Sun Jan 17 19:48:14 UTC 2021 I: starting to build r-base/buster/arm64 on jenkins on '2021-01-17 19:47' Sun Jan 17 19:48:14 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_28/16581/console.log Sun Jan 17 19:48:14 UTC 2021 I: Downloading source for buster/r-base=3.5.2-1 --2021-01-17 19:48:14-- http://deb.debian.org/debian/pool/main/r/r-base/r-base_3.5.2-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3008 (2.9K) Saving to: ‘r-base_3.5.2-1.dsc’ 0K .. 100% 282M=0s 2021-01-17 19:48:14 (282 MB/s) - ‘r-base_3.5.2-1.dsc’ saved [3008/3008] Sun Jan 17 19:48:14 UTC 2021 I: r-base_3.5.2-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) 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: any all Version: 3.5.2-1 Maintainer: Dirk Eddelbuettel Homepage: http://www.r-project.org/ Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/edd/r-base Vcs-Git: https://salsa.debian.org/edd/r-base.git Build-Depends: gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk [!arm !hppa !kfreebsd-i386 !kfreebsd-amd64 !hurd-i386] | openjdk-10-jdk [!arm !hppa !kfreebsd-i386 !kfreebsd-amd64 !hurd-i386], mpack, bash-completion Package-List: r-base deb gnu-r optional arch=all r-base-core deb gnu-r optional arch=any r-base-core-dbg deb debug optional arch=any r-base-dev deb gnu-r optional arch=all r-base-html deb doc optional arch=all r-doc-html deb doc optional arch=all r-doc-info deb doc optional arch=all r-doc-pdf deb doc optional arch=all r-mathlib deb gnu-r optional arch=any r-recommended deb gnu-r optional arch=all Checksums-Sha1: 057ea91daed3e68a12b2a473ee1283cf26f360e2 30186438 r-base_3.5.2.orig.tar.gz 5da3359e5a7698b005b8cf4a703ff5b151860527 88304 r-base_3.5.2-1.debian.tar.xz Checksums-Sha256: e53d8c3cf20f2b8d7a9c1631b6f6a22874506fb392034758b3bb341c586c5b62 30186438 r-base_3.5.2.orig.tar.gz 10a7e638a267f277dc03644c11dcfe282bc522133f804b1232b2be40d199b419 88304 r-base_3.5.2-1.debian.tar.xz Files: 3e4b40b2bbd4a2f8133ac45dbef6a485 30186438 r-base_3.5.2.orig.tar.gz fce75a6167de945bf9cf12eb9bf3f615 88304 r-base_3.5.2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIVAwUBXBuArqFIn+KrmaIaAQg1Ng//QN3kau0Cg/jaL17As6D8sfiKoIwJ1Ao+ SFmYf+qviLQEvE5Ebjf4x4yLnwG1ZcC33/F54W4CPlP70AJlVEm1BmpyyeuU06AE 5vAu0AjVwB3YY49F4pCSO20bUg88Hsnxjfr2vYBH1nXa/8IMA8U/GNpgvKXplk8B x0bnnynjWYjL5SY5bGQm0jI5JKqELNZJGtylCHFpN1crllAh7/q5cYuaY3VaKyug x+cIjUbrm07SoO9QBw4IBROvqyr2yq9ORQxZOqOprLuIlAThMe7tZhsQe+ZLfHKN PFJCWx7TJ2fbInxFmHRgG3hjIVF/KX+GrgMj+AGWaYE9kWHeqTYoOP86DBt/mBP/ C1BWEq1vKJjooLYIiauDvQArzT/7WTnpqSb1i6VCRzEqPhD3K3DJRVgsNxkk5VP+ 0Hhf8ihqXHMYLbTp8rF0ueNGPyrUxuc3ixczMmD/H6P+RGuCQYPH+upQ2qgiYPfB YGX9qB68YM8RYx77Aj9OeyW4RxJVwbylezX2nPouLI5Aov6pMBC3OkVAR+BGTzgJ OXB0CyjkYmZvy81L+JL/GxMDJjCceMGPNMB+6vDFWMY0I4HGiRKXvxx7u0X01bPf zJJhgs3CJu+WGslzRVdKiZJau47P7TvdgKo7vgbjmSN+Sp/6i2UKxZ7Ww+Oow1m4 hoQYFBWegrk= =ocMK -----END PGP SIGNATURE----- Sun Jan 17 19:48:14 UTC 2021 I: Checking whether the package is not for us Sun Jan 17 19:48:14 UTC 2021 I: Starting 1st build on remote node codethink15-arm64.debian.net. Sun Jan 17 19:48:14 UTC 2021 I: Preparing to do remote build '1' on codethink15-arm64.debian.net. Sun Jan 17 20:34:08 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 19 14:11:40 -12 2022 I: pbuilder-time-stamp: 1645323100 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [r-base_3.5.2-1.dsc] I: copying [./r-base_3.5.2.orig.tar.gz] I: copying [./r-base_3.5.2-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Dec 19 23:44:46 2018 -12 gpgv: using RSA key A1489FE2AB99A21A gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-base_3.5.2-1.dsc dpkg-source: info: extracting r-base in r-base-3.5.2 dpkg-source: info: unpacking r-base_3.5.2.orig.tar.gz dpkg-source: info: unpacking r-base_3.5.2-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14484/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='14484' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.cCDsfdUQXN/pbuilderrc_rpm0 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cCDsfdUQXN/b1 --logfile b1/build.log r-base_3.5.2-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink15-arm64 4.4.0-190-generic #220-Ubuntu SMP Fri Aug 28 23:03:33 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 6 2021 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/14484/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk | openjdk-10-jdk, mpack, bash-completion dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on gfortran (>= 4:4.1.0); however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev (>= 3.1.1); however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on tcl8.6-dev; however: Package tcl8.6-dev is not installed. pbuilder-satisfydepends-dummy depends on tk8.6-dev; however: Package tk8.6-dev is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on groff-base; however: Package groff-base is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 7.2.3); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on texinfo (>= 4.1-2); however: Package texinfo is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libpcre3-dev; however: Package libpcre3-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-openssl-dev | libcurl4-dev; however: Package libcurl4-openssl-dev is not installed. Package libcurl4-dev is not installed. pbuilder-satisfydepends-dummy depends on xdg-utils; however: Package xdg-utils is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on libjpeg-dev; however: Package libjpeg-dev is not installed. pbuilder-satisfydepends-dummy depends on libx11-dev; however: Package libx11-dev is not installed. pbuilder-satisfydepends-dummy depends on libxt-dev; however: Package libxt-dev is not installed. pbuilder-satisfydepends-dummy depends on x11proto-core-dev; however: Package x11proto-core-dev is not installed. pbuilder-satisfydepends-dummy depends on libpango1.0-dev; however: Package libpango1.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libcairo2-dev; however: Package libcairo2-dev is not installed. pbuilder-satisfydepends-dummy depends on libtiff5-dev; however: Package libtiff5-dev is not installed. pbuilder-satisfydepends-dummy depends on xvfb; however: Package xvfb is not installed. pbuilder-satisfydepends-dummy depends on xauth; however: Package xauth is not installed. pbuilder-satisfydepends-dummy depends on xfonts-base; however: Package xfonts-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-base; however: Package texlive-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-generic-recommended; however: Package texlive-generic-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-extra; however: Package texlive-fonts-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-extra-utils; however: Package texlive-extra-utils is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on default-jdk | openjdk-10-jdk; however: Package default-jdk is not installed. Package openjdk-10-jdk is not installed. pbuilder-satisfydepends-dummy depends on mpack; however: Package mpack is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bison{a} bsdmainutils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} gir1.2-freedesktop{a} gir1.2-glib-2.0{a} gir1.2-harfbuzz-0.0{a} gir1.2-pango-1.0{a} groff-base{a} icu-devtools{a} intltool-debian{a} java-common{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbison-dev{a} libblas-dev{a} libblas3{a} libblkid-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcroco3{a} libcups2{a} libcupsimage2{a} libcurl4{a} libcurl4-openssl-dev{a} libdatrie1{a} libdbus-1-3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-etnaviv1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontconfig1-dev{a} libfontenc1{a} libfreetype6{a} libfreetype6-dev{a} libfribidi-dev{a} libfribidi0{a} libgfortran-8-dev{a} libgfortran5{a} libgif7{a} libgirepository-1.0-1{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgraphite2-dev{a} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libharfbuzz-dev{a} libharfbuzz-gobject0{a} libharfbuzz-icu0{a} libharfbuzz0b{a} libice-dev{a} libice6{a} libicu-dev{a} libicu63{a} libidn11{a} libijs-0.35{a} libjbig-dev{a} libjbig0{a} libjbig2dec0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} libllvm7{a} liblzma-dev{a} liblzo2-2{a} libmagic-mgc{a} libmagic1{a} libmime-charset-perl{a} libmount-dev{a} libmpdec2{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpango-1.0-0{a} libpango1.0-dev{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpangoxft-1.0-0{a} libpaper-utils{a} libpaper1{a} libpcre16-3{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpng-dev{a} libpng16-16{a} libpotrace0{a} libpsl5{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline-dev{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsensors-config{a} libsensors5{a} libsepol1-dev{a} libsigsegv2{a} libsm-dev{a} libsm6{a} libsombok3{a} libssh2-1{a} libssl1.1{a} libsynctex2{a} libtcl8.6{a} libteckit0{a} libtexlua52{a} libtexlua53{a} libtext-unidecode-perl{a} libthai-data{a} libthai0{a} libtiff-dev{a} libtiff5{a} libtiff5-dev{a} libtiffxx5{a} libtk8.6{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{a} libunwind8{a} libwebp6{a} libwoff1{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb-sync1{a} libxcb1{a} libxcb1-dev{a} libxdamage1{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes3{a} libxfont2{a} libxft-dev{a} libxft2{a} libxi6{a} libxkbfile1{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml2{a} libxmu6{a} libxmuu1{a} libxpm4{a} libxrender-dev{a} libxrender1{a} libxshmfence1{a} libxss-dev{a} libxss1{a} libxt-dev{a} libxt6{a} libxtst6{a} libxxf86vm1{a} libxxhash0{a} libzzip-0-13{a} lsb-base{a} m4{a} man-db{a} mime-support{a} mpack{a} openjdk-11-jdk{a} openjdk-11-jdk-headless{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openssl{a} pango1.0-tools{a} pkg-config{a} po-debconf{a} poppler-data{a} preview-latex-style{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} t1utils{a} tcl8.6{a} tcl8.6-dev{a} tex-common{a} texinfo{a} texlive-base{a} texlive-binaries{a} texlive-extra-utils{a} texlive-fonts-extra{a} texlive-fonts-recommended{a} texlive-generic-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} texlive-plain-generic{a} tk8.6{a} tk8.6-dev{a} ucf{a} uuid-dev{a} x11-common{a} x11-xkb-utils{a} x11proto-core-dev{a} x11proto-dev{a} x11proto-scrnsaver-dev{a} x11proto-xext-dev{a} xauth{a} xdg-utils{a} xfonts-base{a} xfonts-encodings{a} xfonts-utils{a} xkb-data{a} xorg-sgml-doctools{a} xserver-common{a} xtrans-dev{a} xvfb{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl dbus deepin-terminal eterm fonts-adf-accanthis fonts-adf-berenis fonts-adf-gillius fonts-adf-universalis fonts-cabin fonts-comfortaa fonts-croscore