[]X, the De-bian @reducedrm GNU@textr m /Linux @reducedrm CRAN @textrm check Underfull \hbox (badness 10000) in paragraph at lines 1879--1889 @textrm sys-tems use rea-son-ably re-cent ver-sions of the De-bian TexLive dis- tri-bu-tion [25] [26] [27] [28] [29] [30] [31] [32] Underfull \hbox (badness 3333) in paragraph at lines 2591--2593 []@textrm Some notes on is-sues spe-cific to port-ing to x64 Win-dows are avail -able at [33] [34] [35] Underfull \hbox (badness 2401) in paragraph at lines 2797--2802 []@textrm The pro-ce-dures make use of @texttt msgfmt[] @textrm and @texttt xge ttext[] @textrm which are part of @reducedrm GNU [36] [37] [38] [39] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3104--3104 []@texttt msgfmt -c -o share/locale/it/LC_MESSAGES/RGui.mo $R_SRC_HOME/po/RGui -it.gmo[] [40] Chapter 2 [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 7595) in paragraph at lines 4258--4266 []@textrm Occasionally the best con-tent for one out-put for-mat is dif-fer-ent from the Underfull \hbox (badness 7796) in paragraph at lines 4258--4266 @textrm best con-tent for an-other. For this sit-u-a-tion, the @texttt \if{@tex tttsl format@texttt }{@textttsl text@texttt }[] @textrm or Underfull \hbox (badness 3503) in paragraph at lines 4275--4281 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [56] [57] [58] Underfull \hbox (badness 6526) in paragraph at lines 4470--4475 @textrm command, and this needs to be matched by a suit-able in-vo-ca-tion of t he Underfull \hbox (badness 4096) in paragraph at lines 4470--4475 @texttt \usepackage{inputenc}[] @textrm com-mand. The R util-ity @texttt R CMD Rd2dvi[] @textrm looks at the Chapter 3 [59] [60] [61] [62] [63] Underfull \hbox (badness 2941) in paragraph at lines 4911--4914 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see [][]@texttt http:// [64] [65] Underfull \hbox (badness 2343) in paragraph at lines 5002--5006 @texttt Shark[] @textrm (see [][]@texttt http://developer.apple.com/tools/shark optimize.html[][][] @textrm and [][]@texttt http:// Chapter 4 [66] [67] [68] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5208--5208 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [69] Overfull \hbox (25.25755pt too wide) in paragraph at lines 5248--5248 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [70] Overfull \hbox (20.53261pt too wide) in paragraph at lines 5352--5352 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 5382--5391 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [71] [72] [73] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5583--5583 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5586--5586 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [74] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5653--5653 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [75] [76] Chapter 5 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] Overfull \hbox (135.6642pt too wide) in paragraph at lines 6626--6626 []@texttt PKGB_PATH=`echo 'cat(system.file("libs", .Platform$r_arch, package=" packB", mustWork=TRUE))' \[] Overfull \hbox (135.6642pt too wide) in paragraph at lines 6639--6639 []@texttt PKGB_PATH=`echo 'cat(system.file("libs", .Platform$r_arch, package=" packB", mustWork=TRUE))' \[] [88] Overfull \hbox (37.93651pt too wide) in paragraph at lines 6660--6660 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] Overfull \hbox (59.61772pt too wide) in paragraph at lines 6709--6709 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7462--7462 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [99] Underfull \hbox (badness 10000) in paragraph at lines 7523--7525 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8361--8361 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [110] [111] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8451--8451 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [112] Overfull \hbox (43.6852pt too wide) in paragraph at lines 8528--8528 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [113] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8610--8610 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] Underfull \hbox (badness 6332) in paragraph at lines 10026--10029 []@textrm The header files which R in-stalls are in di-rec-tory `@textttsl R_IN CLUDE_DIR[]@textrm '[] (de-fault Underfull \hbox (badness 10000) in paragraph at lines 10082--10084 @textrm definitions for ex-ports from `@texttt R.dll[]@textrm '[] on [131] Underfull \hbox (badness 10000) in paragraph at lines 10087--10092 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Chapter 7 [132] [133] Chapter 8 [134] Underfull \hbox (badness 2213) in paragraph at lines 10327--10332 []@textrm Setting @texttt LD_LIBRARY_PATH[] @textrm to in-clude the di-rec-to- ries used in link-ing R. This [135] [136] Overfull \hbox (20.69044pt too wide) in paragraph at lines 10467--10467 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] [137] [138] [139] Underfull \hbox (badness 2547) in paragraph at lines 10703--10710 @texttt modules/internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet /nanohttp.c[]@textrm '[] and `@texttt src/ [140] [141] Overfull \hbox (34.81801pt too wide) in paragraph at lines 10825--10830 @textrm Its phi-los-o-phy is dis-cussed in [][]@texttt http://www.omegahat.org /RDCOMServer/Docs/Paradigm.html[][][] [142] [143] Underfull \hbox (badness 2671) in paragraph at lines 10961--10968 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 4084) in paragraph at lines 10961--10968 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [144] [145] (Function and variable index) [146] (Concept index) [147] [148] ) (see the transcript file for additional information) Output written on R-exts.pdf (151 pages, 794179 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) Chapter 1 [1] [2] Underfull \hbox (badness 3049) in paragraph at lines 267--276 [][]@texttt http://www.debian.org/doc/debian-policy/ch-controlfields.html[][][] @textrm : R does not [3] Underfull \hbox (badness 3826) in paragraph at lines 304--321 []@textrm The names of ab-bre-vi-a-tions of free or open source soft-ware (FOS S, e.g., Underfull \hbox (badness 2608) in paragraph at lines 304--321 @textrm soft-ware (see [][]@texttt http://www.opensource.org/licenses/bsd-lice nse.php[][][]@textrm ) li-censes [4] [5] Underfull \hbox (badness 6741) in paragraph at lines 442--446 []@textrm Packages whose name space only is needed to load the pack-age us-ing Underfull \hbox (badness 3118) in paragraph at lines 446--450 []@textrm Packages that need to be at-tached to suc-cess-fully load the pack-a ge us-ing [6] Underfull \hbox (badness 4543) in paragraph at lines 546--556 []@textrm Finally, an `@texttt Language[]@textrm '[] field can be used to in-di -cate if the pack-age doc- Underfull \hbox (badness 8038) in paragraph at lines 546--556 @textrm u-men-ta-tion is not in En-glish: this should be a comma-separated list of Underfull \hbox (badness 10000) in paragraph at lines 546--556 @textrm stan-dard (not pri-vate use or grand-fa-thered) IETF lan-guage tags as cur- Underfull \hbox (badness 7012) in paragraph at lines 546--556 @textrm rently de-fined by RFC 5646 ([][]@texttt http://tools.ietf.org/html/rfc 5646[][][]@textrm , see also [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (16.92342pt too wide) in paragraph at lines 1359--1359 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [18] Overfull \hbox (8.1238pt too wide) in paragraph at lines 1444--1446 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as `@smalltt ~/.R/check.Renviron.i386[]@smallrm '[] [19] [20] [21] Underfull \hbox (badness 3291) in paragraph at lines 1634--1647 []@textbf Multiple sub-architectures: @textrm On sys-tems which sup-port mul-t i-ple sub- [22] [23] l.1823: Undefined cross reference `Customizing package compilation-snt'. l.1823: Undefined cross reference `Customizing package compilation-snt'. l.1823: Undefined cross reference `Customizing package compilation-pg'. [24] Underfull \hbox (badness 2951) in paragraph at lines 1845--1849 []@textrm Read through the PDF man-ual that was pro-duced by @texttt R CMD che ck[] @textrm at Underfull \hbox (badness 7576) in paragraph at lines 1879--1889 []@textrm Note also that for run-ning L[]T[]X, the De-bian @reducedrm GNU@textr m /Linux @reducedrm CRAN @textrm check Underfull \hbox (badness 10000) in paragraph at lines 1879--1889 @textrm sys-tems use rea-son-ably re-cent ver-sions of the De-bian TexLive dis- tri-bu-tion [25] [26] [27] [28] [29] [30] [31] [32] Underfull \hbox (badness 3333) in paragraph at lines 2591--2593 []@textrm Some notes on is-sues spe-cific to port-ing to x64 Win-dows are avail -able at [33] [34] [35] Underfull \hbox (badness 2401) in paragraph at lines 2797--2802 []@textrm The pro-ce-dures make use of @texttt msgfmt[] @textrm and @texttt xge ttext[] @textrm which are part of @reducedrm GNU [36] [37] [38] [39] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3104--3104 []@texttt msgfmt -c -o share/locale/it/LC_MESSAGES/RGui.mo $R_SRC_HOME/po/RGui -it.gmo[] [40] Chapter 2 [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 7595) in paragraph at lines 4258--4266 []@textrm Occasionally the best con-tent for one out-put for-mat is dif-fer-ent from the Underfull \hbox (badness 7796) in paragraph at lines 4258--4266 @textrm best con-tent for an-other. For this sit-u-a-tion, the @texttt \if{@tex tttsl format@texttt }{@textttsl text@texttt }[] @textrm or Underfull \hbox (badness 3503) in paragraph at lines 4275--4281 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [56] [57] Underfull \hbox (badness 6526) in paragraph at lines 4470--4475 @textrm command, and this needs to be matched by a suit-able in-vo-ca-tion of t he Underfull \hbox (badness 4096) in paragraph at lines 4470--4475 @texttt \usepackage{inputenc}[] @textrm com-mand. The R util-ity @texttt R CMD Rd2dvi[] @textrm looks at the [58] Chapter 3 [59] [60] [61] [62] [63] Underfull \hbox (badness 2941) in paragraph at lines 4911--4914 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see [][]@texttt http:// [64] [65] Underfull \hbox (badness 2343) in paragraph at lines 5002--5006 @texttt Shark[] @textrm (see [][]@texttt http://developer.apple.com/tools/shark optimize.html[][][] @textrm and [][]@texttt http:// Chapter 4 [66] [67] [68] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5208--5208 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [69] Overfull \hbox (25.25755pt too wide) in paragraph at lines 5248--5248 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [70] Overfull \hbox (20.53261pt too wide) in paragraph at lines 5352--5352 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 5382--5391 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [71] [72] [73] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5583--5583 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5586--5586 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [74] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5653--5653 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [75] [76] Chapter 5 [77] [78] [79] [80] [81] [82] [83] [84] l.6384: Undefined cross reference `Customizing package compilation-snt'. l.6384: Undefined cross reference `Customizing package compilation-snt'. l.6384: Undefined cross reference `Customizing package compilation-pg'. [85] [86] [87] Overfull \hbox (135.6642pt too wide) in paragraph at lines 6626--6626 []@texttt PKGB_PATH=`echo 'cat(system.file("libs", .Platform$r_arch, package=" packB", mustWork=TRUE))' \[] Overfull \hbox (135.6642pt too wide) in paragraph at lines 6639--6639 []@texttt PKGB_PATH=`echo 'cat(system.file("libs", .Platform$r_arch, package=" packB", mustWork=TRUE))' \[] [88] Overfull \hbox (37.93651pt too wide) in paragraph at lines 6660--6660 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] Overfull \hbox (59.61772pt too wide) in paragraph at lines 6709--6709 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7462--7462 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [99] Underfull \hbox (badness 10000) in paragraph at lines 7523--7525 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8361--8361 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [110] [111] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8451--8451 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [112] Overfull \hbox (43.6852pt too wide) in paragraph at lines 8528--8528 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [113] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8610--8610 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] Underfull \hbox (badness 6332) in paragraph at lines 10026--10029 []@textrm The header files which R in-stalls are in di-rec-tory `@textttsl R_IN CLUDE_DIR[]@textrm '[] (de-fault Underfull \hbox (badness 10000) in paragraph at lines 10082--10084 @textrm definitions for ex-ports from `@texttt R.dll[]@textrm '[] on [131] Underfull \hbox (badness 10000) in paragraph at lines 10087--10092 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Chapter 7 [132] [133] Chapter 8 [134] Underfull \hbox (badness 2213) in paragraph at lines 10327--10332 []@textrm Setting @texttt LD_LIBRARY_PATH[] @textrm to in-clude the di-rec-to- ries used in link-ing R. This [135] [136] Overfull \hbox (20.69044pt too wide) in paragraph at lines 10467--10467 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] [137] [138] [139] Underfull \hbox (badness 2547) in paragraph at lines 10703--10710 @texttt modules/internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet /nanohttp.c[]@textrm '[] and `@texttt src/ [140] [141] Overfull \hbox (34.81801pt too wide) in paragraph at lines 10825--10830 @textrm Its phi-los-o-phy is dis-cussed in [][]@texttt http://www.omegahat.org /RDCOMServer/Docs/Paradigm.html[][][] [142] [143] Underfull \hbox (badness 2671) in paragraph at lines 10961--10968 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 4084) in paragraph at lines 10961--10968 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [144] [145] (Function and variable index) [146] (./R-exts.vrs [147] [148]) (Concept index) [149] (./R-exts.cps [150]) [151] ) (see the transcript file for additional information) Output written on R-exts.pdf (157 pages, 955095 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-exts.toc [-1] [-2] [-3]) [-4] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) Chapter 1 [1] [2] Underfull \hbox (badness 3049) in paragraph at lines 267--276 [][]@texttt http://www.debian.org/doc/debian-policy/ch-controlfields.html[][][] @textrm : R does not [3] Underfull \hbox (badness 3826) in paragraph at lines 304--321 []@textrm The names of ab-bre-vi-a-tions of free or open source soft-ware (FOS S, e.g., Underfull \hbox (badness 2608) in paragraph at lines 304--321 @textrm soft-ware (see [][]@texttt http://www.opensource.org/licenses/bsd-lice nse.php[][][]@textrm ) li-censes [4] [5] Underfull \hbox (badness 6741) in paragraph at lines 442--446 []@textrm Packages whose name space only is needed to load the pack-age us-ing Underfull \hbox (badness 3118) in paragraph at lines 446--450 []@textrm Packages that need to be at-tached to suc-cess-fully load the pack-a ge us-ing [6] Underfull \hbox (badness 4543) in paragraph at lines 546--556 []@textrm Finally, an `@texttt Language[]@textrm '[] field can be used to in-di -cate if the pack-age doc- Underfull \hbox (badness 8038) in paragraph at lines 546--556 @textrm u-men-ta-tion is not in En-glish: this should be a comma-separated list of Underfull \hbox (badness 10000) in paragraph at lines 546--556 @textrm stan-dard (not pri-vate use or grand-fa-thered) IETF lan-guage tags as cur- Underfull \hbox (badness 7012) in paragraph at lines 546--556 @textrm rently de-fined by RFC 5646 ([][]@texttt http://tools.ietf.org/html/rfc 5646[][][]@textrm , see also [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (16.92342pt too wide) in paragraph at lines 1359--1359 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [18] Overfull \hbox (8.1238pt too wide) in paragraph at lines 1444--1446 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as `@smalltt ~/.R/check.Renviron.i386[]@smallrm '[] [19] [20] [21] Underfull \hbox (badness 3291) in paragraph at lines 1634--1647 []@textbf Multiple sub-architectures: @textrm On sys-tems which sup-port mul-t i-ple sub- [22] [23] l.1823: Undefined cross reference `Customizing package compilation-snt'. l.1823: Undefined cross reference `Customizing package compilation-snt'. l.1823: Undefined cross reference `Customizing package compilation-pg'. [24] Underfull \hbox (badness 2951) in paragraph at lines 1845--1849 []@textrm Read through the PDF man-ual that was pro-duced by @texttt R CMD che ck[] @textrm at Underfull \hbox (badness 7576) in paragraph at lines 1879--1889 []@textrm Note also that for run-ning L[]T[]X, the De-bian @reducedrm GNU@textr m /Linux @reducedrm CRAN @textrm check Underfull \hbox (badness 10000) in paragraph at lines 1879--1889 @textrm sys-tems use rea-son-ably re-cent ver-sions of the De-bian TexLive dis- tri-bu-tion [25] [26] [27] [28] [29] [30] [31] [32] Underfull \hbox (badness 3333) in paragraph at lines 2591--2593 []@textrm Some notes on is-sues spe-cific to port-ing to x64 Win-dows are avail -able at [33] [34] [35] Underfull \hbox (badness 2401) in paragraph at lines 2797--2802 []@textrm The pro-ce-dures make use of @texttt msgfmt[] @textrm and @texttt xge ttext[] @textrm which are part of @reducedrm GNU [36] [37] [38] [39] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3104--3104 []@texttt msgfmt -c -o share/locale/it/LC_MESSAGES/RGui.mo $R_SRC_HOME/po/RGui -it.gmo[] [40] Chapter 2 [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 7595) in paragraph at lines 4258--4266 []@textrm Occasionally the best con-tent for one out-put for-mat is dif-fer-ent from the Underfull \hbox (badness 7796) in paragraph at lines 4258--4266 @textrm best con-tent for an-other. For this sit-u-a-tion, the @texttt \if{@tex tttsl format@texttt }{@textttsl text@texttt }[] @textrm or Underfull \hbox (badness 3503) in paragraph at lines 4275--4281 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [56] [57] Underfull \hbox (badness 6526) in paragraph at lines 4470--4475 @textrm command, and this needs to be matched by a suit-able in-vo-ca-tion of t he Underfull \hbox (badness 4096) in paragraph at lines 4470--4475 @texttt \usepackage{inputenc}[] @textrm com-mand. The R util-ity @texttt R CMD Rd2dvi[] @textrm looks at the [58] Chapter 3 [59] [60] [61] [62] [63] Underfull \hbox (badness 2941) in paragraph at lines 4911--4914 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see [][]@texttt http:// [64] [65] Underfull \hbox (badness 2343) in paragraph at lines 5002--5006 @texttt Shark[] @textrm (see [][]@texttt http://developer.apple.com/tools/shark optimize.html[][][] @textrm and [][]@texttt http:// Chapter 4 [66] [67] [68] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5208--5208 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [69] Overfull \hbox (25.25755pt too wide) in paragraph at lines 5248--5248 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [70] Overfull \hbox (20.53261pt too wide) in paragraph at lines 5352--5352 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 5382--5391 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [71] [72] [73] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5583--5583 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5586--5586 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [74] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5653--5653 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [75] [76] Chapter 5 [77] [78] [79] [80] [81] [82] [83] [84] l.6384: Undefined cross reference `Customizing package compilation-snt'. l.6384: Undefined cross reference `Customizing package compilation-snt'. l.6384: Undefined cross reference `Customizing package compilation-pg'. [85] [86] [87] Overfull \hbox (135.6642pt too wide) in paragraph at lines 6626--6626 []@texttt PKGB_PATH=`echo 'cat(system.file("libs", .Platform$r_arch, package=" packB", mustWork=TRUE))' \[] Overfull \hbox (135.6642pt too wide) in paragraph at lines 6639--6639 []@texttt PKGB_PATH=`echo 'cat(system.file("libs", .Platform$r_arch, package=" packB", mustWork=TRUE))' \[] [88] Overfull \hbox (37.93651pt too wide) in paragraph at lines 6660--6660 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] Overfull \hbox (59.61772pt too wide) in paragraph at lines 6709--6709 []@texttt PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="pa ckB"))' \[] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7462--7462 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [99] Underfull \hbox (badness 10000) in paragraph at lines 7523--7525 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8361--8361 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [110] [111] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8451--8451 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [112] Overfull \hbox (43.6852pt too wide) in paragraph at lines 8528--8528 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [113] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8610--8610 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] Underfull \hbox (badness 6332) in paragraph at lines 10026--10029 []@textrm The header files which R in-stalls are in di-rec-tory `@textttsl R_IN CLUDE_DIR[]@textrm '[] (de-fault Underfull \hbox (badness 10000) in paragraph at lines 10082--10084 @textrm definitions for ex-ports from `@texttt R.dll[]@textrm '[] on [131] Underfull \hbox (badness 10000) in paragraph at lines 10087--10092 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Chapter 7 [132] [133] Chapter 8 [134] Underfull \hbox (badness 2213) in paragraph at lines 10327--10332 []@textrm Setting @texttt LD_LIBRARY_PATH[] @textrm to in-clude the di-rec-to- ries used in link-ing R. This [135] [136] Overfull \hbox (20.69044pt too wide) in paragraph at lines 10467--10467 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] [137] [138] [139] Underfull \hbox (badness 2547) in paragraph at lines 10703--10710 @texttt modules/internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet /nanohttp.c[]@textrm '[] and `@texttt src/ [140] [141] Overfull \hbox (34.81801pt too wide) in paragraph at lines 10825--10830 @textrm Its phi-los-o-phy is dis-cussed in [][]@texttt http://www.omegahat.org /RDCOMServer/Docs/Paradigm.html[][][] [142] [143] Underfull \hbox (badness 2671) in paragraph at lines 10961--10968 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 4084) in paragraph at lines 10961--10968 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [144] [145] (Function and variable index) [146] (./R-exts.vrs [147] [148]) (Concept index) [149] (./R-exts.cps [150]) [151] ) (see the transcript file for additional information) Output written on R-exts.pdf (157 pages, 955094 bytes). Transcript written on R-exts.log. /bin/bash: line 0: test: too many arguments TEXINPUTS=".:$TEXINPUTS" /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Chapter 6 [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] [35] [36] <./images/hist.pdf> <./images/ecdf.pdf> [37] <./images/QQ.pdf> [38] <./images/ice.pdf> [39] [40] Chapter 9 [41] [42] Chapter 10 [43] [44] [45] [46] [47] [48] [49] [50] [51] Chapter 11 [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Chapter 12 [66] [67] [68] [69] [70] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5738--5738 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [71] [72] [73] [74] [75] <./images/fig11.pdf> [76] <./images/fig12.pdf> [77] [78] Underfull \hbox (badness 3240) in paragraph at lines 6220--6223 []@textrm More com-pli-cated ar-range-ments of mul-ti-ple fig-ures can be pro-d uced by the [79] [80] Underfull \hbox (badness 7832) in paragraph at lines 6409--6412 @textrm and these can be ac-cessed from R via the pack-age @textbf rggobi@textr m , de-scribed at Chapter 13 [81] Underfull \hbox (badness 10000) in paragraph at lines 6444--6449 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [82] Appendix A [83] [84] [85] [86] Appendix B [87] [88] [89] [90] [91] [92] [93] Appendix C [94] [95] Appendix D [96] Appendix E [97] Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (102 pages, 645987 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-intro.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc) (Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Chapter 6 [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] [35] [36] <./images/hist.pdf> <./images/ecdf.pdf> [37] <./images/QQ.pdf> [38] <./images/ice.pdf> [39] [40] Chapter 9 [41] [42] Chapter 10 [43] [44] [45] [46] [47] [48] [49] [50] [51] Chapter 11 [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Chapter 12 [66] [67] [68] [69] [70] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5738--5738 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [71] [72] [73] [74] [75] <./images/fig11.pdf> [76] <./images/fig12.pdf> [77] [78] Underfull \hbox (badness 3240) in paragraph at lines 6220--6223 []@textrm More com-pli-cated ar-range-ments of mul-ti-ple fig-ures can be pro-d uced by the [79] [80] Underfull \hbox (badness 7832) in paragraph at lines 6409--6412 @textrm and these can be ac-cessed from R via the pack-age @textbf rggobi@textr m , de-scribed at Chapter 13 [81] Underfull \hbox (badness 10000) in paragraph at lines 6444--6449 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [82] Appendix A [83] [84] [85] [86] Appendix B [87] [88] [89] [90] [91] [92] [93] Appendix C [94] [95] Appendix D [96] (./R-intro.vrs [97] [98]) Appendix E [99] (./R-intro.cps [100]) Appendix F [101] [102] ) (see the transcript file for additional information) Output written on R-intro.pdf (108 pages, 783803 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-intro.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc) (Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Chapter 6 [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] [35] [36] <./images/hist.pdf> <./images/ecdf.pdf> [37] <./images/QQ.pdf> [38] <./images/ice.pdf> [39] [40] Chapter 9 [41] [42] Chapter 10 [43] [44] [45] [46] [47] [48] [49] [50] [51] Chapter 11 [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Chapter 12 [66] [67] [68] [69] [70] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5738--5738 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [71] [72] [73] [74] [75] <./images/fig11.pdf> [76] <./images/fig12.pdf> [77] [78] Underfull \hbox (badness 3240) in paragraph at lines 6220--6223 []@textrm More com-pli-cated ar-range-ments of mul-ti-ple fig-ures can be pro-d uced by the [79] [80] Underfull \hbox (badness 7832) in paragraph at lines 6409--6412 @textrm and these can be ac-cessed from R via the pack-age @textbf rggobi@textr m , de-scribed at Chapter 13 [81] Underfull \hbox (badness 10000) in paragraph at lines 6444--6449 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [82] Appendix A [83] [84] [85] [86] Appendix B [87] [88] [89] [90] [91] [92] [93] Appendix C [94] [95] Appendix D [96] (./R-intro.vrs [97] [98]) Appendix E [99] (./R-intro.cps [100]) Appendix F [101] [102] ) (see the transcript file for additional information) Output written on R-intro.pdf (108 pages, 783818 bytes). Transcript written on R-intro.log. /bin/bash: line 0: test: too many arguments TEXINPUTS=".:$TEXINPUTS" /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Overfull \hbox (5.29526pt too wide) in paragraph at lines 1960--1965 []@textrm Lazy-load data-bases are cre-ated by the code in `@texttt src/library /tools/R/makeLazyLoad.R[]@textrm '[]: [24] Chapter 2 [25] [26] [27] [28] Overfull \hbox (0.64153pt too wide) in paragraph at lines 2305--2312 []@textrm Those prim-i-tives which are in @texttt .GenericArgsEnv[] @textrm are checked (via `@texttt tests/primitives.R[]@textrm '[]) Chapter 3 [29] [30] Chapter 4 [31] [32] [33] Chapter 5 [34] Overfull \hbox (0.6417pt too wide) in paragraph at lines 2611--2614 []@textrm Some notes on the changes for 1.4.0 can be found at [][]@texttt http: //www.stat.auckland.ac.nz/ Underfull \hbox (badness 10000) in paragraph at lines 2611--2614 @texttt ~paul/R/basegraph.html[][][] @textrm and [][]@texttt http://www.stat.au ckland.ac.nz/~paul/R/ [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 5832) in paragraph at lines 3135--3151 []@textrm Users may use @texttt grDevices::setGraphicsEventEnv[] @textrm to set the @texttt eventEnv[] @textrm en- Underfull \hbox (badness 2556) in paragraph at lines 3135--3151 @textrm vi-ron-ment in the de-vice driver to hold event han-dlers. When the use r calls [42] [43] [44] Underfull \hbox (badness 2245) in paragraph at lines 3362--3366 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in Chapter 6 [45] [46] [47] Chapter 7 [48] [49] Chapter 8 [50] Chapter 9 [51] Chapter 10 [52] [53] (Function and variable index) [54] (Concept index) [55] [56] ) (see the transcript file for additional information) Output written on R-ints.pdf (59 pages, 385362 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-ints.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Overfull \hbox (5.29526pt too wide) in paragraph at lines 1960--1965 []@textrm Lazy-load data-bases are cre-ated by the code in `@texttt src/library /tools/R/makeLazyLoad.R[]@textrm '[]: [24] Chapter 2 [25] [26] [27] [28] Overfull \hbox (0.64153pt too wide) in paragraph at lines 2305--2312 []@textrm Those prim-i-tives which are in @texttt .GenericArgsEnv[] @textrm are checked (via `@texttt tests/primitives.R[]@textrm '[]) Chapter 3 [29] [30] Chapter 4 [31] [32] [33] Chapter 5 [34] Overfull \hbox (0.6417pt too wide) in paragraph at lines 2611--2614 []@textrm Some notes on the changes for 1.4.0 can be found at [][]@texttt http: //www.stat.auckland.ac.nz/ Underfull \hbox (badness 10000) in paragraph at lines 2611--2614 @texttt ~paul/R/basegraph.html[][][] @textrm and [][]@texttt http://www.stat.au ckland.ac.nz/~paul/R/ [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 5832) in paragraph at lines 3135--3151 []@textrm Users may use @texttt grDevices::setGraphicsEventEnv[] @textrm to set the @texttt eventEnv[] @textrm en- Underfull \hbox (badness 2556) in paragraph at lines 3135--3151 @textrm vi-ron-ment in the de-vice driver to hold event han-dlers. When the use r calls [42] [43] [44] Underfull \hbox (badness 2245) in paragraph at lines 3362--3366 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in Chapter 6 [45] [46] [47] Chapter 7 [48] [49] Chapter 8 [50] Chapter 9 [51] Chapter 10 [52] [53] (Function and variable index) [54] (./R-ints.vrs [55]) (Concept index) [56] (./R-ints.cps) [57] ) (see the transcript file for additional information) Output written on R-ints.pdf (61 pages, 474091 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-ints.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-ints.toc [-1]) [-2] (./R-ints.toc) (./R-ints.toc) Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Overfull \hbox (5.29526pt too wide) in paragraph at lines 1960--1965 []@textrm Lazy-load data-bases are cre-ated by the code in `@texttt src/library /tools/R/makeLazyLoad.R[]@textrm '[]: [24] Chapter 2 [25] [26] [27] [28] Overfull \hbox (0.64153pt too wide) in paragraph at lines 2305--2312 []@textrm Those prim-i-tives which are in @texttt .GenericArgsEnv[] @textrm are checked (via `@texttt tests/primitives.R[]@textrm '[]) Chapter 3 [29] [30] Chapter 4 [31] [32] [33] Chapter 5 [34] Overfull \hbox (0.6417pt too wide) in paragraph at lines 2611--2614 []@textrm Some notes on the changes for 1.4.0 can be found at [][]@texttt http: //www.stat.auckland.ac.nz/ Underfull \hbox (badness 10000) in paragraph at lines 2611--2614 @texttt ~paul/R/basegraph.html[][][] @textrm and [][]@texttt http://www.stat.au ckland.ac.nz/~paul/R/ [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 5832) in paragraph at lines 3135--3151 []@textrm Users may use @texttt grDevices::setGraphicsEventEnv[] @textrm to set the @texttt eventEnv[] @textrm en- Underfull \hbox (badness 2556) in paragraph at lines 3135--3151 @textrm vi-ron-ment in the de-vice driver to hold event han-dlers. When the use r calls [42] [43] [44] Underfull \hbox (badness 2245) in paragraph at lines 3362--3366 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in Chapter 6 [45] [46] [47] Chapter 7 [48] [49] Chapter 8 [50] Chapter 9 [51] Chapter 10 [52] [53] (Function and variable index) [54] (./R-ints.vrs [55]) (Concept index) [56] (./R-ints.cps) [57] ) (see the transcript file for additional information) Output written on R-ints.pdf (61 pages, 474091 bytes). Transcript written on R-ints.log. /bin/bash: line 0: test: too many arguments TEXINPUTS=".:$TEXINPUTS" /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 300--301 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] [44] Chapter 8 [45] [46] Chapter 9 [47] [48] [49] Chapter 10 [50] [51] [52] Underfull \hbox (badness 3623) in paragraph at lines 4328--4330 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [53] [54] [55] [56] [57] (Function and Variable Index) [58] (Concept Index) [59] Appendix A [60] [61] ) (see the transcript file for additional information) Output written on R-lang.pdf (64 pages, 377464 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-lang.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1 Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 300--301 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] [44] Chapter 8 [45] [46] Chapter 9 [47] [48] [49] Chapter 10 [50] [51] [52] Underfull \hbox (badness 3623) in paragraph at lines 4328--4330 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [53] [54] [55] [56] [57] (Function and Variable Index) [58] (./R-lang.vrs [59]) (Concept Index) [60] (./R-lang.cps) Appendix A [61] [62] ) (see the transcript file for additional information) Output written on R-lang.pdf (67 pages, 499566 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (/build/buildd/r-base-2.12.1/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.3 <23 July 2005> ) localization, formatting, and turning on texinfo input format.) (./R-lang.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1 Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 300--301 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] [44] Chapter 8 [45] [46] Chapter 9 [47] [48] [49] Chapter 10 [50] [51] [52] Underfull \hbox (badness 3623) in paragraph at lines 4328--4330 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [53] [54] [55] [56] [57] (Function and Variable Index) [58] (./R-lang.vrs [59]) (Concept Index) [60] (./R-lang.cps) Appendix A [61] [62] ) (see the transcript file for additional information) Output written on R-lang.pdf (67 pages, 499566 bytes). Transcript written on R-lang.log. installing R manuals in PDF format ... make[2]: Leaving directory `/build/buildd/r-base-2.12.1/doc/manual' make[1]: Leaving directory `/build/buildd/r-base-2.12.1' make prefix=/build/buildd/r-base-2.12.1/debian/r-base-core/usr \ infodir=/build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info install-info make[1]: Entering directory `/build/buildd/r-base-2.12.1' make[2]: Entering directory `/build/buildd/r-base-2.12.1/doc/manual' /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-admin.texi R-admin.texi:726: warning: unlikely character ( in @var. R-admin.texi:726: warning: unlikely character ) in @var. /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-data.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-exts.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-intro.