fonts-crosextra-caladea fonts-crosextra-carlito fonts-dejavu-extra fonts-droid-fallback fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga fonts-gfs-solomos fonts-go fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobstertwo fonts-noto-hinted fonts-noto-mono fonts-oflb-asana-math fonts-open-sans fonts-roboto-unhinted fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix ghostscript gnome-terminal kitty konsole krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libcupsfilters1 libfile-homedir-perl libfile-mimeinfo-perl libgpm2 liblog-log4perl-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libwww-perl libx11-protocol-perl libxml-sax-expat-perl libyaml-tiny-perl lilyterm lmodern lxterminal lynx mate-terminal mlterm mlterm-tiny pterm publicsuffix qterminal ruby rxvt-unicode sakura shared-mime-info stterm terminator terminology termit tex-gyre texlive-fonts-extra-links tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs xfce4-terminal xiterm+thai xterm 0 packages upgraded, 314 newly installed, 0 to remove and 0 not upgraded. Need to get 936 MB of archives. After unpacking 2534 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 poppler-data all 0.4.9-2 [1473 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libpython3.7-minimal arm64 3.7.3-2+deb10u2 [588 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 python3.7-minimal arm64 3.7.3-2+deb10u2 [1404 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 python3-minimal arm64 3.7.3-1 [36.6 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libmpdec2 arm64 2.4.2-2 [77.7 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libpython3.7-stdlib arm64 3.7.3-2+deb10u2 [1641 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 python3.7 arm64 3.7.3-2+deb10u2 [330 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libpython3-stdlib arm64 3.7.3-1 [20.0 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 python3 arm64 3.7.3-1 [61.5 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 ucf all 3.0038+nmu1 [69.0 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 tex-common all 6.11 [53.1 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 bash-completion all 1:2.8-6 [208 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libbison-dev arm64 2:3.3.2.dfsg-1 [500 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 bison arm64 2:3.3.2.dfsg-1 [855 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 openssl arm64 1.1.1d-0+deb10u3 [823 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 ca-certificates all 20190110 [157 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 java-common all 0.71 [14.4 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libavahi-common-data arm64 0.7-4+b1 [122 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libavahi-common3 arm64 0.7-4+b1 [53.5 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libdbus-1-3 arm64 1.12.20-0+deb10u1 [206 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libavahi-client3 arm64 0.7-4+b1 [56.8 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3+deb10u1 [64.9 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3+deb10u1 [123 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3+deb10u1 [351 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3+deb10u1 [150 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libcups2 arm64 2.2.10-6+deb10u4 [310 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 liblcms2-2 arm64 2.9-3 [137 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libjpeg62-turbo arm64 1:1.5.2-2+deb10u1 [123 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libpng16-16 arm64 1.6.36-6 [287 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libfreetype6 arm64 2.9.1-3+deb10u2 [355 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 fontconfig-config all 2.13.1-2 [280 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 libfontconfig1 arm64 2.13.1-2 [343 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libnspr4 arm64 2:4.20-1 [105 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 libnss3 arm64 2:3.42.1-1+deb10u3 [1082 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 libasound2-data all 1.1.8-1 [59.6 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 libasound2 arm64 1.1.8-1 [333 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 libpcsclite1 arm64 1.8.24-1 [58.1 kB] Get: 72 http://deb.debian.org/debian buster/main arm64 libxau6 arm64 1:1.0.8-1+b2 [19.3 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 74 http://deb.debian.org/debian buster/main arm64 libxcb1 arm64 1.13.1-2 [135 kB] Get: 75 http://deb.debian.org/debian buster/main arm64 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 libx11-6 arm64 2:1.6.7-1+deb10u1 [734 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 libxext6 arm64 2:1.3.3-1+b2 [48.6 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 libxi6 arm64 2:1.7.9-1 [79.0 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 lsb-base all 10.2019051400 [28.4 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 x11-common all 1:7.7+19 [251 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 libxtst6 arm64 2:1.2.3-1 [26.7 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 openjdk-11-jre-headless arm64 11.0.9.1+1-1~deb10u2 [36.8 MB] Get: 84 http://deb.debian.org/debian buster/main arm64 default-jre-headless arm64 2:1.11-71 [10.9 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 ca-certificates-java all 20190405 [15.7 kB] Get: 86 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 87 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 88 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 89 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 90 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 91 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 92 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 93 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 94 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 95 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+deb10u1 [625 kB] Get: 96 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 97 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 98 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 99 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 100 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 101 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 102 http://deb.debian.org/debian buster/main arm64 libglvnd0 arm64 1.1.0-1 [42.4 kB] Get: 103 http://deb.debian.org/debian buster/main arm64 libdrm-common all 2.4.97-1 [13.8 kB] Get: 104 http://deb.debian.org/debian buster/main arm64 libdrm2 arm64 2.4.97-1 [39.5 kB] Get: 105 http://deb.debian.org/debian buster/main arm64 libglapi-mesa arm64 18.3.6-2+deb10u1 [74.8 kB] Get: 106 http://deb.debian.org/debian buster/main arm64 libx11-xcb1 arm64 2:1.6.7-1+deb10u1 [190 kB] Get: 107 http://deb.debian.org/debian buster/main arm64 libxcb-dri2-0 arm64 1.13.1-2 [101 kB] Get: 108 http://deb.debian.org/debian buster/main arm64 libxcb-dri3-0 arm64 1.13.1-2 [100 kB] Get: 109 http://deb.debian.org/debian buster/main arm64 libxcb-glx0 arm64 1.13.1-2 [116 kB] Get: 110 http://deb.debian.org/debian buster/main arm64 libxcb-present0 arm64 1.13.1-2 [99.1 kB] Get: 111 http://deb.debian.org/debian buster/main arm64 libxcb-sync1 arm64 1.13.1-2 [102 kB] Get: 112 http://deb.debian.org/debian buster/main arm64 libxfixes3 arm64 1:5.0.3-1 [21.0 kB] Get: 113 http://deb.debian.org/debian buster/main arm64 libxdamage1 arm64 1:1.1.4-3+b3 [14.8 kB] Get: 114 http://deb.debian.org/debian buster/main arm64 libxshmfence1 arm64 1.3-1 [8712 B] Get: 115 http://deb.debian.org/debian buster/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 116 http://deb.debian.org/debian buster/main arm64 libdrm-amdgpu1 arm64 2.4.97-1 [26.6 kB] Get: 117 http://deb.debian.org/debian buster/main arm64 libdrm-etnaviv1 arm64 2.4.97-1 [21.0 kB] Get: 118 http://deb.debian.org/debian buster/main arm64 libdrm-nouveau2 arm64 2.4.97-1 [25.5 kB] Get: 119 http://deb.debian.org/debian buster/main arm64 libdrm-radeon1 arm64 2.4.97-1 [30.0 kB] Get: 120 http://deb.debian.org/debian buster/main arm64 libedit2 arm64 3.1-20181209-1 [91.2 kB] Get: 121 http://deb.debian.org/debian buster/main arm64 libllvm7 arm64 1:7.0.1-8+deb10u2 [10.8 MB] Get: 122 http://deb.debian.org/debian buster/main arm64 libsensors-config all 1:3.5.0-3 [31.6 kB] Get: 123 http://deb.debian.org/debian buster/main arm64 libsensors5 arm64 1:3.5.0-3 [51.8 kB] Get: 124 http://deb.debian.org/debian buster/main arm64 libgl1-mesa-dri arm64 18.3.6-2+deb10u1 [4910 kB] Get: 125 http://deb.debian.org/debian buster/main arm64 libglx-mesa0 arm64 18.3.6-2+deb10u1 [180 kB] Get: 126 http://deb.debian.org/debian buster/main arm64 libglx0 arm64 1.1.0-1 [29.0 kB] Get: 127 http://deb.debian.org/debian buster/main arm64 libgl1 arm64 1.1.0-1 [92.5 kB] Get: 128 http://deb.debian.org/debian buster/main arm64 libgif7 arm64 5.1.4-3 [41.7 kB] Get: 129 http://deb.debian.org/debian buster/main arm64 openjdk-11-jre arm64 11.0.9.1+1-1~deb10u2 [32.8 kB] Get: 130 http://deb.debian.org/debian buster/main arm64 default-jre arm64 2:1.11-71 [1044 B] Get: 131 http://deb.debian.org/debian buster/main arm64 openjdk-11-jdk-headless arm64 11.0.9.1+1-1~deb10u2 [218 MB] Get: 132 http://deb.debian.org/debian buster/main arm64 default-jdk-headless arm64 2:1.11-71 [1104 B] Get: 133 http://deb.debian.org/debian buster/main arm64 openjdk-11-jdk arm64 11.0.9.1+1-1~deb10u2 [13.5 kB] Get: 134 http://deb.debian.org/debian buster/main arm64 default-jdk arm64 2:1.11-71 [1056 B] Get: 135 http://deb.debian.org/debian buster/main arm64 fontconfig arm64 2.13.1-2 [405 kB] Get: 136 http://deb.debian.org/debian buster/main arm64 fonts-lmodern all 2.004.5-6 [4539 kB] Get: 137 http://deb.debian.org/debian buster/main arm64 libgfortran5 arm64 8.3.0-6 [298 kB] Get: 138 http://deb.debian.org/debian buster/main arm64 libgfortran-8-dev arm64 8.3.0-6 [346 kB] Get: 139 http://deb.debian.org/debian buster/main arm64 gfortran-8 arm64 8.3.0-6 [7861 kB] Get: 140 http://deb.debian.org/debian buster/main arm64 gfortran arm64 4:8.3.0-1 [1420 B] Get: 141 http://deb.debian.org/debian buster/main arm64 libgirepository-1.0-1 arm64 1.58.3-2 [85.1 kB] Get: 142 http://deb.debian.org/debian buster/main arm64 gir1.2-glib-2.0 arm64 1.58.3-2 [143 kB] Get: 143 http://deb.debian.org/debian buster/main arm64 libpixman-1-0 arm64 0.36.0-1 [436 kB] Get: 144 http://deb.debian.org/debian buster/main arm64 libxcb-render0 arm64 1.13.1-2 [108 kB] Get: 145 http://deb.debian.org/debian buster/main arm64 libxcb-shm0 arm64 1.13.1-2 [99.3 kB] Get: 146 http://deb.debian.org/debian buster/main arm64 libcairo2 arm64 1.16.0-4 [644 kB] Get: 147 http://deb.debian.org/debian buster/main arm64 libcairo-gobject2 arm64 1.16.0-4 [124 kB] Get: 148 http://deb.debian.org/debian buster/main arm64 gir1.2-freedesktop arm64 1.58.3-2 [20.3 kB] Get: 149 http://deb.debian.org/debian buster/main arm64 libgraphite2-3 arm64 1.3.13-7 [75.8 kB] Get: 150 http://deb.debian.org/debian buster/main arm64 libharfbuzz0b arm64 2.3.1-1 [1155 kB] Get: 151 http://deb.debian.org/debian buster/main arm64 libharfbuzz-gobject0 arm64 2.3.1-1 [847 kB] Get: 152 http://deb.debian.org/debian buster/main arm64 gir1.2-harfbuzz-0.0 arm64 2.3.1-1 [853 kB] Get: 153 http://deb.debian.org/debian buster/main arm64 libfribidi0 arm64 1.0.5-3.1+deb10u1 [63.6 kB] Get: 154 http://deb.debian.org/debian buster/main arm64 libthai-data all 0.1.28-2 [170 kB] Get: 155 http://deb.debian.org/debian buster/main arm64 libdatrie1 arm64 0.2.12-2 [38.6 kB] Get: 156 http://deb.debian.org/debian buster/main arm64 libthai0 arm64 0.1.28-2 [52.8 kB] Get: 157 http://deb.debian.org/debian buster/main arm64 libpango-1.0-0 arm64 1.42.4-8~deb10u1 [179 kB] Get: 158 http://deb.debian.org/debian buster/main arm64 libpangoft2-1.0-0 arm64 1.42.4-8~deb10u1 [65.7 kB] Get: 159 http://deb.debian.org/debian buster/main arm64 libpangocairo-1.0-0 arm64 1.42.4-8~deb10u1 [54.0 kB] Get: 160 http://deb.debian.org/debian buster/main arm64 libxft2 arm64 2.3.2-2 [51.3 kB] Get: 161 http://deb.debian.org/debian buster/main arm64 libpangoxft-1.0-0 arm64 1.42.4-8~deb10u1 [49.1 kB] Get: 162 http://deb.debian.org/debian buster/main arm64 gir1.2-pango-1.0 arm64 1.42.4-8~deb10u1 [55.8 kB] Get: 163 http://deb.debian.org/debian buster/main arm64 icu-devtools arm64 63.1-6+deb10u1 [179 kB] Get: 164 http://deb.debian.org/debian buster/main arm64 libblas3 arm64 3.8.0-2 [100 kB] Get: 165 http://deb.debian.org/debian buster/main arm64 libblas-dev arm64 3.8.0-2 [105 kB] Get: 166 http://deb.debian.org/debian buster/main arm64 uuid-dev arm64 2.33.1-0.1 [93.8 kB] Get: 167 http://deb.debian.org/debian buster/main arm64 libblkid-dev arm64 2.33.1-0.1 [229 kB] Get: 168 http://deb.debian.org/debian buster/main arm64 libbrotli1 arm64 1.0.7-2 [261 kB] Get: 169 http://deb.debian.org/debian buster/main arm64 libbz2-dev arm64 1.0.6-9.2~deb10u1 [30.9 kB] Get: 170 http://deb.debian.org/debian buster/main arm64 liblzo2-2 arm64 2.10-0.1 [49.0 kB] Get: 171 http://deb.debian.org/debian buster/main arm64 libcairo-script-interpreter2 arm64 1.16.0-4 [157 kB] Get: 172 http://deb.debian.org/debian buster/main arm64 libexpat1-dev arm64 2.2.6-2+deb10u1 [128 kB] Get: 173 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Get: 174 http://deb.debian.org/debian buster/main arm64 libpng-dev arm64 1.6.36-6 [297 kB] Get: 175 http://deb.debian.org/debian buster/main arm64 libfreetype6-dev arm64 2.9.1-3+deb10u2 [526 kB] Get: 176 http://deb.debian.org/debian buster/main arm64 pkg-config arm64 0.29-6 [62.2 kB] Get: 177 http://deb.debian.org/debian buster/main arm64 libfontconfig1-dev arm64 2.13.1-2 [964 kB] Get: 178 http://deb.debian.org/debian buster/main arm64 xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get: 179 http://deb.debian.org/debian buster/main arm64 x11proto-dev all 2018.4-4 [251 kB] Get: 180 http://deb.debian.org/debian buster/main arm64 x11proto-core-dev all 2018.4-4 [3128 B] Get: 181 http://deb.debian.org/debian buster/main arm64 libxau-dev arm64 1:1.0.8-1+b2 [22.8 kB] Get: 182 http://deb.debian.org/debian buster/main arm64 libxdmcp-dev arm64 1:1.1.2-3 [41.2 kB] Get: 183 http://deb.debian.org/debian buster/main arm64 xtrans-dev all 1.3.5-1 [100 kB] Get: 184 http://deb.debian.org/debian buster/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5336 B] Get: 185 http://deb.debian.org/debian buster/main arm64 libxcb1-dev arm64 1.13.1-2 [174 kB] Get: 186 http://deb.debian.org/debian buster/main arm64 libx11-dev arm64 2:1.6.7-1+deb10u1 [811 kB] Get: 187 http://deb.debian.org/debian buster/main arm64 libxrender-dev arm64 1:0.9.10-1 [38.8 kB] Get: 188 http://deb.debian.org/debian buster/main arm64 x11proto-xext-dev all 2018.4-4 [3128 B] Get: 189 http://deb.debian.org/debian buster/main arm64 libxext-dev arm64 2:1.3.3-1+b2 [104 kB] Get: 190 http://deb.debian.org/debian buster/main arm64 libice6 arm64 2:1.0.9-2 [52.0 kB] Get: 191 http://deb.debian.org/debian buster/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 192 http://deb.debian.org/debian buster/main arm64 libice-dev arm64 2:1.0.9-2 [62.0 kB] Get: 193 http://deb.debian.org/debian buster/main arm64 libsm-dev arm64 2:1.2.3-1 [37.4 kB] Get: 194 http://deb.debian.org/debian buster/main arm64 libpixman-1-dev arm64 0.36.0-1 [453 kB] Get: 195 http://deb.debian.org/debian buster/main arm64 libxcb-render0-dev arm64 1.13.1-2 [113 kB] Get: 196 http://deb.debian.org/debian buster/main arm64 libxcb-shm0-dev arm64 1.13.1-2 [101 kB] Get: 197 http://deb.debian.org/debian buster/main arm64 libffi-dev arm64 3.2.1-9 [155 kB] Get: 198 http://deb.debian.org/debian buster/main arm64 libglib2.0-data all 2.58.3-2+deb10u2 [1110 kB] Get: 199 http://deb.debian.org/debian buster/main arm64 libglib2.0-bin arm64 2.58.3-2+deb10u2 [122 kB] Get: 200 http://deb.debian.org/debian buster/main arm64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 201 http://deb.debian.org/debian buster/main arm64 python3-distutils all 3.7.3-1 [142 kB] Get: 202 http://deb.debian.org/debian buster/main arm64 libglib2.0-dev-bin arm64 2.58.3-2+deb10u2 [156 kB] Get: 203 http://deb.debian.org/debian buster/main arm64 libmount-dev arm64 2.33.1-0.1 [238 kB] Get: 204 http://deb.debian.org/debian buster/main arm64 libpcre16-3 arm64 2:8.39-12 [236 kB] Get: 205 http://deb.debian.org/debian buster/main arm64 libpcre32-3 arm64 2:8.39-12 [230 kB] Get: 206 http://deb.debian.org/debian buster/main arm64 libpcrecpp0v5 arm64 2:8.39-12 [151 kB] Get: 207 http://deb.debian.org/debian buster/main arm64 libpcre3-dev arm64 2:8.39-12 [578 kB] Get: 208 http://deb.debian.org/debian buster/main arm64 libsepol1-dev arm64 2.8-1 [308 kB] Get: 209 http://deb.debian.org/debian buster/main arm64 libselinux1-dev arm64 2.8-1+b1 [163 kB] Get: 210 http://deb.debian.org/debian buster/main arm64 libglib2.0-dev arm64 2.58.3-2+deb10u2 [1509 kB] Get: 211 http://deb.debian.org/debian buster/main arm64 libcairo2-dev arm64 1.16.0-4 [706 kB] Get: 212 http://deb.debian.org/debian buster/main arm64 libcupsimage2 arm64 2.2.10-6+deb10u4 [132 kB] Get: 213 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 214 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 215 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u4 [89.8 kB] Get: 216 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u4 [216 kB] Get: 217 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 218 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 219 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 220 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 221 http://deb.debian.org/debian buster/main arm64 libcurl4 arm64 7.64.0-4+deb10u1 [312 kB] Get: 222 http://deb.debian.org/debian buster/main arm64 libcurl4-openssl-dev arm64 7.64.0-4+deb10u1 [409 kB] Get: 223 http://deb.debian.org/debian buster/main arm64 libfontenc1 arm64 1:1.1.3-1+b2 [22.7 kB] Get: 224 http://deb.debian.org/debian buster/main arm64 libfribidi-dev arm64 1.0.5-3.1+deb10u1 [101 kB] Get: 225 http://deb.debian.org/debian buster/main arm64 libgraphite2-dev arm64 1.3.13-7 [23.1 kB] Get: 226 http://deb.debian.org/debian buster/main arm64 libgs9-common all 9.27~dfsg-2+deb10u4 [5136 kB] Get: 227 http://deb.debian.org/debian buster/main arm64 libidn11 arm64 1.33-2.2 [113 kB] Get: 228 http://deb.debian.org/debian buster/main arm64 libijs-0.35 arm64 0.35-14 [17.9 kB] Get: 229 http://deb.debian.org/debian buster/main arm64 libjbig2dec0 arm64 0.16-1 [58.1 kB] Get: 230 http://deb.debian.org/debian buster/main arm64 libopenjp2-7 arm64 2.3.0-2+deb10u1 [148 kB] Get: 231 http://deb.debian.org/debian buster/main arm64 libpaper1 arm64 1.1.28 [21.1 kB] Get: 232 http://deb.debian.org/debian buster/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 233 http://deb.debian.org/debian buster/main arm64 libwebp6 arm64 0.6.1-2 [233 kB] Get: 234 http://deb.debian.org/debian buster/main arm64 libtiff5 arm64 4.1.0+git191117-2~deb10u1 [259 kB] Get: 235 http://deb.debian.org/debian buster/main arm64 libgs9 arm64 9.27~dfsg-2+deb10u4 [2027 kB] Get: 236 http://deb.debian.org/debian buster/main arm64 libharfbuzz-icu0 arm64 2.3.1-1 [834 kB] Get: 237 http://deb.debian.org/debian buster/main arm64 libicu-dev arm64 63.1-6+deb10u1 [9062 kB] Get: 238 http://deb.debian.org/debian buster/main arm64 libharfbuzz-dev arm64 2.3.1-1 [1282 kB] Get: 239 http://deb.debian.org/debian buster/main arm64 libjbig-dev arm64 2.1-3.1+b2 [28.3 kB] Get: 240 http://deb.debian.org/debian buster/main arm64 libjpeg62-turbo-dev arm64 1:1.5.2-2+deb10u1 [195 kB] Get: 241 http://deb.debian.org/debian buster/main arm64 libjpeg-dev all 1:1.5.2-2+deb10u1 [57.7 kB] Get: 242 http://deb.debian.org/debian buster/main arm64 libkpathsea6 arm64 2018.20181218.49446-1 [164 kB] Get: 243 http://deb.debian.org/debian buster/main arm64 liblapack3 arm64 3.8.0-2 [1489 kB] Get: 244 http://deb.debian.org/debian buster/main arm64 liblapack-dev arm64 3.8.0-2 [1524 kB] Get: 245 http://deb.debian.org/debian buster/main arm64 liblzma-dev arm64 5.2.4-1 [209 kB] Get: 246 http://deb.debian.org/debian buster/main arm64 libmime-charset-perl all 1.012.2-1 [35.4 kB] Get: 247 http://deb.debian.org/debian buster/main arm64 libncurses-dev arm64 6.1+20181013-2+deb10u2 [324 kB] Get: 248 http://deb.debian.org/debian buster/main arm64 libncurses5-dev arm64 6.1+20181013-2+deb10u2 [948 B] Get: 249 http://deb.debian.org/debian buster/main arm64 libxft-dev arm64 2.3.2-2 [64.3 kB] Get: 250 http://deb.debian.org/debian buster/main arm64 pango1.0-tools arm64 1.42.4-8~deb10u1 [55.2 kB] Get: 251 http://deb.debian.org/debian buster/main arm64 libpango1.0-dev arm64 1.42.4-8~deb10u1 [139 kB] Get: 252 http://deb.debian.org/debian buster/main arm64 libpaper-utils arm64 1.1.28 [18.0 kB] Get: 253 http://deb.debian.org/debian buster/main arm64 libpotrace0 arm64 1.15-1 [23.6 kB] Get: 254 http://deb.debian.org/debian buster/main arm64 libptexenc1 arm64 2018.20181218.49446-1 [60.3 kB] Get: 255 http://deb.debian.org/debian buster/main arm64 libreadline-dev arm64 7.0-5 [128 kB] Get: 256 http://deb.debian.org/debian buster/main arm64 libsombok3 arm64 2.4.0-2 [27.7 kB] Get: 257 http://deb.debian.org/debian buster/main arm64 libsynctex2 arm64 2018.20181218.49446-1 [77.8 kB] Get: 258 http://deb.debian.org/debian buster/main arm64 libtcl8.6 