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-ints.texi /usr/bin/makeinfo --enable-encoding -D UseExternalXrefs -I. R-lang.texi mkdir -p -- /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info /usr/bin/install -c -m 644 "./dir" "/build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info" installing R info pages ... updating '/build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/dir' ... install-info: warning: don't call programs like install-info with an absolute path, install-info: warning: /usr/sbin/install-info provided by dpkg is deprecated and will go away soon; install-info: warning: its replacement lives in /usr/bin/. install-info: warning: nothing done since /usr/bin/install-info doesn't exist, install-info: warning: you might want to install an info-browser package. install-info: warning: don't call programs like install-info with an absolute path, install-info: warning: /usr/sbin/install-info provided by dpkg is deprecated and will go away soon; install-info: warning: its replacement lives in /usr/bin/. install-info: warning: nothing done since /usr/bin/install-info doesn't exist, install-info: warning: you might want to install an info-browser package. install-info: warning: don't call programs like install-info with an absolute path, install-info: warning: /usr/sbin/install-info provided by dpkg is deprecated and will go away soon; install-info: warning: its replacement lives in /usr/bin/. install-info: warning: nothing done since /usr/bin/install-info doesn't exist, install-info: warning: you might want to install an info-browser package. install-info: warning: don't call programs like install-info with an absolute path, install-info: warning: /usr/sbin/install-info provided by dpkg is deprecated and will go away soon; install-info: warning: its replacement lives in /usr/bin/. install-info: warning: nothing done since /usr/bin/install-info doesn't exist, install-info: warning: you might want to install an info-browser package. install-info: warning: don't call programs like install-info with an absolute path, install-info: warning: /usr/sbin/install-info provided by dpkg is deprecated and will go away soon; install-info: warning: its replacement lives in /usr/bin/. install-info: warning: nothing done since /usr/bin/install-info doesn't exist, install-info: warning: you might want to install an info-browser package. install-info: warning: don't call programs like install-info with an absolute path, install-info: warning: /usr/sbin/install-info provided by dpkg is deprecated and will go away soon; install-info: warning: its replacement lives in /usr/bin/. install-info: warning: nothing done since /usr/bin/install-info doesn't exist, install-info: warning: you might want to install an info-browser package. install-info: warning: don't call programs like install-info with an absolute path, install-info: warning: /usr/sbin/install-info provided by dpkg is deprecated and will go away soon; install-info: warning: its replacement lives in /usr/bin/. install-info: warning: nothing done since /usr/bin/install-info doesn't exist, install-info: warning: you might want to install an info-browser package. make[2]: Leaving directory `/build/buildd/r-base-2.12.1/doc/manual' make[1]: Leaving directory `/build/buildd/r-base-2.12.1' dh_movefiles --sourcedir=debian/r-base-core -pr-doc-pdf dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html touch install-indep-stamp gunzip -9v /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/*.gz /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-FAQ.info.gz: 66.9% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-FAQ.info /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-admin.info.gz: 68.2% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-admin.info /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-data.info.gz: 70.1% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-data.info /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-exts.info-1.gz: 67.3% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-exts.info-1 /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-exts.info-2.gz: 72.7% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-exts.info-2 /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-exts.info.gz: 63.1% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-exts.info /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-intro.info.gz: 70.0% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-intro.info /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-ints.info.gz: 67.1% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-ints.info /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-lang.info.gz: 71.2% -- replaced with /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/info/R-lang.info dh_movefiles --sourcedir=debian/r-base-core -pr-doc-info rm -vf /build/buildd/r-base-2.12.1/debian/r-doc-info/usr/share/info/dir \ /build/buildd/r-base-2.12.1/debian/r-doc-info/usr/share/info/dir.old removed `/build/buildd/r-base-2.12.1/debian/r-doc-info/usr/share/info/dir' dh_installdirs -pr-mathlib usr/include usr/lib \ usr/share/lintian/overrides \ usr/lib/pkgconfig dh_movefiles --sourcedir=debian/r-base-core -pr-mathlib (cd /build/buildd/r-base-2.12.1/debian/r-mathlib/usr/lib; \ ls -l ; \ mv -v libRmath.so libRmath.so.1.0.0; \ ln -sv libRmath.so.1.0.0 libRmath.so.1; \ ln -sv libRmath.so.1 libRmath.so) total 2112 -rw-r--r-- 1 root root 1484334 Jan 14 03:40 libRmath.a -rwxr-xr-x 1 root root 660327 Jan 14 03:40 libRmath.so drwxr-xr-x 2 root root 4096 Jan 14 03:42 pkgconfig `libRmath.so' -> `libRmath.so.1.0.0' `libRmath.so.1' -> `libRmath.so.1.0.0' `libRmath.so' -> `libRmath.so.1' install -m 0644 src/include/Rmath.h \ /build/buildd/r-base-2.12.1/debian/r-mathlib/usr/include install -m 0644 debian/Rprofile.site /build/buildd/r-base-2.12.1/debian/r-base-core/etc/R install -m 0644 debian/Renviron.site /build/buildd/r-base-2.12.1/debian/r-base-core/etc/R (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/etc; \ cat /build/buildd/r-base-2.12.1/debian/Renviron-R_LIBS.patch | patch --verbose; \ mv Makeconf repositories ldpaths ../../../../etc/R/; \ mv Renviron Renviron.ucf; \ ln -s /etc/R/Makeconf .; \ ln -s /etc/R/Renviron .; \ ln -s /etc/R/Renviron.site .; \ ln -s /etc/R/Rprofile.site .; \ ln -s /etc/R/ldpaths .; \ ln -s /etc/R/repositories . ) Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |--- Renviron.orig 2003-04-04 06:52:22.000000000 -0500 |+++ Renviron 2003-04-04 06:49:05.000000000 -0500 -------------------------- Patching file Renviron using Plan A... Hunk #1 succeeded at 46 with fuzz 2 (offset 13 lines). done (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/bin; \ cat /build/buildd/r-base-2.12.1/debian/javareconf.patch | patch --verbose ) Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |--- javareconf.orig 2008-08-25 06:26:13.000000000 -0500 |+++ javareconf 2008-08-25 06:30:49.000000000 -0500 -------------------------- Patching file javareconf using Plan A... Hunk #1 succeeded at 312 with fuzz 2 (offset 20 lines). done install -m 0644 debian/R.bash_completion \ debian/r-base-core/etc/bash_completion.d/R (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/; \ ln -sv R/lib/libR.so . ) `./libR.so' -> `R/lib/libR.so' touch install-arch-stamp *** binary-arch *** dh_testdir -a dh_testroot -a dh_installdocs -pr-base-core NEWS ONEWS OONEWS README \ debian/README.Atlas \ debian/README.mathlib dh_installdocs -pr-mathlib NEWS ONEWS OONEWS README \ debian/README.mathlib dh_installdocs -pr-base-core-dbg dh_installexamples -pr-mathlib src/nmath/standalone/test.c dh_installmenu -a # (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .) (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .) (cd /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/library .) install -p -m 0644 debian/r-base-core.lintian \ /build/buildd/r-base-2.12.1/debian/r-base-core/usr/share/lintian/overrides/r-base-core install -p -m 0644 debian/r-recommended.lintian \ /build/buildd/r-base-2.12.1/debian/r-recommended/usr/share/lintian/overrides/r-recommended install -p -m 0644 debian/r-mathlib.lintian \ /build/buildd/r-base-2.12.1/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib install -p -m 0644 debian/r-base-core-dbg.lintian \ /build/buildd/r-base-2.12.1/debian/r-base-core-dbg/usr/share/lintian/overrides/r-base-core-dbg dh_installchangelogs -a -k NEWS dh_strip --sourcedir=/build/buildd/r-base-2.12.1/debian/r-base-core --dbg-package=r-base-core-dbg dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given Unknown option: sourcedir dh_strip --sourcedir=/build/buildd/r-base-2.12.1/debian/r-mathlib dh_strip debug symbol extraction: disabling for PPA build dh_strip debug symbol extraction: not doing anything since NO_PKG_MANGLE is given Unknown option: sourcedir dh_compress -a dh_fixperms -a dh_link -a dh_makeshlibs -a dh_installdeb -a dh_perl -a dh_shlibdeps -a -l /build/buildd/r-base-2.12.1/debian/r-base-core/usr/lib/R/lib dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: Can't extract name and version from library name `libR.so' dpkg-shlibdeps: warning: dependency on libglib-2.0.so.0 could be avoided if "debian/r-base-core/usr/lib/R/modules/R_X11.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: dependency on libXss.so.1 could be avoided if "debian/r-base-core/usr/lib/R/library/tcltk/libs/tcltk.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: dependency on librt.so.1 could be avoided if "debian/r-base-core/usr/lib/R/modules/R_X11.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: dependency on libXext.so.6 could be avoided if "debian/r-base-core/usr/lib/R/library/tcltk/libs/tcltk.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: dependency on libpthread.so.0 could be avoided if "debian/r-base-core/usr/lib/R/modules/R_X11.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: dependency on libgmodule-2.0.so.0 could be avoided if "debian/r-base-core/usr/lib/R/modules/R_X11.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: dependency on libSM.so.6 could be avoided if "debian/r-base-core/usr/lib/R/modules/R_X11.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: dependency on libgthread-2.0.so.0 could be avoided if "debian/r-base-core/usr/lib/R/modules/R_X11.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: dependency on libICE.so.6 could be avoided if "debian/r-base-core/usr/lib/R/modules/R_X11.so" were not uselessly linked against it (they use none of its symbols). dpkg-shlibdeps: warning: symbol hypot used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol fmod used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol trunc used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol sincos used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol sinh used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol floor used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol log10 used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol pow used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol expm1 used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: symbol exp used by debian/r-mathlib/usr/lib/libRmath.so.1.0.0 found in none of the libraries. dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all). dh_gencontrol -a dh_md5sums -a -X'usr/bin/R' -X'usr/bin/Rscript' \ -X'usr/lib/debug/usr/bin/Rscript' \ -X'usr/lib/R/bin/Rscript' \ -X'usr/lib/R/etc/Renviron.ucf' \ -XLibIndex -Xindex.txt \ -Xfunction.html -Xpackages.html dh_builddeb -a INFO: pkgstriptranslations version 75 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build dpkg-deb: building package `r-base-core' in `../r-base-core_2.12.1-1~ppa1~maverick1_amd64.deb'. INFO: pkgstriptranslations version 75 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build dpkg-deb: building package `r-mathlib' in `../r-mathlib_2.12.1-1~ppa1~maverick1_amd64.deb'. INFO: pkgstriptranslations version 75 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build dpkg-deb: building package `r-base-core-dbg' in `../r-base-core-dbg_2.12.1-1~ppa1~maverick1_amd64.deb'. dpkg-genchanges -B -mUbuntu Build Daemon >../r-base_2.12.1-1~ppa1~maverick1_amd64.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: warning: the current version (2.12.1-1~ppa1~maverick1) is earlier than the previous one (2.12.1-1) dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build r-base-2.12.1 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20110114-0343 chroot-autobuild/build/buildd/r-base-core_2.12.1-1~ppa1~maverick1_amd64.deb: new debian package, version 2.0. size 14128890 bytes: control archive= 22374 bytes. 118 bytes, 6 lines conffiles 2699 bytes, 44 lines control 53442 bytes, 702 lines md5sums 2453 bytes, 73 lines * postinst #!/bin/sh 160 bytes, 5 lines * postrm #!/bin/sh 667 bytes, 34 lines * preinst #!/bin/sh 689 bytes, 26 lines * prerm #!/bin/sh 30 bytes, 1 lines shlibs Package: r-base-core Source: r-base Version: 2.12.1-1~ppa1~maverick1 Architecture: amd64 Maintainer: Dirk Eddelbuettel Installed-Size: 27252 Depends: perl, zip, unzip, libpaper-utils, xdg-utils, libblas3gf | libblas.so.3gf | libatlas3gf-base, libbz2-1.0, libc6 (>= 2.11), libcairo2 (>= 1.2.4), libgfortran3 (>= 4.3), libglib2.0-0 (>= 2.12.0), libice6 (>= 1:1.0.0), libjpeg62, liblapack3gf | liblapack.so.3gf | libatlas3gf-base, liblzma2 (>= 4.999.9beta+20091116), libpango1.0-0 (>= 1.14.0), libpcre3 (>= 7.7), libpng12-0 (>= 1.2.13-4), libreadline6 (>= 6.0), libsm6, libtiff4, libx11-6, libxext6, libxss1, libxt6, tcl8.5 (>= 8.5.0), tk8.5 (>= 8.5.0), zlib1g (>= 1:1.1.4), ucf (>= 3.0) Recommends: r-recommended, r-base-dev, r-doc-html Suggests: ess, r-doc-info | r-doc-pdf, r-mathlib, r-base-html Conflicts: r-base-latex, r-cran-rcompgen, r-gnome Replaces: r-base (<= 1.4.1-1), r-base-latex (<= 2.9.2-4), r-cran-rcompgen (<= 0.1-17-1), r-gnome (<= 2.3.1), r-recommended (<< 1.9.0) Provides: r-base-latex, r-cran-rcompgen, r-gnome Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R core of statistical computation and graphics system R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, over thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'. . This package provides the core GNU R system from which only the optional documentation packages r-base-html, r-doc-html, r-doc-pdf and r-doc-info have been split off to somewhat reduce the size of this package. chroot-autobuild/build/buildd/r-mathlib_2.12.1-1~ppa1~maverick1_amd64.deb: new debian package, version 2.0. size 619362 bytes: control archive= 1784 bytes. 1806 bytes, 39 lines control 867 bytes, 13 lines md5sums 135 bytes, 7 lines * postinst #!/bin/sh 132 bytes, 7 lines * postrm #!/bin/sh 30 bytes, 1 lines shlibs Package: r-mathlib Source: r-base Version: 2.12.1-1~ppa1~maverick1 Architecture: amd64 Maintainer: Dirk Eddelbuettel Installed-Size: 1280 Depends: libc6 (>= 2.3.4) Recommends: r-base-core (= 2.12.1-1~ppa1~maverick1), r-base-dev (= 2.12.1-1~ppa1~maverick1) Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R standalone mathematics library R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, over thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'. . This package provides the libRmath shared and static libraries which can be called from standalone C or C++ code. chroot-autobuild/build/buildd/r-base-core-dbg_2.12.1-1~ppa1~maverick1_amd64.deb: new debian package, version 2.0. size 2560724 bytes: control archive= 1746 bytes. 1809 bytes, 38 lines control 1447 bytes, 18 lines md5sums Package: r-base-core-dbg Source: r-base Version: 2.12.1-1~ppa1~maverick1 Architecture: amd64 Maintainer: Dirk Eddelbuettel Installed-Size: 8452 Depends: r-base-core (= 2.12.1-1~ppa1~maverick1), r-base-dev (= 2.12.1-1~ppa1~maverick1) Section: debug Priority: extra Homepage: http://www.r-project.org/ Description: GNU R debug symbols for statistical comp. language and environment R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, over thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'. . This package contains debugging symbol tables for the binaries and dynamic libraries in the r-base-core package. chroot-autobuild/build/buildd/r-base-core_2.12.1-1~ppa1~maverick1_amd64.deb: drwxr-xr-x root/root 0 2011-01-14 03:42 ./ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/help/ -rw-r--r-- root/root 1714385 2011-01-14 03:40 ./usr/lib/R/library/base/help/base.rdb -rw-r--r-- root/root 10609 2011-01-14 03:40 ./usr/lib/R/library/base/help/aliases.rds -rw-r--r-- root/root 8477 2011-01-14 03:40 ./usr/lib/R/library/base/help/base.rdx -rw-r--r-- root/root 2869 2011-01-14 03:40 ./usr/lib/R/library/base/help/paths.rds -rw-r--r-- root/root 29459 2011-01-14 03:40 ./usr/lib/R/library/base/help/AnIndex -rw-r--r-- root/root 1046 2011-01-14 03:40 ./usr/lib/R/library/base/CITATION drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/demo/ -rw-r--r-- root/root 4135 2011-01-14 03:40 ./usr/lib/R/library/base/demo/is.things.R -rw-r--r-- root/root 2072 2011-01-14 03:40 ./usr/lib/R/library/base/demo/recursion.R -rw-r--r-- root/root 1519 2011-01-14 03:40 ./usr/lib/R/library/base/demo/scoping.R drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/R/ -rw-r--r-- root/root 2885 2011-01-14 03:40 ./usr/lib/R/library/base/R/base -rw-r--r-- root/root 289887 2011-01-14 03:40 ./usr/lib/R/library/base/R/base.rdb -rw-r--r-- root/root 4782 2011-01-14 03:40 ./usr/lib/R/library/base/R/Rprofile -rw-r--r-- root/root 11841 2011-01-14 03:40 ./usr/lib/R/library/base/R/base.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/Meta/ -rw-r--r-- root/root 11423 2011-01-14 03:40 ./usr/lib/R/library/base/Meta/links.rds -rw-r--r-- root/root 19539 2011-01-14 03:40 ./usr/lib/R/library/base/Meta/Rd.rds -rw-r--r-- root/root 20136 2011-01-14 03:40 ./usr/lib/R/library/base/Meta/hsearch.rds -rw-r--r-- root/root 212 2011-01-14 03:40 ./usr/lib/R/library/base/Meta/demo.rds -rw-r--r-- root/root 466 2011-01-14 03:40 ./usr/lib/R/library/base/Meta/package.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 51626 2011-01-14 03:40 ./usr/lib/R/library/base/po/ru/LC_MESSAGES/R-base.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/it/LC_MESSAGES/ -rw-r--r-- root/root 33353 2011-01-14 03:40 ./usr/lib/R/library/base/po/it/LC_MESSAGES/R-base.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 61948 2011-01-14 03:40 ./usr/lib/R/library/base/po/ja/LC_MESSAGES/R-base.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 48010 2011-01-14 03:40 ./usr/lib/R/library/base/po/zh_CN/LC_MESSAGES/R-base.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 50819 2011-01-14 03:40 ./usr/lib/R/library/base/po/en@quot/LC_MESSAGES/R-base.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 54889 2011-01-14 03:40 ./usr/lib/R/library/base/po/fr/LC_MESSAGES/R-base.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/de/LC_MESSAGES/ -rw-r--r-- root/root 52142 2011-01-14 03:40 ./usr/lib/R/library/base/po/de/LC_MESSAGES/R-base.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 34201 2011-01-14 03:40 ./usr/lib/R/library/base/po/pt_BR/LC_MESSAGES/R-base.