arm64 8.6.9+dfsg-2 [950 kB] Get: 259 http://deb.debian.org/debian buster/main arm64 libteckit0 arm64 2.5.8+ds2-5 [284 kB] Get: 260 http://deb.debian.org/debian buster/main arm64 libtexlua52 arm64 2018.20181218.49446-1 [107 kB] Get: 261 http://deb.debian.org/debian buster/main arm64 libtexlua53 arm64 2018.20181218.49446-1 [118 kB] Get: 262 http://deb.debian.org/debian buster/main arm64 libtext-unidecode-perl all 1.30-1 [103 kB] Get: 263 http://deb.debian.org/debian buster/main arm64 libtiffxx5 arm64 4.1.0+git191117-2~deb10u1 [117 kB] Get: 264 http://deb.debian.org/debian buster/main arm64 libtiff-dev arm64 4.1.0+git191117-2~deb10u1 [384 kB] Get: 265 http://deb.debian.org/debian buster/main arm64 libtiff5-dev arm64 4.1.0+git191117-2~deb10u1 [114 kB] Get: 266 http://deb.debian.org/debian buster/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 267 http://deb.debian.org/debian buster/main arm64 libtk8.6 arm64 8.6.9-2 [728 kB] Get: 268 http://deb.debian.org/debian buster/main arm64 libunicode-linebreak-perl arm64 0.0.20190101-1 [102 kB] Get: 269 http://deb.debian.org/debian buster/main arm64 libunwind8 arm64 1.2.1-10~deb10u1 [50.6 kB] Get: 270 http://deb.debian.org/debian buster/main arm64 libwoff1 arm64 1.0.2-1 [40.7 kB] Get: 271 http://deb.debian.org/debian buster/main arm64 libxt6 arm64 1:1.1.5-1+b3 [175 kB] Get: 272 http://deb.debian.org/debian buster/main arm64 libxmu6 arm64 2:1.1.2-2+b3 [57.8 kB] Get: 273 http://deb.debian.org/debian buster/main arm64 libxpm4 arm64 1:3.5.12-1 [43.9 kB] Get: 274 http://deb.debian.org/debian buster/main arm64 libxaw7 arm64 2:1.0.13-1+b2 [167 kB] Get: 275 http://deb.debian.org/debian buster/main arm64 libxfont2 arm64 1:2.0.3-1 [122 kB] Get: 276 http://deb.debian.org/debian buster/main arm64 libxkbfile1 arm64 1:1.0.9-2+b11 [71.4 kB] Get: 277 http://deb.debian.org/debian buster/main arm64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get: 278 http://deb.debian.org/debian buster/main arm64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get: 279 http://deb.debian.org/debian buster/main arm64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get: 280 http://deb.debian.org/debian buster/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-1 [334 kB] Get: 281 http://deb.debian.org/debian buster/main arm64 libxmuu1 arm64 2:1.1.2-2+b3 [24.1 kB] Get: 282 http://deb.debian.org/debian buster/main arm64 x11proto-scrnsaver-dev all 2018.4-4 [3136 B] Get: 283 http://deb.debian.org/debian buster/main arm64 libxss-dev arm64 1:1.2.3-1 [23.5 kB] Get: 284 http://deb.debian.org/debian buster/main arm64 libxt-dev arm64 1:1.1.5-1+b3 [424 kB] Get: 285 http://deb.debian.org/debian buster/main arm64 libxxhash0 arm64 0.6.5-2 [7684 B] Get: 286 http://deb.debian.org/debian buster/main arm64 libzzip-0-13 arm64 0.13.62-3.2 [55.5 kB] Get: 287 http://deb.debian.org/debian buster/main arm64 mpack arm64 1.6-8.2 [32.6 kB] Get: 288 http://deb.debian.org/debian buster/main arm64 preview-latex-style all 11.91-2 [201 kB] Get: 289 http://deb.debian.org/debian buster/main arm64 t1utils arm64 1.41-3 [59.7 kB] Get: 290 http://deb.debian.org/debian buster/main arm64 tcl8.6 arm64 8.6.9+dfsg-2 [123 kB] Get: 291 http://deb.debian.org/debian buster/main arm64 tcl8.6-dev arm64 8.6.9+dfsg-2 [982 kB] Get: 292 http://deb.debian.org/debian buster/main arm64 texinfo arm64 6.5.0.dfsg.1-4+b1 [1427 kB] Get: 293 http://deb.debian.org/debian buster/main arm64 texlive-binaries arm64 2018.20181218.49446-1 [8464 kB] Get: 294 http://deb.debian.org/debian buster/main arm64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 295 http://deb.debian.org/debian buster/main arm64 texlive-base all 2018.20190227-2 [19.7 MB] Get: 296 http://deb.debian.org/debian buster/main arm64 texlive-latex-base all 2018.20190227-2 [984 kB] Get: 297 http://deb.debian.org/debian buster/main arm64 texlive-extra-utils all 2018.20190227-2 [39.4 MB] Get: 298 http://deb.debian.org/debian buster/main arm64 texlive-fonts-extra all 2018.20190227-2 [412 MB] Get: 299 http://deb.debian.org/debian buster/main arm64 texlive-fonts-recommended all 2018.20190227-2 [5228 kB] Get: 300 http://deb.debian.org/debian buster/main arm64 texlive-plain-generic all 2018.20190227-2 [24.3 MB] Get: 301 http://deb.debian.org/debian buster/main arm64 texlive-generic-recommended all 2018.20190227-2 [32.2 kB] Get: 302 http://deb.debian.org/debian buster/main arm64 texlive-latex-recommended all 2018.20190227-2 [15.2 MB] Get: 303 http://deb.debian.org/debian buster/main arm64 texlive-pictures all 2018.20190227-2 [8201 kB] Get: 304 http://deb.debian.org/debian buster/main arm64 texlive-latex-extra all 2018.20190227-2 [12.3 MB] Get: 305 http://deb.debian.org/debian buster/main arm64 tk8.6 arm64 8.6.9-2 [72.2 kB] Get: 306 http://deb.debian.org/debian buster/main arm64 tk8.6-dev arm64 8.6.9-2 [747 kB] Get: 307 http://deb.debian.org/debian buster/main arm64 x11-xkb-utils arm64 7.7+4 [146 kB] Get: 308 http://deb.debian.org/debian buster/main arm64 xauth arm64 1:1.0.10-1 [38.2 kB] Get: 309 http://deb.debian.org/debian buster/main arm64 xfonts-encodings all 1:1.0.4-2 [574 kB] Get: 310 http://deb.debian.org/debian buster/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 311 http://deb.debian.org/debian buster/main arm64 xfonts-base all 1:1.0.5 [5897 kB] Get: 312 http://deb.debian.org/debian buster/main arm64 xkb-data all 2.26-2 [681 kB] Get: 313 http://deb.debian.org/debian buster/main arm64 xserver-common all 2:1.20.4-1+deb10u1 [2235 kB] Get: 314 http://deb.debian.org/debian buster/main arm64 xvfb arm64 2:1.20.4-1+deb10u1 [2934 kB] Fetched 936 MB in 2min 4s (7560 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... 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Setting up libgs9-common (9.27~dfsg-2+deb10u4) ... Setting up libpcrecpp0v5:arm64 (2:8.39-12) ... Setting up libpipeline1:arm64 (1.5.1-2) ... Setting up libgraphite2-3:arm64 (1.3.13-7) ... Setting up liblcms2-2:arm64 (2.9-3) ... Setting up libpixman-1-0:arm64 (0.36.0-1) ... Setting up lsb-base (10.2019051400) ... Setting up libx11-xcb1:arm64 (2:1.6.7-1+deb10u1) ... Setting up libxau6:arm64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:arm64 (1.6-6) ... Setting up libpsl5:arm64 (0.20.2-2) ... Setting up libpixman-1-dev:arm64 (0.36.0-1) ... Setting up mime-support (3.62) ... Setting up libtexlua52:arm64 (2018.20181218.49446-1) ... Setting up libpcre16-3:arm64 (2:8.39-12) ... Setting up libbison-dev:arm64 (2:3.3.2.dfsg-1) ... Setting up java-common (0.71) ... Setting up libdatrie1:arm64 (0.2.12-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up mpack (1.6-8.2) ... Setting up libtexlua53:arm64 (2018.20181218.49446-1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libglvnd0:arm64 (1.1.0-1) ... Setting up libijs-0.35:arm64 (0.35-14) ... Setting up libbrotli1:arm64 (1.0.7-2) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.5.0-3) ... Setting up libnghttp2-14:arm64 (1.36.0-2+deb10u1) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up libsepol1-dev:arm64 (2.8-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up xkb-data (2.26-2) ... Setting up liblzo2-2:arm64 (2.10-0.1) ... Setting up libzzip-0-13:arm64 (0.13.62-3.2) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libffi-dev:arm64 (3.2.1-9) ... 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Setting up libglib2.0-bin (2.58.3-2+deb10u2) ... Setting up libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u4) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:arm64 (2:3.42.1-1+deb10u3) ... Setting up libxcb-shm0:arm64 (1.13.1-2) ... Setting up libreadline-dev:arm64 (7.0-5) ... Setting up gfortran (4:8.3.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up libxcb-present0:arm64 (1.13.1-2) ... Setting up libthai0:arm64 (0.1.28-2) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libxdmcp-dev:arm64 (1:1.1.2-3) ... Setting up libblas3:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libptexenc1:arm64 (2018.20181218.49446-1) ... Setting up libfreetype6:arm64 (2.9.1-3+deb10u2) ... Setting up libtiff-dev:arm64 (4.1.0+git191117-2~deb10u1) ... Setting up libxcb-sync1:arm64 (1.13.1-2) ... Setting up x11proto-core-dev (2018.4-4) ... Setting up bsdmainutils (11.1.2+b1) ... 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 libgssapi-krb5-2:arm64 (1.17-3+deb10u1) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up gir1.2-glib-2.0:arm64 (1.58.3-2) ... Setting up autoconf (2.69-11) ... Setting up libxcb-dri2-0:arm64 (1.13.1-2) ... Setting up x11proto-xext-dev (2018.4-4) ... Setting up libdrm2:arm64 (2.4.97-1) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libncurses5-dev:arm64 (6.1+20181013-2+deb10u2) ... Setting up bison (2:3.3.2.dfsg-1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libcurl4:arm64 (7.64.0-4+deb10u1) ... Setting up libllvm7:arm64 (1:7.0.1-8+deb10u2) ... Setting up libx11-6:arm64 (2:1.6.7-1+deb10u1) ... Setting up libharfbuzz0b:arm64 (2.3.1-1) ... Setting up libxkbfile1:arm64 (1:1.0.9-2+b11) ... Setting up x11proto-scrnsaver-dev (2018.4-4) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libxfont2:arm64 (1:2.0.3-1) ... Setting up libavahi-client3:arm64 (0.7-4+b1) ... Setting up libmount-dev:arm64 (2.33.1-0.1) ... Setting up libxmuu1:arm64 (2:1.1.2-2+b3) ... Setting up libblas-dev:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libpython3-stdlib:arm64 (3.7.3-1) ... Setting up libdrm-amdgpu1:arm64 (2.4.97-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:arm64 (1.13.1-2) ... Setting up libpaper1:arm64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up python3.7 (3.7.3-2+deb10u2) ... Setting up liblapack3:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libdrm-nouveau2:arm64 (2.4.97-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libharfbuzz-icu0:arm64 (2.3.1-1) ... Setting up libdrm-etnaviv1:arm64 (2.4.97-1) ... Setting up libxcb1-dev:arm64 (1.13.1-2) ... Setting up libxpm4:arm64 (1:3.5.12-1) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up libsombok3:arm64 (2.4.0-2) ... Setting up libsm-dev:arm64 (2:1.2.3-1) ... Setting up libselinux1-dev:arm64 (2.8-1+b1) ... Setting up libdrm-radeon1:arm64 (2.4.97-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libgl1-mesa-dri:arm64 (18.3.6-2+deb10u1) ... Setting up libx11-dev:arm64 (2:1.6.7-1+deb10u1) ... Setting up libxext6:arm64 (2:1.3.3-1+b2) ... Setting up libtiff5-dev (4.1.0+git191117-2~deb10u1) ... Setting up python3 (3.7.3-1) ... Setting up libharfbuzz-gobject0:arm64 (2.3.1-1) ... Setting up libpaper-utils (1.1.28) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gir1.2-harfbuzz-0.0:arm64 (2.3.1-1) ... Setting up python2 (2.7.16-1) ... Setting up