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/base/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 38333 2011-01-14 03:40 ./usr/lib/R/library/base/po/ko/LC_MESSAGES/R-base.mo -rw-r--r-- root/root 21948 2011-01-14 03:40 ./usr/lib/R/library/base/INDEX -rw-r--r-- root/root 282 2011-01-14 03:40 ./usr/lib/R/library/base/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/ -rw-r--r-- root/root 2091 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/TeXtext.enc -rw-r--r-- root/root 2311 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/WinAnsi.enc -rw-r--r-- root/root 2094 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/AdobeStd.enc -rw-r--r-- root/root 2308 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/KOI8-U.enc -rw-r--r-- root/root 2389 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/CP1251.enc -rw-r--r-- root/root 2514 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/AdobeSym.enc -rw-r--r-- root/root 2349 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/Cyrillic.enc -rw-r--r-- root/root 2207 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/PDFDoc.enc -rw-r--r-- root/root 2272 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/ISOLatin7.enc -rw-r--r-- root/root 2213 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/ISOLatin1.enc -rw-r--r-- root/root 2224 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/CP1250.enc -rw-r--r-- root/root 2212 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/Greek.enc -rw-r--r-- root/root 2196 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/ISOLatin9.enc -rw-r--r-- root/root 2187 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/ISOLatin2.enc -rw-r--r-- root/root 2290 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/KOI8-R.enc -rw-r--r-- root/root 2185 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/CP1253.enc -rw-r--r-- root/root 2262 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/MacRoman.enc -rw-r--r-- root/root 2247 2011-01-14 03:40 ./usr/lib/R/library/grDevices/enc/CP1257.enc drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/help/ -rw-r--r-- root/root 1475 2011-01-14 03:40 ./usr/lib/R/library/grDevices/help/grDevices.rdx -rw-r--r-- root/root 1182 2011-01-14 03:40 ./usr/lib/R/library/grDevices/help/aliases.rds -rw-r--r-- root/root 588 2011-01-14 03:40 ./usr/lib/R/library/grDevices/help/paths.rds -rw-r--r-- root/root 2708 2011-01-14 03:40 ./usr/lib/R/library/grDevices/help/AnIndex -rw-r--r-- root/root 290142 2011-01-14 03:40 ./usr/lib/R/library/grDevices/help/grDevices.rdb drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/R/ -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/grDevices/R/grDevices -rw-r--r-- root/root 2235 2011-01-14 03:40 ./usr/lib/R/library/grDevices/R/grDevices.rdx -rw-r--r-- root/root 64465 2011-01-14 03:40 ./usr/lib/R/library/grDevices/R/grDevices.rdb drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/Meta/ -rw-r--r-- root/root 1402 2011-01-14 03:40 ./usr/lib/R/library/grDevices/Meta/links.rds -rw-r--r-- root/root 2873 2011-01-14 03:40 ./usr/lib/R/library/grDevices/Meta/Rd.rds -rw-r--r-- root/root 2829 2011-01-14 03:40 ./usr/lib/R/library/grDevices/Meta/hsearch.rds -rw-r--r-- root/root 523 2011-01-14 03:40 ./usr/lib/R/library/grDevices/Meta/package.rds -rw-r--r-- root/root 1094 2011-01-14 03:40 ./usr/lib/R/library/grDevices/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/ -rw-r--r-- root/root 69269 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Helvetica-Bold.afm -rw-r--r-- root/root 17086 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/hvnb____.afm -rw-r--r-- root/root 15662 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/pob_____.afm -rw-r--r-- root/root 15352 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/cob_____.afm -rw-r--r-- root/root 42749 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/a010015l.afm -rw-r--r-- root/root 43205 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/c059033l.afm -rw-r--r-- root/root 17230 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/hvbo____.afm -rw-r--r-- root/root 17839 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/hv______.afm -rw-r--r-- root/root 17983 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/tib_____.afm -rw-r--r-- root/root 17241 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/agw_____.afm -rw-r--r-- root/root 42708 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/a010033l.afm -rw-r--r-- root/root 74292 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Helvetica.afm -rw-r--r-- root/root 15441 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Courier-Oblique.afm -rw-r--r-- root/root 69365 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Helvetica-BoldOblique.afm -rw-r--r-- root/root 42852 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n019064l.afm -rw-r--r-- root/root 15733 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/poi_____.afm -rw-r--r-- root/root 26866 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n022024l.afm -rw-r--r-- root/root 17781 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/hvn_____.afm -rw-r--r-- root/root 42851 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/c059016l.afm -rw-r--r-- root/root 26742 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n022004l.afm -rw-r--r-- root/root 10040 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/CM_boldx_10.afm -rw-r--r-- root/root 42833 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/a010013l.afm -rw-r--r-- root/root 851 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/README -rw-r--r-- root/root 42632 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/b018015l.afm -rw-r--r-- root/root 42593 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n019004l.afm -rw-r--r-- root/root 43017 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/c059036l.afm -rw-r--r-- root/root 43346 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n021003l.afm -rw-r--r-- root/root 18068 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/tii_____.afm -rw-r--r-- root/root 15278 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/bkdi____.afm -rw-r--r-- root/root 42680 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n019043l.afm -rw-r--r-- root/root 15422 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/cobo____.afm -rw-r--r-- root/root 10074 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/CM_boldx_italic_10.afm -rw-r--r-- root/root 17919 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/hvo_____.afm -rw-r--r-- root/root 15157 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/bkd_____.afm -rw-r--r-- root/root 15339 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/com_____.afm -rw-r--r-- root/root 17195 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/hvnbo___.afm -rw-r--r-- root/root 10050 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/CM_italic_10.afm -rw-r--r-- root/root 43493 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n019023l.afm -rw-r--r-- root/root 42911 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n019063l.afm -rw-r--r-- root/root 15752 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/por_____.afm -rw-r--r-- root/root 17155 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/hvb_____.afm -rw-r--r-- root/root 43396 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/b018032l.afm -rw-r--r-- root/root 17183 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/agd_____.afm -rw-r--r-- root/root 42730 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/p052024l.afm -rw-r--r-- root/root 17255 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/agdo____.afm -rw-r--r-- root/root 43083 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/b018035l.afm -rw-r--r-- root/root 6623 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/CM_symbol_10.afm -rw-r--r-- root/root 43161 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n021004l.afm -rw-r--r-- root/root 9527 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/ZapfDingbats.afm -rw-r--r-- root/root 74392 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Helvetica-Oblique.afm -rw-r--r-- root/root 9686 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/s050000l.afm -rw-r--r-- root/root 43033 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/c059013l.afm -rw-r--r-- root/root 15181 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/bkli____.afm -rw-r--r-- root/root 59642 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Times-BoldItalic.afm -rw-r--r-- root/root 15333 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Courier-Bold.afm -rw-r--r-- root/root 16028 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/ncb_____.afm -rw-r--r-- root/root 17877 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/hvno____.afm -rw-r--r-- root/root 936 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/MustRead.html -rw-r--r-- root/root 26903 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n022023l.afm -rw-r--r-- root/root 16665 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/ncr_____.afm -rw-r--r-- root/root 15335 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Courier.afm -rw-r--r-- root/root 66328 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Times-Italic.afm -rw-r--r-- root/root 17346 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/agwo____.afm -rw-r--r-- root/root 43497 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/p052003l.afm -rw-r--r-- root/root 42882 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n019003l.afm -rw-r--r-- root/root 8879 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/cmbxti10.afm -rw-r--r-- root/root 60460 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Times-Roman.afm -rw-r--r-- root/root 42970 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/b018012l.afm -rw-r--r-- root/root 16920 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/nci_____.afm -rw-r--r-- root/root 15399 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Courier-BoldOblique.afm -rw-r--r-- root/root 9644 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/sy______.afm -rw-r--r-- root/root 42967 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/a010035l.afm -rw-r--r-- root/root 43225 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/p052004l.afm -rw-r--r-- root/root 9740 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Symbol.afm -rw-r--r-- root/root 17942 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/tir_____.afm -rw-r--r-- root/root 15000 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/bkl_____.afm -rw-r--r-- root/root 43482 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/p052023l.afm -rw-r--r-- root/root 43339 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n021023l.afm -rw-r--r-- root/root 8866 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/cmti10.afm -rw-r--r-- root/root 26723 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n022003l.afm -rw-r--r-- root/root 64251 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/Times-Bold.afm -rw-r--r-- root/root 15810 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/pobi____.afm -rw-r--r-- root/root 43405 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n021024l.afm -rw-r--r-- root/root 10028 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/CM_regular_10.afm -rw-r--r-- root/root 18070 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/tibi____.afm -rw-r--r-- root/root 42381 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n019044l.afm -rw-r--r-- root/root 15443 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/coo_____.afm -rw-r--r-- root/root 43133 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/n019024l.afm -rw-r--r-- root/root 17496 2011-01-14 03:40 ./usr/lib/R/library/grDevices/afm/ncbi____.afm drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 11971 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ru/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 13939 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ru/LC_MESSAGES/grDevices.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/it/LC_MESSAGES/ -rw-r--r-- root/root 7443 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/it/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 8644 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/it/LC_MESSAGES/grDevices.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/en_GB/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/en_GB/LC_MESSAGES/ -rw-r--r-- root/root 495 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/en_GB/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 968 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/en_GB/LC_MESSAGES/grDevices.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 14264 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ja/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 17851 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ja/LC_MESSAGES/grDevices.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 11110 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/zh_CN/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 13364 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/zh_CN/LC_MESSAGES/grDevices.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 11709 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/en@quot/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 14069 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/en@quot/LC_MESSAGES/grDevices.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 12882 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/fr/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 15636 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/fr/LC_MESSAGES/grDevices.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/de/LC_MESSAGES/ -rw-r--r-- root/root 12322 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/de/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 15127 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/de/LC_MESSAGES/grDevices.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 7921 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ko/LC_MESSAGES/R-grDevices.mo -rw-r--r-- root/root 7817 2011-01-14 03:40 ./usr/lib/R/library/grDevices/po/ko/LC_MESSAGES/grDevices.mo -rw-r--r-- root/root 2815 2011-01-14 03:40 ./usr/lib/R/library/grDevices/NAMESPACE -rw-r--r-- root/root 3533 2011-01-14 03:40 ./usr/lib/R/library/grDevices/INDEX -rw-r--r-- root/root 383 2011-01-14 03:40 ./usr/lib/R/library/grDevices/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/library/grDevices/libs/ -rw-r--r-- root/root 158616 2011-01-14 03:42 ./usr/lib/R/library/grDevices/libs/grDevices.so drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/help/ -rw-r--r-- root/root 31300 2011-01-14 03:40 ./usr/lib/R/library/stats4/help/stats4.rdb -rw-r--r-- root/root 373 2011-01-14 03:40 ./usr/lib/R/library/stats4/help/aliases.rds -rw-r--r-- root/root 230 2011-01-14 03:40 ./usr/lib/R/library/stats4/help/paths.rds -rw-r--r-- root/root 1194 2011-01-14 03:40 ./usr/lib/R/library/stats4/help/AnIndex -rw-r--r-- root/root 492 2011-01-14 03:40 ./usr/lib/R/library/stats4/help/stats4.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/R/ -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/stats4/R/stats4 -rw-r--r-- root/root 54253 2011-01-14 03:40 ./usr/lib/R/library/stats4/R/stats4.rdb -rw-r--r-- root/root 976 2011-01-14 03:40 ./usr/lib/R/library/stats4/R/stats4.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/Meta/ -rw-r--r-- root/root 453 2011-01-14 03:40 ./usr/lib/R/library/stats4/Meta/links.rds -rw-r--r-- root/root 860 2011-01-14 03:40 ./usr/lib/R/library/stats4/Meta/Rd.rds -rw-r--r-- root/root 880 2011-01-14 03:40 ./usr/lib/R/library/stats4/Meta/hsearch.rds -rw-r--r-- root/root 561 2011-01-14 03:40 ./usr/lib/R/library/stats4/Meta/package.rds -rw-r--r-- root/root 312 2011-01-14 03:40 ./usr/lib/R/library/stats4/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 1444 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ru/LC_MESSAGES/R-stats4.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/it/LC_MESSAGES/ -rw-r--r-- root/root 1256 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/it/LC_MESSAGES/R-stats4.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 1464 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ja/LC_MESSAGES/R-stats4.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 1188 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/zh_CN/LC_MESSAGES/R-stats4.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 1195 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/en@quot/LC_MESSAGES/R-stats4.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 1382 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/fr/LC_MESSAGES/R-stats4.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/de/LC_MESSAGES/ -rw-r--r-- root/root 1283 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/de/LC_MESSAGES/R-stats4.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 1332 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/pt_BR/LC_MESSAGES/R-stats4.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 1396 2011-01-14 03:40 ./usr/lib/R/library/stats4/po/ko/LC_MESSAGES/R-stats4.mo -rw-r--r-- root/root 549 2011-01-14 03:40 ./usr/lib/R/library/stats4/NAMESPACE -rw-r--r-- root/root 1301 2011-01-14 03:40 ./usr/lib/R/library/stats4/INDEX -rw-r--r-- root/root 374 2011-01-14 03:40 ./usr/lib/R/library/stats4/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/help/ -rw-r--r-- root/root 947 2011-01-14 03:40 ./usr/lib/R/library/graphics/help/aliases.rds -rw-r--r-- root/root 593 2011-01-14 03:40 ./usr/lib/R/library/graphics/help/paths.rds -rw-r--r-- root/root 423112 2011-01-14 03:40 ./usr/lib/R/library/graphics/help/graphics.rdb -rw-r--r-- root/root 2326 2011-01-14 03:40 ./usr/lib/R/library/graphics/help/AnIndex -rw-r--r-- root/root 1619 2011-01-14 03:40 ./usr/lib/R/library/graphics/help/graphics.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/demo/ -rw-r--r-- root/root 19928 2011-01-14 03:40 ./usr/lib/R/library/graphics/demo/Hershey.R -rw-r--r-- root/root 8474 2011-01-14 03:40 ./usr/lib/R/library/graphics/demo/plotmath.R -rw-r--r-- root/root 2791 2011-01-14 03:40 ./usr/lib/R/library/graphics/demo/persp.R -rw-r--r-- root/root 34475 2011-01-14 03:40 ./usr/lib/R/library/graphics/demo/Japanese.R -rw-r--r-- root/root 4995 2011-01-14 03:40 ./usr/lib/R/library/graphics/demo/graphics.R -rw-r--r-- root/root 1061 2011-01-14 03:40 ./usr/lib/R/library/graphics/demo/image.R drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/R/ -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/graphics/R/graphics -rw-r--r-- root/root 84679 2011-01-14 03:40 ./usr/lib/R/library/graphics/R/graphics.rdb -rw-r--r-- root/root 1686 2011-01-14 03:40 ./usr/lib/R/library/graphics/R/graphics.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/Meta/ -rw-r--r-- root/root 1257 2011-01-14 03:40 ./usr/lib/R/library/graphics/Meta/links.rds -rw-r--r-- root/root 3128 2011-01-14 03:40 ./usr/lib/R/library/graphics/Meta/Rd.rds -rw-r--r-- root/root 3084 2011-01-14 03:40 ./usr/lib/R/library/graphics/Meta/hsearch.rds -rw-r--r-- root/root 261 2011-01-14 03:40 ./usr/lib/R/library/graphics/Meta/demo.rds -rw-r--r-- root/root 513 2011-01-14 03:40 ./usr/lib/R/library/graphics/Meta/package.rds -rw-r--r-- root/root 835 2011-01-14 03:40 ./usr/lib/R/library/graphics/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 13721 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ru/LC_MESSAGES/R-graphics.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/it/LC_MESSAGES/ -rw-r--r-- root/root 10494 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/it/LC_MESSAGES/R-graphics.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 16143 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ja/LC_MESSAGES/R-graphics.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 12780 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/zh_CN/LC_MESSAGES/R-graphics.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 13531 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/en@quot/LC_MESSAGES/R-graphics.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 14419 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/fr/LC_MESSAGES/R-graphics.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/de/LC_MESSAGES/ -rw-r--r-- root/root 14048 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/de/LC_MESSAGES/R-graphics.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 12235 2011-01-14 03:40 ./usr/lib/R/library/graphics/po/ko/LC_MESSAGES/R-graphics.mo -rw-r--r-- root/root 2074 2011-01-14 03:40 ./usr/lib/R/library/graphics/NAMESPACE -rw-r--r-- root/root 3728 2011-01-14 03:40 ./usr/lib/R/library/graphics/INDEX -rw-r--r-- root/root 322 2011-01-14 03:40 ./usr/lib/R/library/graphics/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/help/ -rw-r--r-- root/root 1267 2011-01-14 03:40 ./usr/lib/R/library/grid/help/aliases.rds -rw-r--r-- root/root 224662 2011-01-14 03:40 ./usr/lib/R/library/grid/help/grid.rdb -rw-r--r-- root/root 672 2011-01-14 03:40 ./usr/lib/R/library/grid/help/paths.rds -rw-r--r-- root/root 3896 2011-01-14 03:40 ./usr/lib/R/library/grid/help/AnIndex -rw-r--r-- root/root 1793 2011-01-14 03:40 ./usr/lib/R/library/grid/help/grid.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/R/ -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/grid/R/grid -rw-r--r-- root/root 149793 2011-01-14 03:40 ./usr/lib/R/library/grid/R/grid.rdb -rw-r--r-- root/root 7060 2011-01-14 03:40 ./usr/lib/R/library/grid/R/grid.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/ -rw-r--r-- root/root 3850 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/saveload.Snw -rw-r--r-- root/root 9698 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/displaylist.Snw -rw-r--r-- root/root 28669 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/grid.Snw -rw-r--r-- root/root 5705 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/frame.R -rw-r--r-- root/root 106363 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/viewports.pdf -rw-r--r-- root/root 1288 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/moveline.R -rw-r--r-- root/root 4355 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/nonfinite.Snw -rw-r--r-- root/root 49438 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/locndimn.pdf -rw-r--r-- root/root 11031 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/viewports.Snw -rw-r--r-- root/root 72031 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/grobs.pdf -rw-r--r-- root/root 49077 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/changes.txt -rw-r--r-- root/root 14706 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/grid.R -rw-r--r-- root/root 207 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/grid.bib -rw-r--r-- root/root 21367 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/plotexample.Snw -rw-r--r-- root/root 6243 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/sharing.R -rw-r--r-- root/root 86497 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/displaylist.pdf -rw-r--r-- root/root 11732 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/grobs.R -rw-r--r-- root/root 3953 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/interactive.R -rw-r--r-- root/root 2119 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/moveline.Snw -rw-r--r-- root/root 49320 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/interactive.pdf -rw-r--r-- root/root 4291 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/interactive.Snw -rw-r--r-- root/root 200364 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/grid.pdf -rw-r--r-- root/root 18763 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/grobs.Snw -rw-r--r-- root/root 5009 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/rotated.Snw -rw-r--r-- root/root 51120 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/moveline.pdf -rw-r--r-- root/root 169684 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/plotexample.pdf -rw-r--r-- root/root 12511 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/viewports.R -rw-r--r-- root/root 45091 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/nonfinite.pdf -rw-r--r-- root/root 67392 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/saveload.pdf -rw-r--r-- root/root 2517 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/nonfinite.R -rw-r--r-- root/root 1519 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/saveload.R -rw-r--r-- root/root 4391 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/locndimn.Snw -rw-r--r-- root/root 8489 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/rotated.R -rw-r--r-- root/root 2955 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/locndimn.R -rw-r--r-- root/root 19175 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/plotexample.R -rw-r--r-- root/root 16076 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/frame.Snw -rw-r--r-- root/root 45488 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/sharing.pdf -rw-r--r-- root/root 1212 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/index.html -rw-r--r-- root/root 5391 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/displaylist.R -rw-r--r-- root/root 102090 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/frame.pdf -rw-r--r-- root/root 2839 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/sharing.Snw -rw-r--r-- root/root 85483 2011-01-14 03:40 ./usr/lib/R/library/grid/doc/rotated.pdf drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/Meta/ -rw-r--r-- root/root 1603 2011-01-14 03:40 ./usr/lib/R/library/grid/Meta/links.rds -rw-r--r-- root/root 3008 2011-01-14 03:40 ./usr/lib/R/library/grid/Meta/Rd.rds -rw-r--r-- root/root 2932 2011-01-14 03:40 ./usr/lib/R/library/grid/Meta/hsearch.rds -rw-r--r-- root/root 676 2011-01-14 03:40 ./usr/lib/R/library/grid/Meta/vignette.rds -rw-r--r-- root/root 589 2011-01-14 03:40 ./usr/lib/R/library/grid/Meta/package.rds -rw-r--r-- root/root 1695 2011-01-14 03:40 ./usr/lib/R/library/grid/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 2419 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ru/LC_MESSAGES/grid.mo -rw-r--r-- root/root 16087 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ru/LC_MESSAGES/R-grid.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/it/LC_MESSAGES/ -rw-r--r-- root/root 1762 2011-01-14 03:40 ./usr/lib/R/library/grid/po/it/LC_MESSAGES/grid.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 2863 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ja/LC_MESSAGES/grid.mo -rw-r--r-- root/root 19362 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ja/LC_MESSAGES/R-grid.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 2320 2011-01-14 03:40 ./usr/lib/R/library/grid/po/zh_CN/LC_MESSAGES/grid.mo -rw-r--r-- root/root 15056 2011-01-14 03:40 ./usr/lib/R/library/grid/po/zh_CN/LC_MESSAGES/R-grid.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 2271 2011-01-14 03:40 ./usr/lib/R/library/grid/po/en@quot/LC_MESSAGES/grid.mo -rw-r--r-- root/root 15909 2011-01-14 03:40 ./usr/lib/R/library/grid/po/en@quot/LC_MESSAGES/R-grid.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 2515 2011-01-14 03:40 ./usr/lib/R/library/grid/po/fr/LC_MESSAGES/grid.mo -rw-r--r-- root/root 16731 2011-01-14 03:40 ./usr/lib/R/library/grid/po/fr/LC_MESSAGES/R-grid.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/de/LC_MESSAGES/ -rw-r--r-- root/root 2476 2011-01-14 03:40 ./usr/lib/R/library/grid/po/de/LC_MESSAGES/grid.mo -rw-r--r-- root/root 16544 2011-01-14 03:40 ./usr/lib/R/library/grid/po/de/LC_MESSAGES/R-grid.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 2382 2011-01-14 03:40 ./usr/lib/R/library/grid/po/pt_BR/LC_MESSAGES/grid.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 1929 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ko/LC_MESSAGES/grid.mo -rw-r--r-- root/root 16149 2011-01-14 03:40 ./usr/lib/R/library/grid/po/ko/LC_MESSAGES/R-grid.mo -rw-r--r-- root/root 10158 2011-01-14 03:40 ./usr/lib/R/library/grid/NAMESPACE -rw-r--r-- root/root 4431 2011-01-14 03:40 ./usr/lib/R/library/grid/INDEX -rw-r--r-- root/root 406 2011-01-14 03:40 ./usr/lib/R/library/grid/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/library/grid/libs/ -rw-r--r-- root/root 129840 2011-01-14 03:42 ./usr/lib/R/library/grid/libs/grid.so drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/help/ -rw-r--r-- root/root 449459 2011-01-14 03:40 ./usr/lib/R/library/methods/help/methods.rdb -rw-r--r-- root/root 1779 2011-01-14 03:40 ./usr/lib/R/library/methods/help/methods.rdx -rw-r--r-- root/root 3883 2011-01-14 03:40 ./usr/lib/R/library/methods/help/aliases.rds -rw-r--r-- root/root 748 2011-01-14 03:40 ./usr/lib/R/library/methods/help/paths.rds -rw-r--r-- root/root 13305 2011-01-14 03:40 ./usr/lib/R/library/methods/help/AnIndex drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/R/ -rw-r--r-- root/root 508597 2011-01-14 03:40 ./usr/lib/R/library/methods/R/methods.rdb -rw-r--r-- root/root 12498 2011-01-14 03:40 ./usr/lib/R/library/methods/R/methods.rdx -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/methods/R/methods drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/Meta/ -rw-r--r-- root/root 3780 2011-01-14 03:40 ./usr/lib/R/library/methods/Meta/links.rds -rw-r--r-- root/root 5355 2011-01-14 03:40 ./usr/lib/R/library/methods/Meta/Rd.rds -rw-r--r-- root/root 5384 2011-01-14 03:40 ./usr/lib/R/library/methods/Meta/hsearch.rds -rw-r--r-- root/root 637 2011-01-14 03:40 ./usr/lib/R/library/methods/Meta/package.rds -rw-r--r-- root/root 1607 2011-01-14 03:40 ./usr/lib/R/library/methods/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 64000 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ru/LC_MESSAGES/R-methods.mo -rw-r--r-- root/root 5986 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ru/LC_MESSAGES/methods.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 76654 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ja/LC_MESSAGES/R-methods.mo -rw-r--r-- root/root 7089 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ja/LC_MESSAGES/methods.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 58231 2011-01-14 03:40 ./usr/lib/R/library/methods/po/zh_CN/LC_MESSAGES/R-methods.mo -rw-r--r-- root/root 5567 2011-01-14 03:40 ./usr/lib/R/library/methods/po/zh_CN/LC_MESSAGES/methods.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 64185 2011-01-14 03:40 ./usr/lib/R/library/methods/po/en@quot/LC_MESSAGES/R-methods.mo -rw-r--r-- root/root 5899 2011-01-14 03:40 ./usr/lib/R/library/methods/po/en@quot/LC_MESSAGES/methods.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 69549 2011-01-14 03:40 ./usr/lib/R/library/methods/po/fr/LC_MESSAGES/R-methods.mo -rw-r--r-- root/root 6620 2011-01-14 03:40 ./usr/lib/R/library/methods/po/fr/LC_MESSAGES/methods.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/de/LC_MESSAGES/ -rw-r--r-- root/root 64537 2011-01-14 03:40 ./usr/lib/R/library/methods/po/de/LC_MESSAGES/R-methods.mo -rw-r--r-- root/root 6197 2011-01-14 03:40 ./usr/lib/R/library/methods/po/de/LC_MESSAGES/methods.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 11605 2011-01-14 03:40 ./usr/lib/R/library/methods/po/pt_BR/LC_MESSAGES/R-methods.mo -rw-r--r-- root/root 5164 2011-01-14 03:40 ./usr/lib/R/library/methods/po/pt_BR/LC_MESSAGES/methods.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 24592 2011-01-14 03:40 ./usr/lib/R/library/methods/po/ko/LC_MESSAGES/R-methods.mo -rw-r--r-- root/root 4955 2011-01-14 03:40 ./usr/lib/R/library/methods/NAMESPACE -rw-r--r-- root/root 4426 2011-01-14 03:40 ./usr/lib/R/library/methods/INDEX -rw-r--r-- root/root 512 2011-01-14 03:40 ./usr/lib/R/library/methods/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/library/methods/libs/ -rw-r--r-- root/root 31136 2011-01-14 03:42 ./usr/lib/R/library/methods/libs/methods.so drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/help/ -rw-r--r-- root/root 35344 2011-01-14 03:40 ./usr/lib/R/library/splines/help/splines.rdb -rw-r--r-- root/root 230 2011-01-14 03:40 ./usr/lib/R/library/splines/help/aliases.rds -rw-r--r-- root/root 445 2011-01-14 03:40 ./usr/lib/R/library/splines/help/splines.rdx -rw-r--r-- root/root 216 2011-01-14 03:40 ./usr/lib/R/library/splines/help/paths.rds -rw-r--r-- root/root 541 2011-01-14 03:40 ./usr/lib/R/library/splines/help/AnIndex drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/R/ -rw-r--r-- root/root 16087 2011-01-14 03:40 ./usr/lib/R/library/splines/R/splines.rdb -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/splines/R/splines -rw-r--r-- root/root 780 2011-01-14 03:40 ./usr/lib/R/library/splines/R/splines.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/Meta/ -rw-r--r-- root/root 320 2011-01-14 03:40 ./usr/lib/R/library/splines/Meta/links.rds -rw-r--r-- root/root 731 2011-01-14 03:40 ./usr/lib/R/library/splines/Meta/Rd.rds -rw-r--r-- root/root 726 2011-01-14 03:40 ./usr/lib/R/library/splines/Meta/hsearch.rds -rw-r--r-- root/root 582 2011-01-14 03:40 ./usr/lib/R/library/splines/Meta/package.rds -rw-r--r-- root/root 471 2011-01-14 03:40 ./usr/lib/R/library/splines/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 591 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ru/LC_MESSAGES/splines.mo -rw-r--r-- root/root 2564 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ru/LC_MESSAGES/R-splines.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 516 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ja/LC_MESSAGES/splines.mo -rw-r--r-- root/root 2933 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ja/LC_MESSAGES/R-splines.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 485 2011-01-14 03:40 ./usr/lib/R/library/splines/po/zh_CN/LC_MESSAGES/splines.mo -rw-r--r-- root/root 2281 2011-01-14 03:40 ./usr/lib/R/library/splines/po/zh_CN/LC_MESSAGES/R-splines.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 497 2011-01-14 03:40 ./usr/lib/R/library/splines/po/en@quot/LC_MESSAGES/splines.mo -rw-r--r-- root/root 2403 2011-01-14 03:40 ./usr/lib/R/library/splines/po/en@quot/LC_MESSAGES/R-splines.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 569 2011-01-14 03:40 ./usr/lib/R/library/splines/po/fr/LC_MESSAGES/splines.mo -rw-r--r-- root/root 2596 2011-01-14 03:40 ./usr/lib/R/library/splines/po/fr/LC_MESSAGES/R-splines.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/de/LC_MESSAGES/ -rw-r--r-- root/root 548 2011-01-14 03:40 ./usr/lib/R/library/splines/po/de/LC_MESSAGES/splines.mo -rw-r--r-- root/root 2511 2011-01-14 03:40 ./usr/lib/R/library/splines/po/de/LC_MESSAGES/R-splines.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 571 2011-01-14 03:40 ./usr/lib/R/library/splines/po/pt_BR/LC_MESSAGES/splines.mo -rw-r--r-- root/root 2548 2011-01-14 03:40 ./usr/lib/R/library/splines/po/pt_BR/LC_MESSAGES/R-splines.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 552 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ko/LC_MESSAGES/splines.mo -rw-r--r-- root/root 2929 2011-01-14 03:40 ./usr/lib/R/library/splines/po/ko/LC_MESSAGES/R-splines.mo -rw-r--r-- root/root 1358 2011-01-14 03:40 ./usr/lib/R/library/splines/NAMESPACE -rw-r--r-- root/root 832 2011-01-14 03:40 ./usr/lib/R/library/splines/INDEX -rw-r--r-- root/root 418 2011-01-14 03:40 ./usr/lib/R/library/splines/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/library/splines/libs/ -rw-r--r-- root/root 10320 2011-01-14 03:42 ./usr/lib/R/library/splines/libs/splines.so drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/help/ -rw-r--r-- root/root 1227 2011-01-14 03:40 ./usr/lib/R/library/tools/help/tools.rdx -rw-r--r-- root/root 914 2011-01-14 03:40 ./usr/lib/R/library/tools/help/aliases.rds -rw-r--r-- root/root 139381 2011-01-14 03:40 ./usr/lib/R/library/tools/help/tools.rdb -rw-r--r-- root/root 542 2011-01-14 03:40 ./usr/lib/R/library/tools/help/paths.rds -rw-r--r-- root/root 2104 2011-01-14 03:40 ./usr/lib/R/library/tools/help/AnIndex drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/R/ -rw-r--r-- root/root 6272 2011-01-14 03:40 ./usr/lib/R/library/tools/R/tools.rdx -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/tools/R/tools -rw-r--r-- root/root 342200 2011-01-14 03:40 ./usr/lib/R/library/tools/R/tools.rdb drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/Meta/ -rw-r--r-- root/root 1134 2011-01-14 03:40 ./usr/lib/R/library/tools/Meta/links.rds -rw-r--r-- root/root 2281 2011-01-14 03:40 ./usr/lib/R/library/tools/Meta/Rd.rds -rw-r--r-- root/root 2237 2011-01-14 03:40 ./usr/lib/R/library/tools/Meta/hsearch.rds -rw-r--r-- root/root 492 2011-01-14 03:40 ./usr/lib/R/library/tools/Meta/package.rds -rw-r--r-- root/root 1059 2011-01-14 03:40 ./usr/lib/R/library/tools/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 850 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ru/LC_MESSAGES/tools.mo -rw-r--r-- root/root 31642 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ru/LC_MESSAGES/R-tools.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/it/LC_MESSAGES/ -rw-r--r-- root/root 648 2011-01-14 03:40 ./usr/lib/R/library/tools/po/it/LC_MESSAGES/tools.mo -rw-r--r-- root/root 5832 2011-01-14 03:40 ./usr/lib/R/library/tools/po/it/LC_MESSAGES/R-tools.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 805 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ja/LC_MESSAGES/tools.mo -rw-r--r-- root/root 38194 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ja/LC_MESSAGES/R-tools.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 669 2011-01-14 03:40 ./usr/lib/R/library/tools/po/zh_CN/LC_MESSAGES/tools.mo -rw-r--r-- root/root 29758 2011-01-14 03:40 ./usr/lib/R/library/tools/po/zh_CN/LC_MESSAGES/R-tools.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 681 2011-01-14 03:40 ./usr/lib/R/library/tools/po/en@quot/LC_MESSAGES/tools.mo -rw-r--r-- root/root 31363 2011-01-14 03:40 ./usr/lib/R/library/tools/po/en@quot/LC_MESSAGES/R-tools.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 795 2011-01-14 03:40 ./usr/lib/R/library/tools/po/fr/LC_MESSAGES/tools.mo -rw-r--r-- root/root 33473 2011-01-14 03:40 ./usr/lib/R/library/tools/po/fr/LC_MESSAGES/R-tools.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/de/LC_MESSAGES/ -rw-r--r-- root/root 742 2011-01-14 03:40 ./usr/lib/R/library/tools/po/de/LC_MESSAGES/tools.mo -rw-r--r-- root/root 32465 2011-01-14 03:40 ./usr/lib/R/library/tools/po/de/LC_MESSAGES/R-tools.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 715 2011-01-14 03:40 ./usr/lib/R/library/tools/po/pt_BR/LC_MESSAGES/tools.