libfreetype6-dev:arm64 (2.9.1-3+deb10u2) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up tex-common (6.11) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxcb-shm0-dev:arm64 (1.13.1-2) ... Setting up libpython-stdlib:arm64 (2.7.16-1) ... Setting up xfonts-base (1:1.0.5) ... Setting up libxfixes3:arm64 (1:5.0.3-1) ... Setting up libcurl4-openssl-dev:arm64 (7.64.0-4+deb10u1) ... Setting up libunicode-linebreak-perl (0.0.20190101-1) ... Setting up liblapack-dev:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libxcb-render0-dev:arm64 (1.13.1-2) ... Setting up libxt6:arm64 (1:1.1.5-1+b3) ... Setting up libxext-dev:arm64 (2:1.3.3-1+b2) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libcups2:arm64 (2.2.10-6+deb10u4) ... Setting up xauth (1:1.0.10-1) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libfontconfig1:arm64 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up libxrender-dev:arm64 (1:0.9.10-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up libglib2.0-dev-bin (2.58.3-2+deb10u2) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.2-2) ... Setting up libxmu6:arm64 (2:1.1.2-2+b3) ... Setting up libfontconfig1-dev:arm64 (2.13.1-2) ... Setting up libxdamage1:arm64 (1:1.1.4-3+b3) ... Setting up libxi6:arm64 (2:1.7.9-1) ... Setting up libxtst6:arm64 (2:1.2.3-1) ... Setting up po-debconf (1.0.21) ... Setting up preview-latex-style (11.91-2) ... Setting up libtk8.6:arm64 (8.6.9-2) ... Setting up libpango-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up libxaw7:arm64 (2:1.0.13-1+b2) ... Setting up libxss-dev:arm64 (1:1.2.3-1) ... Setting up libcairo2:arm64 (1.16.0-4) ... Setting up libcupsimage2:arm64 (2.2.10-6+deb10u4) ... Setting up libglib2.0-dev:arm64 (2.58.3-2+deb10u2) ... Setting up libxt-dev:arm64 (1:1.1.5-1+b3) ... Setting up texinfo (6.5.0.dfsg.1-4+b1) ... Running mktexlsr. This may take some time. ... done. Setting up libcairo-gobject2:arm64 (1.16.0-4) ... Setting up libpangoft2-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up libpangocairo-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up libxft-dev:arm64 (2.3.2-2) ... Setting up libcairo-script-interpreter2:arm64 (1.16.0-4) ... Setting up tk8.6 (8.6.9-2) ... Setting up libharfbuzz-dev:arm64 (2.3.1-1) ... Setting up gir1.2-freedesktop:arm64 (1.58.3-2) ... Setting up libglx-mesa0:arm64 (18.3.6-2+deb10u1) ... Setting up libgs9:arm64 (9.27~dfsg-2+deb10u4) ... Setting up libpangoxft-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up libglx0:arm64 (1.1.0-1) ... Setting up x11-xkb-utils (7.7+4) ... Setting up pango1.0-tools (1.42.4-8~deb10u1) ... Setting up gir1.2-pango-1.0:arm64 (1.42.4-8~deb10u1) ... Setting up libgl1:arm64 (1.1.0-1) ... Setting up tk8.6-dev:arm64 (8.6.9-2) ... Setting up texlive-binaries (2018.20181218.49446-1) ... 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 Setting up libcairo2-dev:arm64 (1.16.0-4) ... Setting up xserver-common (2:1.20.4-1+deb10u1) ... Setting up texlive-base (2018.20190227-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex Setting up xvfb (2:1.20.4-1+deb10u1) ... Setting up texlive-plain-generic (2018.20190227-2) ... Setting up texlive-latex-base (2018.20190227-2) ... Setting up texlive-extra-utils (2018.20190227-2) ... Setting up texlive-fonts-extra (2018.20190227-2) ... Setting up libpango1.0-dev:arm64 (1.42.4-8~deb10u1) ... Setting up texlive-latex-recommended (2018.20190227-2) ... Setting up texlive-generic-recommended (2018.20190227-2) ... Setting up texlive-pictures (2018.20190227-2) ... Setting up texlive-fonts-recommended (2018.20190227-2) ... Setting up texlive-latex-extra (2018.20190227-2) ... Setting up default-jre-headless (2:1.11-71) ... Setting up openjdk-11-jre-headless:arm64 (11.0.9.1+1-1~deb10u2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up debhelper (12.1.1) ... Setting up openjdk-11-jre:arm64 (11.0.9.1+1-1~deb10u2) ... Setting up openjdk-11-jdk-headless:arm64 (11.0.9.1+1-1~deb10u2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre (2:1.11-71) ... Setting up dh-autoreconf (19) ... Setting up default-jdk-headless (2:1.11-71) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up openjdk-11-jdk:arm64 (11.0.9.1+1-1~deb10u2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Taiwan_GRCA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AddTrust_External_Root.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up default-jdk (2:1.11-71) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Processing triggers for tex-common (6.11) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/r-base-3.5.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package r-base dpkg-buildpackage: info: source version 3.5.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dirk Eddelbuettel dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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_SHELL=/bin/bash \ mkdir_p="/bin/mkdir -p" \ MKDIR_P="/bin/mkdir -p" \ R_TEXI2DVICMD=emulation \ R_PAPERSIZE=letter \ R_BROWSER=xdg-open \ R_BZIPCMD=/bin/bzip2 \ R_GZIPCMD="/bin/gzip -n" \ PAGER=/usr/bin/pager \ PERL=/usr/bin/perl \ JAVA_HOME=/usr/lib/jvm/default-java \ R_UNZIPCMD=/usr/bin/unzip \ R_ZIPCMD=/usr/bin/zip \ R_PRINTCMD=/usr/bin/lpr \ TAR=/bin/tar \ LIBnn=lib \ AWK=/usr/bin/awk \ DD=/bin/dd \ GREP=/bin/grep \ FGREP="/bin/grep -F" \ EGREP="/bin/grep -E" \ SED=/bin/sed \ GETWD="/bin/pwd" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ FC=gfortran \ CFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong" \ FCFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong" \ CPPFLAGS= \ LDFLAGS="-Wl,-z,relro" \ 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 aarch64-linux-gnu configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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 whether ln -s works... yes checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for which... /usr/bin/which checking for /usr/bin/pager... /usr/bin/pager checking for /bin/tar... /bin/tar checking for tex... /usr/bin/tex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeindex... /usr/bin/makeindex checking for texi2any... /usr/bin/texi2any checking whether texi2any version is at least 5.1... yes checking for ginstall-info... no checking for install-info... no checking for texi2dvi... /usr/bin/texi2dvi checking for kpsewhich... /usr/bin/kpsewhich checking for latex inconsolata package... found zi4.sty checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip -n 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 working aclocal... found checking for working autoconf... found checking for working autoheader... found checking for bison... bison -y checking for notangle... false checking for realpath... /usr/bin/realpath checking for pkg-config... /usr/bin/pkg-config checking for gcc... gcc -std=gnu99 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 -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether gcc -std=gnu99 needs -traditional... no 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 how to run the C preprocessor... gcc -std=gnu99 -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 whether g++ -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g can compile C++ code... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc -std=gnu99 accepts -fvisibility... yes checking whether g++ accepts -fvisibility... yes checking whether gfortran accepts -fvisibility... 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 ObjC++ compiler found checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc -std=gnu99... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop 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 dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... /usr/bin/awk checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes checking if gcc -std=gnu99 static flag -static works... yes checking if gcc -std=gnu99 supports -c -o file.o... yes checking if gcc -std=gnu99 supports -c -o file.o... 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-L/usr/lib/gcc/aarch64-linux-gnu/8/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/8/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/8/../../.. -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 -std=gnu99 agree on int and double... yes checking whether gfortran and gcc -std=gnu99 agree on double complex... yes checking for gfortran option to support OpenMP... -fopenmp checking whether g++ accepts -M for generating dependencies... yes checking for g++ option to support OpenMP... -fopenmp checking whether we can compute ObjC Make 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checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes 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... 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(cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... yes 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/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/f77_f2c config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib R is now configured for aarch64-unknown-linux-gnu Source directory: . Installation directory: /usr C compiler: gcc -std=gnu99 -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g Fortran 77 compiler: gfortran -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong Default C++ compiler: g++ -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++98 compiler: g++ -std=gnu++98 -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++11 compiler: g++ -std=gnu++11 -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++14 compiler: g++ -std=gnu++14 -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++17 compiler: g++ -std=gnu++17 -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g Fortran 90/95 compiler: gfortran -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong Obj-C compiler: Interfaces supported: X11, tcltk External libraries: readline, BLAS(generic), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, memory profiling Capabilities skipped: Options not enabled: shared BLAS Recommended packages: no touch configure-stamp *** make-arch *** /usr/bin/make CFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong" \ FCFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ LDFLAGS="-Wl,-z,relro" \ PKG_BUILT_STAMP="""" \ R_GZIPCMD="/bin/gzip -n" \ R make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/m4' make[2]: Entering directory '/build/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/tools' make[2]: Entering directory '/build/r-base-3.5.2/doc' make[3]: Entering directory '/build/r-base-3.5.2/doc/html' make[3]: Leaving directory '/build/r-base-3.5.2/doc/html' make[3]: Entering directory '/build/r-base-3.5.2/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/build/r-base-3.5.2/doc' make[2]: Entering directory '/build/r-base-3.5.2/etc' make[2]: Leaving directory '/build/r-base-3.5.2/etc' make[2]: Entering directory '/build/r-base-3.5.2/share' make[2]: Leaving directory '/build/r-base-3.5.2/share' make[2]: Entering directory '/build/r-base-3.5.2/src' make[3]: Entering directory '/build/r-base-3.5.2/src/scripts' creating src/scripts/R.fe make[4]: Entering directory '/build/r-base-3.5.2/src/scripts' mkdir -p -- ../../bin make[4]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Entering directory '/build/r-base-3.5.2/src/include' mkdir -p -- ../../include make[4]: Entering directory '/build/r-base-3.5.2/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[4]: Leaving directory '/build/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/build/r-base-3.5.2/src/include' make[3]: Entering directory '/build/r-base-3.5.2/src/extra' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/build/r-base-3.5.2/src/extra/tre' making regcomp.d from regcomp.c making regerror.d from regerror.c making regexec.d from regexec.c making tre-ast.d from tre-ast.c making tre-compile.d from tre-compile.c making tre-match-approx.d from tre-match-approx.c making tre-match-backtrack.d from tre-match-backtrack.c making tre-match-parallel.d from tre-match-parallel.c making tre-mem.d from tre-mem.c making tre-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/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/build/r-base-3.5.2/src/extra/tre' gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regerror.c -o regerror.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regexec.c -o regexec.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-stack.c -o tre-stack.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c xmalloc.c -o xmalloc.o 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/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/build/r-base-3.5.2/src/extra' make[3]: Entering directory '/build/r-base-3.5.2/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c make[4]: Entering directory '/build/r-base-3.5.2/src/appl' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interv.c -o interv.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c maxcol.c -o maxcol.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pretty.c -o pretty.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uncmin.c -o uncmin.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dchdc.f -o dchdc.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dpbfa.f -o dpbfa.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dpbsl.f -o dpbsl.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dpoco.f -o dpoco.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dpodi.f -o dpodi.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dpofa.f -o dpofa.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dposl.f -o dposl.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dqrdc.f -o dqrdc.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dqrls.f -o dqrls.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dqrsl.f -o dqrsl.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dqrutl.f -o dqrutl.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dsvdc.f -o dsvdc.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dtrco.f -o dtrco.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c dtrsl.f -o dtrsl.o ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[4]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Entering directory '/build/r-base-3.5.2/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making 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 lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_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]: Entering directory '/build/r-base-3.5.2/src/nmath' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mlutils.c -o mlutils.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d1mach.c -o d1mach.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c i1mach.c -o i1mach.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmax2.c -o fmax2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmin2.c -o fmin2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fprec.c -o fprec.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fround.c -o fround.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ftrunc.c -o ftrunc.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sign.c -o sign.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fsign.c -o fsign.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imax2.c -o imax2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imin2.c -o imin2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chebyshev.c -o chebyshev.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log1p.c -o log1p.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgammacor.c -o lgammacor.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gammalims.c -o gammalims.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stirlerr.c -o stirlerr.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bd0.c -o bd0.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma.c -o gamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgamma.c -o lgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma_cody.c -o gamma_cody.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c beta.c -o beta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lbeta.c -o lbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c polygamma.c -o polygamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cospi.c -o cospi.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_i.c -o bessel_i.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_j.c -o bessel_j.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_k.c -o bessel_k.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_y.c -o bessel_y.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c choose.c -o choose.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c snorm.c -o snorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sexp.c -o sexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgamma.c -o dgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgamma.c -o pgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgamma.c -o qgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgamma.c -o rgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbeta.c -o dbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbeta.c -o pbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbeta.c -o qbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbeta.c -o rbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dunif.c -o dunif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c punif.c -o punif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qunif.c -o qunif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c runif.c -o runif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnorm.c -o dnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnorm.c -o pnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnorm.c -o qnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnorm.c -o rnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlnorm.c -o dlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plnorm.c -o plnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlnorm.c -o qlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlnorm.c -o rlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c df.c -o df.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pf.c -o pf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qf.c -o qf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rf.c -o rf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnf.c -o dnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dt.c -o dt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pt.c -o pt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qt.c -o qt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rt.c -o rt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnt.c -o dnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dchisq.c -o dchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pchisq.c -o pchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qchisq.c -o qchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rchisq.c -o rchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnchisq.c -o rnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbinom.c -o dbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbinom.c -o pbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbinom.c -o qbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbinom.c -o rbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rmultinom.c -o rmultinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcauchy.c -o dcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pcauchy.c -o pcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qcauchy.c -o qcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcauchy.c -o rcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dexp.c -o dexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pexp.c -o pexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qexp.c -o qexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rexp.c -o rexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgeom.c -o dgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgeom.c -o pgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgeom.c -o qgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgeom.c -o rgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dhyper.c -o dhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c phyper.c -o phyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qhyper.c -o qhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rhyper.c -o rhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbinom.c -o dnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbinom.c -o pnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbinom.c -o qnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dpois.c -o dpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ppois.c -o ppois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qpois.c -o qpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rpois.c -o rpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dweibull.c -o dweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pweibull.c -o pweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qweibull.c -o qweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rweibull.c -o rweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlogis.c -o dlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plogis.c -o plogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlogis.c -o qlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlogis.c -o rlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnchisq.c -o dnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnchisq.c -o pnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnchisq.c -o qnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbeta.c -o dnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbeta.c -o pnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbeta.c -o qnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnf.c -o pnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnt.c -o pnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnf.c -o qnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnt.c -o qnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptukey.c -o ptukey.