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 714 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ko/LC_MESSAGES/tools.mo -rw-r--r-- root/root 6667 2011-01-14 03:40 ./usr/lib/R/library/tools/po/ko/LC_MESSAGES/R-tools.mo -rw-r--r-- root/root 2628 2011-01-14 03:40 ./usr/lib/R/library/tools/NAMESPACE -rw-r--r-- root/root 2660 2011-01-14 03:40 ./usr/lib/R/library/tools/INDEX -rw-r--r-- root/root 341 2011-01-14 03:40 ./usr/lib/R/library/tools/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/library/tools/libs/ -rw-r--r-- root/root 18712 2011-01-14 03:42 ./usr/lib/R/library/tools/libs/tools.so drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/datasets/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/datasets/help/ -rw-r--r-- root/root 890 2011-01-14 03:40 ./usr/lib/R/library/datasets/help/aliases.rds -rw-r--r-- root/root 182295 2011-01-14 03:40 ./usr/lib/R/library/datasets/help/datasets.rdb -rw-r--r-- root/root 802 2011-01-14 03:40 ./usr/lib/R/library/datasets/help/paths.rds -rw-r--r-- root/root 2009 2011-01-14 03:40 ./usr/lib/R/library/datasets/help/AnIndex -rw-r--r-- root/root 2012 2011-01-14 03:40 ./usr/lib/R/library/datasets/help/datasets.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/datasets/R/ -rw-r--r-- root/root 805 2011-01-14 03:40 ./usr/lib/R/library/datasets/R/datasets drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/datasets/Meta/ -rw-r--r-- root/root 1333 2011-01-14 03:40 ./usr/lib/R/library/datasets/Meta/links.rds -rw-r--r-- root/root 3580 2011-01-14 03:40 ./usr/lib/R/library/datasets/Meta/Rd.rds -rw-r--r-- root/root 3193 2011-01-14 03:40 ./usr/lib/R/library/datasets/Meta/hsearch.rds -rw-r--r-- root/root 468 2011-01-14 03:40 ./usr/lib/R/library/datasets/Meta/package.rds -rw-r--r-- root/root 2646 2011-01-14 03:40 ./usr/lib/R/library/datasets/Meta/data.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/datasets/html/ -rw-r--r-- root/root 5547 2011-01-14 03:40 ./usr/lib/R/library/datasets/INDEX drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/datasets/data/ -rw-r--r-- root/root 111860 2011-01-14 03:40 ./usr/lib/R/library/datasets/data/Rdata.rdb -rw-r--r-- root/root 1507 2011-01-14 03:40 ./usr/lib/R/library/datasets/data/Rdata.rdx -rw-r--r-- root/root 1048 2011-01-14 03:40 ./usr/lib/R/library/datasets/data/Rdata.rds -rw-r--r-- root/root 2122 2011-01-14 03:40 ./usr/lib/R/library/datasets/data/morley.tab -rw-r--r-- root/root 289 2011-01-14 03:40 ./usr/lib/R/library/datasets/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/help/ -rw-r--r-- root/root 496196 2011-01-14 03:40 ./usr/lib/R/library/utils/help/utils.rdb -rw-r--r-- root/root 2825 2011-01-14 03:40 ./usr/lib/R/library/utils/help/utils.rdx -rw-r--r-- root/root 2236 2011-01-14 03:40 ./usr/lib/R/library/utils/help/aliases.rds -rw-r--r-- root/root 1113 2011-01-14 03:40 ./usr/lib/R/library/utils/help/paths.rds -rw-r--r-- root/root 5982 2011-01-14 03:40 ./usr/lib/R/library/utils/help/AnIndex drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/R/ -rw-r--r-- root/root 218390 2011-01-14 03:40 ./usr/lib/R/library/utils/R/utils.rdb -rw-r--r-- root/root 5153 2011-01-14 03:40 ./usr/lib/R/library/utils/R/utils.rdx -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/utils/R/utils drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/Meta/ -rw-r--r-- root/root 2717 2011-01-14 03:40 ./usr/lib/R/library/utils/Meta/links.rds -rw-r--r-- root/root 5401 2011-01-14 03:40 ./usr/lib/R/library/utils/Meta/Rd.rds -rw-r--r-- root/root 5218 2011-01-14 03:40 ./usr/lib/R/library/utils/Meta/hsearch.rds -rw-r--r-- root/root 474 2011-01-14 03:40 ./usr/lib/R/library/utils/Meta/package.rds -rw-r--r-- root/root 1846 2011-01-14 03:40 ./usr/lib/R/library/utils/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 34582 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ru/LC_MESSAGES/R-utils.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 41670 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ja/LC_MESSAGES/R-utils.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 32875 2011-01-14 03:40 ./usr/lib/R/library/utils/po/zh_CN/LC_MESSAGES/R-utils.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 34407 2011-01-14 03:40 ./usr/lib/R/library/utils/po/en@quot/LC_MESSAGES/R-utils.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 36754 2011-01-14 03:40 ./usr/lib/R/library/utils/po/fr/LC_MESSAGES/R-utils.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/de/LC_MESSAGES/ -rw-r--r-- root/root 35276 2011-01-14 03:40 ./usr/lib/R/library/utils/po/de/LC_MESSAGES/R-utils.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 18814 2011-01-14 03:40 ./usr/lib/R/library/utils/po/ko/LC_MESSAGES/R-utils.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/misc/ -rw-r--r-- root/root 242 2011-01-14 03:40 ./usr/lib/R/library/utils/misc/exDIF.dif -rw-r--r-- root/root 38 2011-01-14 03:40 ./usr/lib/R/library/utils/misc/exDIF.csv -rw-r--r-- root/root 5719 2011-01-14 03:40 ./usr/lib/R/library/utils/NAMESPACE -rw-r--r-- root/root 6997 2011-01-14 03:40 ./usr/lib/R/library/utils/INDEX -rw-r--r-- root/root 287 2011-01-14 03:40 ./usr/lib/R/library/utils/DESCRIPTION -rw-r--r-- root/root 13474 2011-01-14 03:40 ./usr/lib/R/library/utils/iconvlist drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/utils/Sweave/ -rw-r--r-- root/root 1550 2011-01-14 03:40 ./usr/lib/R/library/utils/Sweave/Sweave-test-1.Rnw drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/ -rw-r--r-- root/root 550 2011-01-14 03:40 ./usr/lib/R/library/stats/SOURCES.ts -rw-r--r-- root/root 1538 2011-01-14 03:40 ./usr/lib/R/library/stats/COPYRIGHTS.modreg drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/help/ -rw-r--r-- root/root 5275 2011-01-14 03:40 ./usr/lib/R/library/stats/help/aliases.rds -rw-r--r-- root/root 6486 2011-01-14 03:40 ./usr/lib/R/library/stats/help/stats.rdx -rw-r--r-- root/root 2280 2011-01-14 03:40 ./usr/lib/R/library/stats/help/paths.rds -rw-r--r-- root/root 15996 2011-01-14 03:40 ./usr/lib/R/library/stats/help/AnIndex -rw-r--r-- root/root 1343084 2011-01-14 03:40 ./usr/lib/R/library/stats/help/stats.rdb drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/demo/ -rw-r--r-- root/root 2462 2011-01-14 03:40 ./usr/lib/R/library/stats/demo/nlm.R -rw-r--r-- root/root 4916 2011-01-14 03:40 ./usr/lib/R/library/stats/demo/lm.glm.R -rw-r--r-- root/root 700 2011-01-14 03:40 ./usr/lib/R/library/stats/demo/glm.vr.R -rw-r--r-- root/root 1239 2011-01-14 03:40 ./usr/lib/R/library/stats/demo/smooth.R drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/R/ -rw-r--r-- root/root 9957 2011-01-14 03:40 ./usr/lib/R/library/stats/R/stats.rdx -rw-r--r-- root/root 461492 2011-01-14 03:40 ./usr/lib/R/library/stats/R/stats.rdb -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/stats/R/stats drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/Meta/ -rw-r--r-- root/root 6328 2011-01-14 03:40 ./usr/lib/R/library/stats/Meta/links.rds -rw-r--r-- root/root 12614 2011-01-14 03:40 ./usr/lib/R/library/stats/Meta/Rd.rds -rw-r--r-- root/root 12687 2011-01-14 03:40 ./usr/lib/R/library/stats/Meta/hsearch.rds -rw-r--r-- root/root 265 2011-01-14 03:40 ./usr/lib/R/library/stats/Meta/demo.rds -rw-r--r-- root/root 495 2011-01-14 03:40 ./usr/lib/R/library/stats/Meta/package.rds -rw-r--r-- root/root 4188 2011-01-14 03:40 ./usr/lib/R/library/stats/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 6674 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ru/LC_MESSAGES/stats.mo -rw-r--r-- root/root 80073 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ru/LC_MESSAGES/R-stats.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/it/LC_MESSAGES/ -rw-r--r-- root/root 3184 2011-01-14 03:40 ./usr/lib/R/library/stats/po/it/LC_MESSAGES/stats.mo -rw-r--r-- root/root 62149 2011-01-14 03:40 ./usr/lib/R/library/stats/po/it/LC_MESSAGES/R-stats.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 7588 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ja/LC_MESSAGES/stats.mo -rw-r--r-- root/root 93885 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ja/LC_MESSAGES/R-stats.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 6098 2011-01-14 03:40 ./usr/lib/R/library/stats/po/zh_CN/LC_MESSAGES/stats.mo -rw-r--r-- root/root 73466 2011-01-14 03:40 ./usr/lib/R/library/stats/po/zh_CN/LC_MESSAGES/R-stats.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 6323 2011-01-14 03:40 ./usr/lib/R/library/stats/po/en@quot/LC_MESSAGES/stats.mo -rw-r--r-- root/root 78383 2011-01-14 03:40 ./usr/lib/R/library/stats/po/en@quot/LC_MESSAGES/R-stats.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 6790 2011-01-14 03:40 ./usr/lib/R/library/stats/po/fr/LC_MESSAGES/stats.mo -rw-r--r-- root/root 83440 2011-01-14 03:40 ./usr/lib/R/library/stats/po/fr/LC_MESSAGES/R-stats.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/de/LC_MESSAGES/ -rw-r--r-- root/root 6651 2011-01-14 03:40 ./usr/lib/R/library/stats/po/de/LC_MESSAGES/stats.mo -rw-r--r-- root/root 80830 2011-01-14 03:40 ./usr/lib/R/library/stats/po/de/LC_MESSAGES/R-stats.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 5352 2011-01-14 03:40 ./usr/lib/R/library/stats/po/pt_BR/LC_MESSAGES/stats.mo -rw-r--r-- root/root 66127 2011-01-14 03:40 ./usr/lib/R/library/stats/po/pt_BR/LC_MESSAGES/R-stats.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 3701 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ko/LC_MESSAGES/stats.mo -rw-r--r-- root/root 72767 2011-01-14 03:40 ./usr/lib/R/library/stats/po/ko/LC_MESSAGES/R-stats.mo -rw-r--r-- root/root 16898 2011-01-14 03:40 ./usr/lib/R/library/stats/NAMESPACE -rw-r--r-- root/root 18297 2011-01-14 03:40 ./usr/lib/R/library/stats/INDEX -rw-r--r-- root/root 310 2011-01-14 03:40 ./usr/lib/R/library/stats/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/library/stats/libs/ -rw-r--r-- root/root 609112 2011-01-14 03:42 ./usr/lib/R/library/stats/libs/stats.so -rw-r--r-- root/root 1179 2011-01-14 03:40 ./usr/lib/R/library/R.css drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/help/ -rw-r--r-- root/root 2031 2011-01-14 03:40 ./usr/lib/R/library/tcltk/help/aliases.rds -rw-r--r-- root/root 248 2011-01-14 03:40 ./usr/lib/R/library/tcltk/help/paths.rds -rw-r--r-- root/root 49325 2011-01-14 03:40 ./usr/lib/R/library/tcltk/help/tcltk.rdb -rw-r--r-- root/root 7293 2011-01-14 03:40 ./usr/lib/R/library/tcltk/help/AnIndex -rw-r--r-- root/root 492 2011-01-14 03:40 ./usr/lib/R/library/tcltk/help/tcltk.rdx drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/demo/ -rw-r--r-- root/root 2931 2011-01-14 03:40 ./usr/lib/R/library/tcltk/demo/tkttest.R -rw-r--r-- root/root 3432 2011-01-14 03:40 ./usr/lib/R/library/tcltk/demo/tkdensity.R -rw-r--r-- root/root 1185 2011-01-14 03:40 ./usr/lib/R/library/tcltk/demo/tkfaq.R -rw-r--r-- root/root 5184 2011-01-14 03:40 ./usr/lib/R/library/tcltk/demo/tkcanvas.R drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/R/ -rw-r--r-- root/root 41549 2011-01-14 03:40 ./usr/lib/R/library/tcltk/R/tcltk.rdb -rw-r--r-- root/root 3363 2011-01-14 03:40 ./usr/lib/R/library/tcltk/R/tcltk.rdx -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/lib/R/library/tcltk/R/tcltk drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/Meta/ -rw-r--r-- root/root 2035 2011-01-14 03:40 ./usr/lib/R/library/tcltk/Meta/links.rds -rw-r--r-- root/root 2342 2011-01-14 03:40 ./usr/lib/R/library/tcltk/Meta/Rd.rds -rw-r--r-- root/root 2405 2011-01-14 03:40 ./usr/lib/R/library/tcltk/Meta/hsearch.rds -rw-r--r-- root/root 265 2011-01-14 03:40 ./usr/lib/R/library/tcltk/Meta/demo.rds -rw-r--r-- root/root 494 2011-01-14 03:40 ./usr/lib/R/library/tcltk/Meta/package.rds -rw-r--r-- root/root 462 2011-01-14 03:40 ./usr/lib/R/library/tcltk/Meta/nsInfo.rds drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/html/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ru/LC_MESSAGES/ -rw-r--r-- root/root 2457 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ru/LC_MESSAGES/R-tcltk.mo -rw-r--r-- root/root 1430 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ru/LC_MESSAGES/tcltk.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/it/LC_MESSAGES/ -rw-r--r-- root/root 903 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/it/LC_MESSAGES/R-tcltk.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ja/LC_MESSAGES/ -rw-r--r-- root/root 2833 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ja/LC_MESSAGES/R-tcltk.mo -rw-r--r-- root/root 1522 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ja/LC_MESSAGES/tcltk.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 2228 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/zh_CN/LC_MESSAGES/R-tcltk.mo -rw-r--r-- root/root 1274 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/zh_CN/LC_MESSAGES/tcltk.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 2275 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/en@quot/LC_MESSAGES/R-tcltk.mo -rw-r--r-- root/root 1275 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/en@quot/LC_MESSAGES/tcltk.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/fr/LC_MESSAGES/ -rw-r--r-- root/root 2509 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/fr/LC_MESSAGES/R-tcltk.mo -rw-r--r-- root/root 1461 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/fr/LC_MESSAGES/tcltk.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/de/LC_MESSAGES/ -rw-r--r-- root/root 2359 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/de/LC_MESSAGES/R-tcltk.mo -rw-r--r-- root/root 1383 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/de/LC_MESSAGES/tcltk.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 974 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/pt_BR/LC_MESSAGES/R-tcltk.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ko/LC_MESSAGES/ -rw-r--r-- root/root 990 2011-01-14 03:40 ./usr/lib/R/library/tcltk/po/ko/LC_MESSAGES/R-tcltk.mo -rw-r--r-- root/root 976 2011-01-14 03:40 ./usr/lib/R/library/tcltk/NAMESPACE -rw-r--r-- root/root 626 2011-01-14 03:40 ./usr/lib/R/library/tcltk/INDEX -rw-r--r-- root/root 311 2011-01-14 03:40 ./usr/lib/R/library/tcltk/DESCRIPTION drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/library/tcltk/libs/ -rw-r--r-- root/root 31520 2011-01-14 03:42 ./usr/lib/R/library/tcltk/libs/tcltk.so drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/ -rw-r--r-- root/root 32703 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/widget.tcl -rw-r--r-- root/root 5753 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/util-expand.tcl -rw-r--r-- root/root 78634 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/progressbar.tcl -rw-r--r-- root/root 3600 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/util-string.tcl -rw-r--r-- root/root 2235 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/console.tcl -rw-r--r-- root/root 17830 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/util-dump.tcl -rw-r--r-- root/root 7157 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/util-tk.tcl -rw-r--r-- root/root 23267 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/util.tcl -rw-r--r-- root/root 39160 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/hierarchy.tcl -rw-r--r-- root/root 2115 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/util-number.tcl -rw-r--r-- root/root 1343 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/pkgIndex.tcl -rw-r--r-- root/root 219 2011-01-14 03:40 ./usr/lib/R/library/tcltk/exec/Tk-frontend.R drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/lib/ -rw-r--r-- root/root 2896504 2011-01-14 03:42 ./usr/lib/R/lib/libR.so -rw-r--r-- root/root 309818 2011-01-14 03:40 ./usr/lib/R/NEWS.pdf -rw-r--r-- root/root 104203 2011-01-14 03:40 ./usr/lib/R/NEWS -rw-r--r-- root/root 46 2011-01-14 03:40 ./usr/lib/R/SVN-REVISION drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/modules/ -rw-r--r-- root/root 604240 2011-01-14 03:42 ./usr/lib/R/modules/vfonts.so -rw-r--r-- root/root 35112 2011-01-14 03:42 ./usr/lib/R/modules/lapack.so -rw-r--r-- root/root 156688 2011-01-14 03:42 ./usr/lib/R/modules/R_X11.so -rw-r--r-- root/root 60016 2011-01-14 03:42 ./usr/lib/R/modules/internet.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/etc/ -rw-r--r-- root/root 1877 2011-01-14 03:42 ./usr/lib/R/etc/Renviron.ucf -rw-r--r-- root/root 1574 2011-01-14 03:40 ./usr/lib/R/etc/Renviron.orig drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/lib/R/site-library/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/bin/ -rwxr-xr-x root/root 310 2011-01-14 03:40 ./usr/lib/R/bin/Rprof -rwxr-xr-x root/root 16336 2011-01-14 03:40 ./usr/lib/R/bin/Sd2Rd -rwxr-xr-x root/root 11913 2011-01-14 03:42 ./usr/lib/R/bin/javareconf -rwxr-xr-x root/root 4133 2011-01-14 03:40 ./usr/lib/R/bin/rtags -rwxr-xr-x root/root 114 2011-01-14 03:40 ./usr/lib/R/bin/Stangle -rwxr-xr-x root/root 3629 2011-01-14 03:40 ./usr/lib/R/bin/f77_f2c -rwxr-xr-x root/root 316 2011-01-14 03:40 ./usr/lib/R/bin/Rd2dvi -rwxr-xr-x root/root 823 2011-01-14 03:40 ./usr/lib/R/bin/INSTALL -rwxr-xr-x root/root 1843 2011-01-14 03:40 ./usr/lib/R/bin/BATCH -rwxr-xr-x root/root 155 2011-01-14 03:40 ./usr/lib/R/bin/SHLIB -rwxr-xr-x root/root 8413 2011-01-14 03:40 ./usr/lib/R/bin/R -rwxr-xr-x root/root 7513 2011-01-14 03:40 ./usr/lib/R/bin/config -rwxr-xr-x root/root 359 2011-01-14 03:40 ./usr/lib/R/bin/Rdconv -rwxr-xr-x root/root 1395 2011-01-14 03:40 ./usr/lib/R/bin/Rcmd -rwxr-xr-x root/root 158 2011-01-14 03:40 ./usr/lib/R/bin/REMOVE -rwxr-xr-x root/root 11739 2011-01-14 03:40 ./usr/lib/R/bin/javareconf.orig -rwxr-xr-x root/root 304 2011-01-14 03:40 ./usr/lib/R/bin/build -rwxr-xr-x root/root 1594 2011-01-14 03:40 ./usr/lib/R/bin/LINK -rwxr-xr-x root/root 10360 2011-01-14 03:42 ./usr/lib/R/bin/Rscript -rwxr-xr-x root/root 2111 2011-01-14 03:40 ./usr/lib/R/bin/Rdiff -rwxr-xr-x root/root 415 2011-01-14 03:40 ./usr/lib/R/bin/pager -rwxr-xr-x root/root 274111 2011-01-14 03:40 ./usr/lib/R/bin/libtool -rwxr-xr-x root/root 194 2011-01-14 03:40 ./usr/lib/R/bin/Sweave drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/R/bin/exec/ -rwxr-xr-x root/root 6184 2011-01-14 03:42 ./usr/lib/R/bin/exec/R -rwxr-xr-x root/root 2127 2011-01-14 03:40 ./usr/lib/R/bin/COMPILE -rwxr-xr-x root/root 3496 2011-01-14 03:40 ./usr/lib/R/bin/mkinstalldirs -rwxr-xr-x root/root 304 2011-01-14 03:40 ./usr/lib/R/bin/check drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/pkgconfig/ -rw-r--r-- root/root 206 2011-01-14 03:40 ./usr/lib/pkgconfig/libR.pc drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/info/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/lintian/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 5642 2011-01-14 03:33 ./usr/share/lintian/overrides/r-base-core drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/R/doc/ -rw-r--r-- root/root 9987 2011-01-14 03:40 ./usr/share/R/doc/CRAN_mirrors.csv -rw-r--r-- root/root 164850 2011-01-14 03:40 ./usr/share/R/doc/NEWS.rds drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/R/doc/manual/ -rw-r--r-- root/root 13142 2011-01-14 03:40 ./usr/share/R/doc/COPYRIGHTS -rw-r--r-- root/root 3047 2011-01-14 03:40 ./usr/share/R/doc/KEYWORDS.db drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/doc/html/ -rw-r--r-- root/root 1022 2011-01-14 03:40 ./usr/share/R/doc/html/right.jpg -rw-r--r-- root/root 2413 2011-01-14 03:40 ./usr/share/R/doc/html/packages.html -rw-r--r-- root/root 7082 2011-01-14 03:40 ./usr/share/R/doc/html/SearchOn.html -rw-r--r-- root/root 4068 2011-01-14 03:40 ./usr/share/R/doc/html/resources.html -rw-r--r-- root/root 1013 2011-01-14 03:40 ./usr/share/R/doc/html/left.jpg -rw-r--r-- root/root 1406 2011-01-14 03:40 ./usr/share/R/doc/html/favicon.ico -rw-r--r-- root/root 1021 2011-01-14 03:40 ./usr/share/R/doc/html/up.jpg -rw-r--r-- root/root 450 2011-01-14 03:40 ./usr/share/R/doc/html/packages-head-utf8.html -rw-r--r-- root/root 625 2011-01-14 03:40 ./usr/share/R/doc/html/Search.html -rw-r--r-- root/root 1973 2011-01-14 03:40 ./usr/share/R/doc/html/about.html -rw-r--r-- root/root 2001 2011-01-14 03:40 ./usr/share/R/doc/html/index.html -rw-r--r-- root/root 3682 2011-01-14 03:40 ./usr/share/R/doc/html/logosm.jpg -rw-r--r-- root/root 141618 2011-01-14 03:40 ./usr/share/R/doc/html/NEWS.html -rw-r--r-- root/root 1179 2011-01-14 03:40 ./usr/share/R/doc/html/R.css -rw-r--r-- root/root 3173 2011-01-14 03:40 ./usr/share/R/doc/html/logo.jpg -rw-r--r-- root/root 2296 2011-01-14 03:40 ./usr/share/R/doc/THANKS -rw-r--r-- root/root 730 2011-01-14 03:40 ./usr/share/R/doc/AUTHORS -rw-r--r-- root/root 1561 2011-01-14 03:40 ./usr/share/R/doc/RESOURCES -rw-r--r-- root/root 119320 2011-01-14 03:40 ./usr/share/R/doc/FAQ -rw-r--r-- root/root 2530 2011-01-14 03:40 ./usr/share/R/doc/KEYWORDS drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/include/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/include/R_ext/ -rw-r--r-- root/root 1242 2011-01-14 03:40 ./usr/share/R/include/R_ext/Riconv.h -rw-r--r-- root/root 2457 2011-01-14 03:40 ./usr/share/R/include/R_ext/stats_package.h -rw-r--r-- root/root 10915 2011-01-14 03:40 ./usr/share/R/include/R_ext/QuartzDevice.h -rw-r--r-- root/root 3944 2011-01-14 03:40 ./usr/share/R/include/R_ext/Rdynload.h -rw-r--r-- root/root 2787 2011-01-14 03:40 ./usr/share/R/include/R_ext/eventloop.h -rw-r--r-- root/root 3629 2011-01-14 03:40 ./usr/share/R/include/R_ext/Utils.h -rw-r--r-- root/root 1794 2011-01-14 03:40 ./usr/share/R/include/R_ext/Random.h -rw-r--r-- root/root 1287 2011-01-14 03:40 ./usr/share/R/include/R_ext/Error.h -rw-r--r-- root/root 1514 2011-01-14 03:40 ./usr/share/R/include/R_ext/libextern.h -rw-r--r-- root/root 1084 2011-01-14 03:40 ./usr/share/R/include/R_ext/Complex.h -rw-r--r-- root/root 1295 2011-01-14 03:40 ./usr/share/R/include/R_ext/Print.h -rw-r--r-- root/root 2035 2011-01-14 03:40 ./usr/share/R/include/R_ext/R-ftp-http.h -rw-r--r-- root/root 2406 2011-01-14 03:40 ./usr/share/R/include/R_ext/stats_stubs.h -rw-r--r-- root/root 2998 2011-01-14 03:40 ./usr/share/R/include/R_ext/RS.h -rw-r--r-- root/root 1065 2011-01-14 03:40 ./usr/share/R/include/R_ext/Boolean.h -rw-r--r-- root/root 4100 2011-01-14 03:40 ./usr/share/R/include/R_ext/rlocale.h -rw-r--r-- root/root 17810 2011-01-14 03:40 ./usr/share/R/include/R_ext/GraphicsEngine.h -rw-r--r-- root/root 4297 2011-01-14 03:40 ./usr/share/R/include/R_ext/Linpack.h -rw-r--r-- root/root 2615 2011-01-14 03:40 ./usr/share/R/include/R_ext/PrtUtil.h -rw-r--r-- root/root 1359 2011-01-14 03:40 ./usr/share/R/include/R_ext/Memory.h -rw-r--r-- root/root 11003 2011-01-14 03:40 ./usr/share/R/include/R_ext/Applic.h -rw-r--r-- root/root 1495 2011-01-14 03:40 ./usr/share/R/include/R_ext/Constants.h -rw-r--r-- root/root 1292 2011-01-14 03:40 ./usr/share/R/include/R_ext/Parse.h -rw-r--r-- root/root 1173 2011-01-14 03:40 ./usr/share/R/include/R_ext/Visibility.h -rw-r--r-- root/root 28584 2011-01-14 03:40 ./usr/share/R/include/R_ext/GraphicsDevice.h -rw-r--r-- root/root 5209 2011-01-14 03:40 ./usr/share/R/include/R_ext/RConverters.h -rw-r--r-- root/root 2622 2011-01-14 03:40 ./usr/share/R/include/R_ext/RStartup.h -rw-r--r-- root/root 2728 2011-01-14 03:40 ./usr/share/R/include/R_ext/Arith.h -rw-r--r-- root/root 3879 2011-01-14 03:40 ./usr/share/R/include/R_ext/Callbacks.h -rw-r--r-- root/root 1064 2011-01-14 03:40 ./usr/share/R/include/R_ext/GetX11Image.h -rw-r--r-- root/root 15522 2011-01-14 03:40 ./usr/share/R/include/R_ext/BLAS.h -rw-r--r-- root/root 121945 2011-01-14 03:40 ./usr/share/R/include/R_ext/Lapack.h -rw-r--r-- root/root 35085 2011-01-14 03:40 ./usr/share/R/include/Rinternals.h -rw-r--r-- root/root 473 2011-01-14 03:40 ./usr/share/R/include/Rversion.h -rw-r--r-- root/root 16505 2011-01-14 03:40 ./usr/share/R/include/Rmath.h -rw-r--r-- root/root 5620 2011-01-14 03:40 ./usr/share/R/include/Rdefines.h -rw-r--r-- root/root 4305 2011-01-14 03:40 ./usr/share/R/include/Rinterface.h -rw-r--r-- root/root 1959 2011-01-14 03:40 ./usr/share/R/include/R.h -rw-r--r-- root/root 390 2011-01-14 03:40 ./usr/share/R/include/Rconfig.h -rw-r--r-- root/root 1976 2011-01-14 03:40 ./usr/share/R/include/Rembedded.h -rw-r--r-- root/root 2129 2011-01-14 03:40 ./usr/share/R/include/S.h drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/make/ -rw-r--r-- root/root 37 2011-01-14 03:40 ./usr/share/R/share/make/config.mk -rw-r--r-- root/root 5147 2011-01-14 03:40 ./usr/share/R/share/make/basepkg.mk -rw-r--r-- root/root 296 2011-01-14 03:40 ./usr/share/R/share/make/shlib.mk -rw-r--r-- root/root 231 2011-01-14 03:40 ./usr/share/R/share/make/check.mk -rw-r--r-- root/root 448 2011-01-14 03:40 ./usr/share/R/share/make/vars.mk -rw-r--r-- root/root 86 2011-01-14 03:40 ./usr/share/R/share/make/clean.mk -rw-r--r-- root/root 890 2011-01-14 03:40 ./usr/share/R/share/make/winshlib.mk drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/licenses/ -rw-r--r-- root/root 35147 2011-01-14 03:40 ./usr/share/R/share/licenses/GPL-3 -rw-r--r-- root/root 26432 2011-01-14 03:40 ./usr/share/R/share/licenses/LGPL-2.1 -rw-r--r-- root/root 9073 2011-01-14 03:40 ./usr/share/R/share/licenses/Artistic-2.0 -rw-r--r-- root/root 34525 2011-01-14 03:40 ./usr/share/R/share/licenses/AGPL-3 -rw-r--r-- root/root 3025 2011-01-14 03:40 ./usr/share/R/share/licenses/license.db -rw-r--r-- root/root 18011 2011-01-14 03:40 ./usr/share/R/share/licenses/GPL-2 -rw-r--r-- root/root 25292 2011-01-14 03:40 ./usr/share/R/share/licenses/LGPL-2 -rw-r--r-- root/root 7639 2011-01-14 03:40 ./usr/share/R/share/licenses/LGPL-3 -rw-r--r-- root/root 6100 2011-01-14 03:40 ./usr/share/R/share/licenses/Artistic-1.0 drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/R/ -rw-r--r-- root/root 3127 2011-01-14 03:40 ./usr/share/R/share/R/examples-header.R -rw-r--r-- root/root 240 2011-01-14 03:40 ./usr/share/R/share/R/examples-footer.R -rw-r--r-- root/root 384 2011-01-14 03:40 ./usr/share/R/share/R/nspackloader.R -rw-r--r-- root/root 131 2011-01-14 03:40 ./usr/share/R/share/R/tests-startup.R -rw-r--r-- root/root 2994 2011-01-14 03:40 ./usr/share/R/share/R/REMOVE.R -rw-r--r-- root/root 672 2011-01-14 03:40 ./usr/share/R/share/R/packloader.R drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/java/ -rw-r--r-- root/root 1356 2011-01-14 03:40 ./usr/share/R/share/java/getsp.class drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/encodings/ -rw-r--r-- root/root 53369 2011-01-14 03:40 ./usr/share/R/share/encodings/character-sets -rw-r--r-- root/root 74056 2011-01-14 03:40 ./usr/share/R/share/encodings/Adobe-glyphlist drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/nn/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/nn/LC_MESSAGES/ -rw-r--r-- root/root 174084 2011-01-14 03:40 ./usr/share/R/share/locale/nn/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/ru/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/ru/LC_MESSAGES/ -rw-r--r-- root/root 176340 2011-01-14 03:40 ./usr/share/R/share/locale/ru/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/it/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/it/LC_MESSAGES/ -rw-r--r-- root/root 124066 2011-01-14 03:40 ./usr/share/R/share/locale/it/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/en_GB/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/en_GB/LC_MESSAGES/ -rw-r--r-- root/root 1954 2011-01-14 03:40 ./usr/share/R/share/locale/en_GB/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/ja/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/ja/LC_MESSAGES/ -rw-r--r-- root/root 208796 2011-01-14 03:40 ./usr/share/R/share/locale/ja/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/zh_CN/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/zh_CN/LC_MESSAGES/ -rw-r--r-- root/root 161036 2011-01-14 03:40 ./usr/share/R/share/locale/zh_CN/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/en@quot/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/en@quot/LC_MESSAGES/ -rw-r--r-- root/root 170179 2011-01-14 03:40 ./usr/share/R/share/locale/en@quot/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/es/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/es/LC_MESSAGES/ -rw-r--r-- root/root 159239 2011-01-14 03:40 ./usr/share/R/share/locale/es/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/fr/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/fr/LC_MESSAGES/ -rw-r--r-- root/root 186172 2011-01-14 03:40 ./usr/share/R/share/locale/fr/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/de/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/de/LC_MESSAGES/ -rw-r--r-- root/root 178481 2011-01-14 03:40 ./usr/share/R/share/locale/de/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/pt_BR/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/pt_BR/LC_MESSAGES/ -rw-r--r-- root/root 127841 2011-01-14 03:40 ./usr/share/R/share/locale/pt_BR/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/ko/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/ko/LC_MESSAGES/ -rw-r--r-- root/root 138199 2011-01-14 03:40 ./usr/share/R/share/locale/ko/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/en/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/en/LC_MESSAGES/ -rw-r--r-- root/root 818 2011-01-14 03:40 ./usr/share/R/share/locale/en/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/zh_TW/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/locale/zh_TW/LC_MESSAGES/ -rw-r--r-- root/root 117292 2011-01-14 03:40 ./usr/share/R/share/locale/zh_TW/LC_MESSAGES/R.mo drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/sh/ -rwxr-xr-x root/root 27 2011-01-14 03:40 ./usr/share/R/share/sh/echo.sh drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/texmf/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/texmf/bibtex/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/texmf/bibtex/bib/ -rw-r--r-- root/root 12375 2011-01-14 03:40 ./usr/share/R/share/texmf/bibtex/bib/RJournal.bib -rw-r--r-- root/root 72349 2011-01-14 03:40 ./usr/share/R/share/texmf/bibtex/bib/Rnews.bib drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/texmf/bibtex/bst/ -rw-r--r-- root/root 32335 2011-01-14 03:40 ./usr/share/R/share/texmf/bibtex/bst/jss.bst drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/ -rw-r--r-- root/root 607 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/omscmtt.fd -rw-r--r-- root/root 14180 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/jss.cls -rw-r--r-- root/root 931 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/Sweave.sty -rw-r--r-- root/root 13132 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/Rd.sty -rw-r--r-- root/root 607 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/omsaett.fd -rw-r--r-- root/root 2699 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/upquote.sty -rw-r--r-- root/root 644 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/omsaer.fd -rw-r--r-- root/root 299 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/ts1aett.fd -rw-r--r-- root/root 534 2011-01-14 03:40 ./usr/share/R/share/texmf/tex/latex/ts1aer.fd drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/doc/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/doc/r-base-core/ -rw-r--r-- root/root 20761 2011-01-14 03:33 ./usr/share/doc/r-base-core/copyright -rw-r--r-- root/root 3922 2010-10-08 22:05 ./usr/share/doc/r-base-core/README -rw-r--r-- root/root 24090 2011-01-14 03:33 ./usr/share/doc/r-base-core/changelog.Debian.gz -rw-r--r-- root/root 154392 2010-09-16 22:02 ./usr/share/doc/r-base-core/OONEWS.gz -rw-r--r-- root/root 2739 2011-01-14 03:33 ./usr/share/doc/r-base-core/README.Atlas.gz -rw-r--r-- root/root 140671 2010-09-16 22:02 ./usr/share/doc/r-base-core/ONEWS.gz -rw-r--r-- root/root 3026 2011-01-14 03:33 ./usr/share/doc/r-base-core/README.mathlib -rw-r--r-- root/root 37320 2011-01-14 03:39 ./usr/share/doc/r-base-core/changelog.gz drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/texmf/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/texmf/tex/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/texmf/tex/latex/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/menu/ -rw-r--r-- root/root 128 2011-01-14 03:33 ./usr/share/menu/r-base-core drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/man/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/man/man1/ -rw-r--r-- root/root 657 2011-01-14 03:40 ./usr/share/man/man1/Rscript.1.gz -rw-r--r-- root/root 2481 2011-01-14 03:40 ./usr/share/man/man1/R.1.gz drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/bin/ -rwxr-xr-x root/root 8413 2011-01-14 03:40 ./usr/bin/R -rwxr-xr-x root/root 10360 2011-01-14 03:42 ./usr/bin/Rscript drwxr-xr-x root/root 0 2011-01-14 03:40 ./etc/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./etc/bash_completion.d/ -rw-r--r-- root/root 12841 2011-01-14 03:42 ./etc/bash_completion.d/R drwxr-xr-x root/root 0 2011-01-14 03:42 ./etc/R/ -rw-r--r-- root/root 608 2011-01-14 03:42 ./etc/R/Renviron.site -rw-r--r-- root/root 792 2011-01-14 03:42 ./etc/R/Rprofile.site -rw-r--r-- root/root 1220 2011-01-14 03:40 ./etc/R/repositories -rw-r--r-- root/root 4047 2011-01-14 03:40 ./etc/R/Makeconf -rw-r--r-- root/root 531 2011-01-14 03:40 ./etc/R/ldpaths drwxr-xr-x root/root 0 2011-01-14 03:40 ./etc/ld.so.conf.d/ lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/R/COPYING -> ../../share/common-licenses/GPL-2 lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/R/etc/Renviron.site -> /etc/R/Renviron.site lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/R/etc/Rprofile.site -> /etc/R/Rprofile.site lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/R/etc/repositories -> /etc/R/repositories lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/R/etc/Renviron -> /etc/R/Renviron lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/R/etc/Makeconf -> /etc/R/Makeconf lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/R/etc/ldpaths -> /etc/R/ldpaths lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/libR.so -> R/lib/libR.so lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/share/R/doc/COPYING -> ../../common-licenses/GPL-2 lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/share/R/doc/COPYING.LIB -> ../../common-licenses/LGPL-2.1 lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/share/doc/r-base-core/library -> ../../../lib/R/library lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/share/doc/r-base-core/doc -> ../../R/doc lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/share/doc/r-base-core/NEWS.gz -> changelog.gz lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/share/texmf/tex/latex/R -> ../../../R/share/texmf chroot-autobuild/build/buildd/r-mathlib_2.12.1-1~ppa1~maverick1_amd64.deb: drwxr-xr-x root/root 0 2011-01-14 03:42 ./ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/ -rw-r--r-- root/root 585398 2011-01-14 03:42 ./usr/lib/libRmath.a drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/pkgconfig/ -rw-r--r-- root/root 174 2011-01-14 03:40 ./usr/lib/pkgconfig/libRmath.pc -rw-r--r-- root/root 215752 2011-01-14 03:42 ./usr/lib/libRmath.so.1.0.0 drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/include/ -rw-r--r-- root/root 16505 2011-01-14 03:42 ./usr/include/Rmath.h drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/lintian/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 175 2011-01-14 03:33 ./usr/share/lintian/overrides/r-mathlib drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/doc/r-mathlib/ -rw-r--r-- root/root 20761 2011-01-14 03:33 ./usr/share/doc/r-mathlib/copyright -rw-r--r-- root/root 3922 2010-10-08 22:05 ./usr/share/doc/r-mathlib/README -rw-r--r-- root/root 24090 2011-01-14 03:33 ./usr/share/doc/r-mathlib/changelog.Debian.gz -rw-r--r-- root/root 154392 2010-09-16 22:02 ./usr/share/doc/r-mathlib/OONEWS.gz -rw-r--r-- root/root 140671 2010-09-16 22:02 ./usr/share/doc/r-mathlib/ONEWS.gz drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/doc/r-mathlib/examples/ -rw-r--r-- root/root 1382 2010-03-17 14:43 ./usr/share/doc/r-mathlib/examples/test.c -rw-r--r-- root/root 3026 2011-01-14 03:33 ./usr/share/doc/r-mathlib/README.mathlib -rw-r--r-- root/root 37320 2011-01-14 03:39 ./usr/share/doc/r-mathlib/changelog.gz lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/libRmath.so.1 -> libRmath.so.1.0.0 lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/lib/libRmath.so -> libRmath.so.1 lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/share/doc/r-mathlib/NEWS.gz -> changelog.gz chroot-autobuild/build/buildd/r-base-core-dbg_2.12.1-1~ppa1~maverick1_amd64.deb: drwxr-xr-x root/root 0 2011-01-14 03:42 ./ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/grDevices/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/grDevices/libs/ -rw-r--r-- root/root 328069 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/grDevices/libs/grDevices.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/grid/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/grid/libs/ -rw-r--r-- root/root 263079 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/grid/libs/grid.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/methods/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/methods/libs/ -rw-r--r-- root/root 58173 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/methods/libs/methods.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/splines/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/splines/libs/ -rw-r--r-- root/root 16320 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/splines/libs/splines.