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qtukey.c -o qtukey.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c toms708.c -o toms708.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wilcox.c -o wilcox.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signrank.c -o signrank.o 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 lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[4]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Entering directory '/build/r-base-3.5.2/src/unix' config.status: creating src/unix/Makefile making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c make[4]: Entering directory '/build/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rembedded.c -o Rembedded.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dynload.c -o dynload.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c system.c -o system.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-unix.c -o sys-unix.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-std.c -o sys-std.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c X11.c -o X11.o ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[4]: Entering directory '/build/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/build/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Entering directory '/build/r-base-3.5.2/src/main' config.status: creating src/main/Makefile 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 altrep.d from altrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making radixsort.d from radixsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making times.d from times.c making unique.d from unique.c making util.d from util.c making version.d from version.c making 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 making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[4]: Entering directory '/build/r-base-3.5.2/src/main' gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CommandLineArgs.c -o CommandLineArgs.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rdynload.c -o Rdynload.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Renviron.c -o Renviron.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RNG.c -o RNG.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c agrep.c -o agrep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c altrep.c -o altrep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c apply.c -o apply.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arithmetic.c -o arithmetic.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c array.c -o array.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attrib.c -o attrib.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bind.c -o bind.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c builtin.c -o builtin.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c character.c -o character.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coerce.c -o coerce.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complex.c -o complex.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connections.c -o connections.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c context.c -o context.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cum.c -o cum.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcf.c -o dcf.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c datetime.c -o datetime.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c debug.c -o debug.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deparse.c -o deparse.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dotcode.c -o dotcode.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dounzip.c -o dounzip.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dstruct.c -o dstruct.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c duplicate.c -o duplicate.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c edit.c -o edit.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c engine.c -o engine.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c errors.c -o errors.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c eval.c -o eval.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c format.c -o format.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gevents.c -o gevents.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram.c -o gram.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram-ex.c -o gram-ex.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grep.c -o grep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c identical.c -o identical.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inlined.c -o inlined.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inspect.c -o inspect.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c internet.c -o internet.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c iosupport.c -o iosupport.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lapack.c -o lapack.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c list.c -o list.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c localecharset.c -o localecharset.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c logic.c -o logic.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c main.c -o main.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mapply.c -o mapply.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match.c -o match.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c memory.c -o memory.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c names.c -o names.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c objects.c -o objects.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c options.c -o options.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c paste.c -o paste.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c platform.c -o platform.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plotmath.c -o plotmath.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c print.c -o print.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printarray.c -o printarray.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printvector.c -o printvector.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printutils.c -o printutils.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qsort.c -o qsort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c radixsort.c -o radixsort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raw.c -o raw.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c registration.c -o registration.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c relop.c -o relop.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlocale.c -o rlocale.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c saveload.c -o saveload.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scan.c -o scan.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c seq.c -o seq.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c serialize.c -o serialize.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sort.c -o sort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c source.c -o source.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c split.c -o split.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sprintf.c -o sprintf.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c startup.c -o startup.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subassign.c -o subassign.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subscript.c -o subscript.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subset.c -o subset.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c summary.c -o summary.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sysutils.c -o sysutils.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c times.c -o times.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unique.c -o unique.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c version.c -o version.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_alab_her.c -o g_alab_her.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_cntrlify.c -o g_cntrlify.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_fontdb.c -o g_fontdb.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_her_glyph.c -o g_her_glyph.o gfortran -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c xxxpr.f -o xxxpr.o gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lblas -lgfortran -lm -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[5]: Entering directory '/build/r-base-3.5.2/src/main' mkdir -p -- /build/r-base-3.5.2/bin/exec mkdir -p -- /build/r-base-3.5.2/lib make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmain.c -o Rmain.o gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,-z,relro -o R.bin Rmain.o -lR make[5]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Entering directory '/build/r-base-3.5.2/src/modules' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/internet' making Rhttpd.d from Rhttpd.c making Rsock.d from Rsock.c making internet.d from internet.c making libcurl.d from libcurl.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/r-base-3.5.2/src/modules/internet' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c internet.c -o internet.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c libcurl.c -o libcurl.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c nanoftp.c -o nanoftp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c nanohttp.c -o nanohttp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sock.c -o sock.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR make[6]: Entering directory '/build/r-base-3.5.2/src/modules/internet' mkdir -p -- /build/r-base-3.5.2/modules make[6]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' making Lapack.d from Lapack.c make[5]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Lapack.c -o Lapack.