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/tools/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/tools/libs/ -rw-r--r-- root/root 25628 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/tools/libs/tools.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/stats/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/stats/libs/ -rw-r--r-- root/root 963455 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/stats/libs/stats.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/tcltk/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/tcltk/libs/ -rw-r--r-- root/root 44151 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/library/tcltk/libs/tcltk.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/lib/ -rw-r--r-- root/root 5630753 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/lib/libR.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/modules/ -rw-r--r-- root/root 51930 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/modules/vfonts.so -rw-r--r-- root/root 52705 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/modules/lapack.so -rw-r--r-- root/root 290468 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/modules/R_X11.so -rw-r--r-- root/root 136999 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/modules/internet.so drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/bin/ -rw-r--r-- root/root 12876 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/bin/Rscript drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/bin/exec/ -rw-r--r-- root/root 8049 2011-01-14 03:42 ./usr/lib/debug/usr/lib/R/bin/exec/R -rw-r--r-- root/root 446983 2011-01-14 03:42 ./usr/lib/debug/usr/lib/libRmath.so.1.0.0 drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/lib/debug/usr/bin/ -rw-r--r-- root/root 12876 2011-01-14 03:42 ./usr/lib/debug/usr/bin/Rscript drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/ drwxr-xr-x root/root 0 2011-01-14 03:40 ./usr/share/lintian/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 148 2011-01-14 03:33 ./usr/share/lintian/overrides/r-base-core-dbg drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2011-01-14 03:42 ./usr/share/doc/r-base-core-dbg/ -rw-r--r-- root/root 20761 2011-01-14 03:33 ./usr/share/doc/r-base-core-dbg/copyright -rw-r--r-- root/root 24090 2011-01-14 03:33 ./usr/share/doc/r-base-core-dbg/changelog.Debian.gz -rw-r--r-- root/root 37320 2011-01-14 03:39 ./usr/share/doc/r-base-core-dbg/changelog.gz lrwxrwxrwx root/root 0 2011-01-14 03:42 ./usr/share/doc/r-base-core-dbg/NEWS.gz -> changelog.gz r-base_2.12.1-1~ppa1~maverick1_amd64.changes: Format: 1.8 Date: Thu, 13 Jan 2011 18:07:46 -0800 Source: r-base Binary: r-base r-base-core r-base-dev r-mathlib r-base-html r-doc-pdf r-doc-html r-doc-info r-recommended r-base-core-dbg Architecture: amd64 Version: 2.12.1-1~ppa1~maverick1 Distribution: maverick Urgency: low Maintainer: Ubuntu Build Daemon Changed-By: Nicola Ferralis Description: r-base - GNU R statistical computation and graphics system r-base-core - GNU R core of statistical computation and graphics system r-base-core-dbg - GNU R debug symbols for statistical comp. language and environmen r-base-dev - GNU R installation of auxiliary GNU R packages r-base-html - GNU R html docs for statistical computing system functions r-doc-html - GNU R html manuals for statistical computing system r-doc-info - GNU R info manuals statistical computing system r-doc-pdf - GNU R pdf manuals for statistical computing system r-mathlib - GNU R standalone mathematics library r-recommended - GNU R collection of recommended packages [metapackage] Changes: r-base (2.12.1-1~ppa1~maverick1) maverick; urgency=low . * Backport to Maverickbleed ppa. Checksums-Sha1: 99a002169dd784ef9ff1b0f3f159c8b2cc6a190a 14128890 r-base-core_2.12.1-1~ppa1~maverick1_amd64.deb 449935fc17fafd9872ba9a7468504d146d78b7e6 619362 r-mathlib_2.12.1-1~ppa1~maverick1_amd64.deb 4e643bdc41ee96ccc44ac1ff6f05df3ca721cf81 2560724 r-base-core-dbg_2.12.1-1~ppa1~maverick1_amd64.deb Checksums-Sha256: 4b1e038385fd0f71172446ea8e9a96539e9b1b861fa9823d4ce528c4eba65965 14128890 r-base-core_2.12.1-1~ppa1~maverick1_amd64.deb 4273fe5d3a57f7cd9e1f528ab5923847f85c2964686ce0693675754418a3c9a4 619362 r-mathlib_2.12.1-1~ppa1~maverick1_amd64.deb 854d0222a4c5285b89f7f7b248426e9444e40ef1d0bbd8c807a198ce7d13ddbb 2560724 r-base-core-dbg_2.12.1-1~ppa1~maverick1_amd64.deb Files: 247a244c3a11be0f63fc326e0f0a3dd7 14128890 gnu-r optional r-base-core_2.12.1-1~ppa1~maverick1_amd64.deb 52574f7a518947ca63c1b7d10453fcb5 619362 gnu-r optional r-mathlib_2.12.1-1~ppa1~maverick1_amd64.deb f3772ebad30dffee82d786d0c65c3dd1 2560724 debug extra r-base-core-dbg_2.12.1-1~ppa1~maverick1_amd64.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/r-base-2.12.1 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge groff-base libavahi-common3 libx11-data m4 fontconfig-config gettext file zlib1g-dev libxaw7 libcairo2 texlive-common openjdk-6-jdk x11-common openjdk-6-jre-lib libcairo-gobject2 python2.6 libx11-dev libvorbis0a tk8.5-dev libvorbisenc2 libfontenc1 libxi6 libpcre3-dev libjpeg62 libxcursor1 xvfb libwrap0 x11proto-input-dev libexpat1-dev libgdk-pixbuf2.0-0 libjasper1 libpixman-1-dev libjpeg62-dev libaccess-bridge-java-jni libfontconfig1 libtiffxx0c2 libnspr4-0d libblas3gf libgfortran3 texlive-latex-extra libxcb-shm0-dev libpcrecpp0 texlive-fonts-recommended libx11-xcb1 libx11-6 xtrans-dev tk8.5 libgif4 libnewt0.52 libpango1.0-common libglib2.0-data libxdamage1 libxt6 x11-xkb-utils texlive-base libkpathsea5 libxss1 bison texlive-doc-base libglib2.0-dev x11proto-scrnsaver-dev libxml2 x11proto-xext-dev pkg-config libthai-data libice6 xserver-common xauth intltool-debian libavahi-client3 libxrender1 libfontconfig1-dev texlive-extra-utils texlive-latex-base libxext-dev libcups2 libxau-dev libdatrie1 libxrender-dev openjdk-6-jre xfonts-utils libpng12-dev libavahi-common-data libxtst6 libxft2 x11proto-render-dev libxext6 libasound2 libsqlite3-0 libxinerama1 preview-latex-style libblas-dev tzdata-java libsm-dev ca-certificates-java libxkbfile1 libxmu6 xfonts-encodings defoma libxdmcp-dev ttf-dejavu-core libpulse0 libcairo2-dev fontconfig libxcb-render0-dev texi2html libxpm4 libcroco3 libxmuu1 gfortran liblapack-dev libxt-dev libpopt0 xdg-utils libfreetype6 texlive-generic-recommended libice-dev texlive-latex-recommended libatk1.0-0 libfreetype6-dev texlive-pictures libgtk2.0-0 libxss-dev liblapack3gf libflac8 libxcb-atom1 libxcb1 tex-common libnss3-1d html2text libsndfile1 libreadline6-dev debhelper libpthread-stubs0 libxrandr2 liblzma-dev libthai0 python libncurses5-dev tcl8.5 libmagic1 libtiff4 libxcb-shm0 libexpat1 tcl8.5-dev bsdmainutils libxau6 libpango1.0-dev libxcomposite1 mime-support x11proto-core-dev whiptail libogg0 libxcb1-dev shared-mime-info libxdmcp6 libxfixes3 po-debconf openjdk-6-jre-headless libxft-dev liblcms1 libxfont1 ed libpython2.6 libbz2-dev xfonts-base man-db xkb-data x11proto-kb-dev texinfo libpixman-1-0 libreadline-dev luatex libpango1.0-0 libpthread-stubs0-dev ucf libgtk2.0-common gettext-base libtiff4-dev libaccess-bridge-java libunistring0 libsm6 gfortran-4.4 libxcb-render0 texlive-binaries libpoppler7 libglib2.0-bin java-common (Reading database ... 34710 files and directories currently installed.) Removing openjdk-6-jdk ... Purging configuration files for openjdk-6-jdk ... Removing tk8.5-dev ... Removing libpcre3-dev ... Removing xvfb ... Removing texlive-latex-extra ... Purging configuration files for texlive-latex-extra ... Removing libpcrecpp0 ... Purging configuration files for libpcrecpp0 ... Removing texlive-fonts-recommended ... Purging configuration files for texlive-fonts-recommended ... Removing tk8.5 ... Purging configuration files for tk8.5 ... Removing bison ... Removing xserver-common ... Removing xauth ... Removing texlive-extra-utils ... Purging configuration files for texlive-extra-utils ... Removing preview-latex-style ... Purging configuration files for preview-latex-style ... Removing texi2html ... Removing libxmuu1 ... Purging configuration files for libxmuu1 ... Removing gfortran ... Removing liblapack-dev ... Removing libxt-dev ... Removing xdg-utils ... Removing texlive-generic-recommended ... Purging configuration files for texlive-generic-recommended ... Removing texlive-latex-recommended ... Purging configuration files for texlive-latex-recommended ... Removing texlive-pictures ... Purging configuration files for texlive-pictures ... Removing libxss-dev ... Removing liblapack3gf ... Purging configuration files for liblapack3gf ... Removing debhelper ... Removing liblzma-dev ... Removing python ... Purging configuration files for python ... Removing tcl8.5-dev ... Removing libpango1.0-dev ... Removing po-debconf ... Removing libxft-dev ... Removing libbz2-dev ... Removing xfonts-base ... Purging configuration files for xfonts-base ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing xkb-data ... Purging configuration files for xkb-data ... Removing texinfo ... Running update-fmtutil. This may take some time. ... done. Running mktexlsr. This may take some time. ... done. Purging configuration files for texinfo ... Removing libreadline-dev ... Removing libtiff4-dev ... Removing gfortran-4.4 ... Removing groff-base ... Purging configuration files for groff-base ... Removing m4 ... Removing libjpeg62-dev ... Removing libtiffxx0c2 ... Purging configuration files for libtiffxx0c2 ... Removing x11-xkb-utils ... Removing libxss1 ... Purging configuration files for libxss1 ... Removing x11proto-scrnsaver-dev ... Removing intltool-debian ... Removing texlive-latex-base ... Purging configuration files for texlive-latex-base ... Removing libxext-dev ... Removing xfonts-utils ... Purging configuration files for xfonts-utils ... Removing libblas-dev ... Removing libxkbfile1 ... Purging configuration files for libxkbfile1 ... Removing xfonts-encodings ... Removing libcairo2-dev ... Removing libxcb-render0-dev ... Removing html2text ... Purging configuration files for html2text ... Removing libreadline6-dev ... Removing libncurses5-dev ... Removing tcl8.5 ... Purging configuration files for tcl8.5 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing libxfont1 ... Purging configuration files for libxfont1 ... Removing gettext ... Removing libcairo-gobject2 ... Purging configuration files for libcairo-gobject2 ... Removing libfontenc1 ... Purging configuration files for libfontenc1 ... Removing libpixman-1-dev ... Removing libblas3gf ... Purging configuration files for libblas3gf ... Removing libgfortran3 ... Purging configuration files for libgfortran3 ... Removing libxcb-shm0-dev ... Removing texlive-base ... Purging configuration files for texlive-base ... Removing texlive-doc-base ... Purging configuration files for texlive-doc-base ... Removing libglib2.0-dev ... Removing x11proto-xext-dev ... Removing libfontconfig1-dev ... Removing libxrender-dev ... Removing libpng12-dev ... Removing x11proto-render-dev ... Removing libsm-dev ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libice-dev ... Removing libfreetype6-dev ... Removing luatex ... Removing gettext-base ... Removing libunistring0 ... Purging configuration files for libunistring0 ... Removing texlive-binaries ... Removing libpoppler7 ... Purging configuration files for libpoppler7 ... Removing libglib2.0-bin ... Removing zlib1g-dev ... Removing libxaw7 ... Purging configuration files for libxaw7 ... Removing texlive-common ... Removing libx11-dev ... Removing x11proto-input-dev ... Removing libexpat1-dev ... Removing xtrans-dev ... Removing libglib2.0-data ... Removing libkpathsea5 ... Purging configuration files for libkpathsea5 ... Removing pkg-config ... Removing libxmu6 ... Purging configuration files for libxmu6 ... Removing libxpm4 ... Purging configuration files for libxpm4 ... Removing tex-common ... Purging configuration files for tex-common ... Removing libxcb1-dev ... Removing ed ... Removing x11proto-kb-dev ... Removing libpthread-stubs0-dev ... Removing libxt6 ... Purging configuration files for libxt6 ... Removing libxau-dev ... Removing libxdmcp-dev ... Removing libpthread-stubs0 ... Removing x11proto-core-dev ... Removing openjdk-6-jre-lib ... Removing openjdk-6-jre ... Purging configuration files for openjdk-6-jre ... Removing libasound2 ... Purging configuration files for libasound2 ... Removing ca-certificates-java ... Purging configuration files for ca-certificates-java ... Removing libpulse0 ... Purging configuration files for libpulse0 ... Removing libxcb-atom1 ... Purging configuration files for libxcb-atom1 ... Removing libsndfile1 ... Purging configuration files for libsndfile1 ... Removing openjdk-6-jre-headless ... Purging configuration files for openjdk-6-jre-headless ... Removing liblcms1 ... Purging configuration files for liblcms1 ... Removing libpython2.6 ... Purging configuration files for libpython2.6 ... Removing libsm6 ... Purging configuration files for libsm6 ... Removing java-common ... Removing python2.6 ... Purging configuration files for python2.6 ... Removing libvorbisenc2 ... Purging configuration files for libvorbisenc2 ... Removing libwrap0 ... Purging configuration files for libwrap0 ... Removing libaccess-bridge-java-jni ... Purging configuration files for libaccess-bridge-java-jni ... Removing libx11-xcb1 ... Purging configuration files for libx11-xcb1 ... Removing libgif4 ... Purging configuration files for libgif4 ... Removing libice6 ... Purging configuration files for libice6 ... Removing libxtst6 ... Purging configuration files for libxtst6 ... Removing tzdata-java ... Removing libgtk2.0-0 ... Purging configuration files for libgtk2.0-0 ... dpkg: warning: while removing libgtk2.0-0, directory '/usr/lib/gtk-2.0/2.10.0' not empty so not removed. dpkg: warning: while removing libgtk2.0-0, directory '/usr/lib/gtk-2.0' not empty so not removed. Removing libflac8 ... Purging configuration files for libflac8 ... Removing libnss3-1d ... Purging configuration files for libnss3-1d ... Removing libxrandr2 ... Purging configuration files for libxrandr2 ... Removing libxcomposite1 ... Purging configuration files for libxcomposite1 ... Removing mime-support ... Purging configuration files for mime-support ... Removing shared-mime-info ... Purging configuration files for shared-mime-info ... Removing libpango1.0-0 ... Purging configuration files for libpango1.0-0 ... Removing libgtk2.0-common ... Removing libaccess-bridge-java ... Removing libcairo2 ... Purging configuration files for libcairo2 ... Removing x11-common ... Purging configuration files for x11-common ... Removing libvorbis0a ... Purging configuration files for libvorbis0a ... Removing libxi6 ... Purging configuration files for libxi6 ... Removing libxcursor1 ... Purging configuration files for libxcursor1 ... Removing libgdk-pixbuf2.0-0 ... Purging configuration files for libgdk-pixbuf2.0-0 ... Removing libjasper1 ... Purging configuration files for libjasper1 ... Removing libnspr4-0d ... Purging configuration files for libnspr4-0d ... Removing libpango1.0-common ... Purging font configuration of pango... Purging category xfont.. Purging configuration files for libpango1.0-common ... Removing libxdamage1 ... Purging configuration files for libxdamage1 ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing libcups2 ... Purging configuration files for libcups2 ... Removing libxft2 ... Purging configuration files for libxft2 ... Removing libsqlite3-0 ... Purging configuration files for libsqlite3-0 ... Removing libxinerama1 ... Purging configuration files for libxinerama1 ... Removing defoma ... Purging configuration files for defoma ... dpkg: warning: while removing defoma, directory '/etc/defoma' not empty so not removed. Removing fontconfig ... Purging configuration files for fontconfig ... Removing libatk1.0-0 ... Purging configuration files for libatk1.0-0 ... Removing libthai0 ... Purging configuration files for libthai0 ... Removing libtiff4 ... Purging configuration files for libtiff4 ... Removing libxcb-shm0 ... Purging configuration files for libxcb-shm0 ... Removing whiptail ... Removing libogg0 ... Purging configuration files for libogg0 ... Removing libxfixes3 ... Purging configuration files for libxfixes3 ... Removing libpixman-1-0 ... Purging configuration files for libpixman-1-0 ... Removing libxcb-render0 ... Purging configuration files for libxcb-render0 ... Removing file ... Purging configuration files for file ... Removing libjpeg62 ... Removing libfontconfig1 ... Purging configuration files for libfontconfig1 ... Removing libnewt0.52 ... Purging configuration files for libnewt0.52 ... Removing libthai-data ... Removing libavahi-client3 ... Purging configuration files for libavahi-client3 ... Removing libxrender1 ... Purging configuration files for libxrender1 ... Removing libdatrie1 ... Purging configuration files for libdatrie1 ... Removing libxext6 ... Purging configuration files for libxext6 ... Removing libpopt0 ... Purging configuration files for libpopt0 ... Removing libfreetype6 ... Purging configuration files for libfreetype6 ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libexpat1 ... Purging configuration files for libexpat1 ... Removing libavahi-common3 ... Purging configuration files for libavahi-common3 ... Removing fontconfig-config ... Purging configuration files for fontconfig-config ... Removing libx11-6 ... Purging configuration files for libx11-6 ... Removing libavahi-common-data ... Removing ttf-dejavu-core ... Removing libxcb1 ... Purging configuration files for libxcb1 ... Removing libxau6 ... Purging configuration files for libxau6 ... Removing libxdmcp6 ... Purging configuration files for libxdmcp6 ... Removing ucf ... Purging configuration files for ucf ... Removing libx11-data ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for libglib2.0-0 ... No schema files found: doing nothing. ****************************************************************************** Finished at 20110114-0345 Build needed 00:10:14, 241052k disk space Can't open average time db /var/debbuild/avg-build-times Can't open average space db /var/debbuild/avg-build-space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '9104a2a6755e804c098d2bd63e011ff2840520ce'] Scanning for processes to kill in build /home/buildd/build-9104a2a6755e804c098d2bd63e011ff2840520ce/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '9104a2a6755e804c098d2bd63e011ff2840520ce'] Unmounting chroot for build 9104a2a6755e804c098d2bd63e011ff2840520ce... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '9104a2a6755e804c098d2bd63e011ff2840520ce'] Removing build 9104a2a6755e804c098d2bd63e011ff2840520ce