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o lapack.so Lapack.o -lR -llapack -lblas -lgfortran -lm make[6]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[6]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/X11' making devX11.d from devX11.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c make[5]: Entering directory '/build/r-base-3.5.2/src/modules/X11' gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/aarch64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devX11.c -o devX11.o gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/aarch64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rotated.c -o rotated.o gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/aarch64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbitmap.c -o rbitmap.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/aarch64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dataentry.c -o dataentry.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/X11' make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/build/r-base-3.5.2/src/modules' make[3]: Entering directory '/build/r-base-3.5.2/src/library' mkdir -p -- ../../library make[4]: Entering directory '/build/r-base-3.5.2/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[4]: Leaving directory '/build/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/build/r-base-3.5.2/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[5]: Entering directory '/build/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/build/r-base-3.5.2/src/library/base' mkdir -p -- ../../../library/base/demo make[5]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' mkdir -p -- ../../../library/tools/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/build/r-base-3.5.2/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c text.c -o text.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmd5.c -o Rmd5.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signals.c -o signals.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c install.c -o install.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getfmts.c -o getfmts.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http.c -o http.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramLatex.c -o gramLatex.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramRd.c -o gramRd.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[7]: Entering directory '/build/r-base-3.5.2/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[7]: Leaving directory '/build/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/build/r-base-3.5.2/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[5]: Entering directory '/build/r-base-3.5.2/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/build/r-base-3.5.2/src/library/compiler' byte-compiling package 'compiler' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' byte-compiling package 'base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tools' byte-compiling package 'tools' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/build/r-base-3.5.2/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/build/r-base-3.5.2/src/library/utils/src' making init.d from init.c making io.d from io.c making size.d from size.c making sock.d from sock.c making stubs.d from stubs.c making utils.d from utils.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c size.c -o size.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sock.c -o sock.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[7]: Entering directory '/build/r-base-3.5.2/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[7]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' byte-compiling package 'utils' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' making axis_scales.d from axis_scales.c making chull.d from chull.c making devices.d from devices.c making init.d from init.c making stubs.d from stubs.c making colors.d from colors.c making devCairo.d from devCairo.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c making devQuartz.d from devQuartz.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c axis_scales.c -o axis_scales.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chull.c -o chull.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devCairo.c -o devCairo.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPicTeX.c -o devPicTeX.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPS.c -o devPS.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devQuartz.c -o devQuartz.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[7]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[8]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[9]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' gcc -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../../../src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cairoBM.c -o cairoBM.o gcc -std=gnu99 -shared -L"../../../../../lib" -Wl,-z,relro -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm make[10]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' byte-compiling package 'grDevices' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/build/r-base-3.5.2/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/build/r-base-3.5.2/src/library/graphics/src' making init.d from init.c making base.d from base.c making graphics.d from graphics.c making par.d from par.c making plot.d from plot.c making plot3d.d from plot3d.c making stem.d from stem.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base.c -o base.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c par.c -o par.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stem.c -o stem.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[7]: Entering directory '/build/r-base-3.5.2/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[7]: Leaving directory '/build/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' byte-compiling package 'graphics' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/build/r-base-3.5.2/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' mkdir -p -- ../../../library/stats/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/build/r-base-3.5.2/src/library/stats/src' making init.d from init.c making kmeans.d from kmeans.c making ansari.d from ansari.c making bandwidths.d from bandwidths.c making chisqsim.d from chisqsim.c making d2x2xk.d from d2x2xk.c making fexact.d from fexact.c making kendall.d from kendall.c making ks.d from ks.c making line.d from line.c making smooth.d from smooth.c making prho.d from prho.c making swilk.d from swilk.c making ksmooth.d from ksmooth.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making dblcen.d from dblcen.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making burg.d from burg.c making filter.d from filter.c making mAR.d from mAR.c making pacf.d from pacf.c making starma.d from starma.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making loglin.d from loglin.c making lowess.d from lowess.c making massdist.d from massdist.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fft.d from fft.c making fourier.d from fourier.c making model.d from model.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making zeroin.d from zeroin.c making rcont.d from rcont.c making influence.d from influence.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kmeans.c -o kmeans.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ansari.c -o ansari.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bandwidths.c -o bandwidths.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chisqsim.c -o chisqsim.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d2x2xk.c -o d2x2xk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fexact.c -o fexact.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kendall.c -o kendall.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ks.c -o ks.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c line.c -o line.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c smooth.c -o smooth.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prho.c -o prho.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c swilk.c -o swilk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ksmooth.c -o ksmooth.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loessc.c -o loessc.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c monoSpl.c -o monoSpl.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c isoreg.c -o isoreg.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Srunmed.c -o Srunmed.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dblcen.c -o dblcen.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distance.c -o distance.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hclust-utils.c -o hclust-utils.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nls.c -o nls.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rWishart.c -o rWishart.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HoltWinters.c -o HoltWinters.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PPsum.c -o PPsum.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arima.c -o arima.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c burg.c -o burg.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filter.c -o filter.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mAR.c -o mAR.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pacf.c -o pacf.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c starma.c -o starma.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c port.c -o port.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c family.c -o family.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sbart.c -o sbart.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c approx.c -o approx.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loglin.c -o loglin.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowess.c -o lowess.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c massdist.c -o massdist.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complete_cases.c -o complete_cases.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cov.c -o cov.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deriv.c -o deriv.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fft.c -o fft.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fourier.c -o fourier.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c model.c -o model.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optimize.c -o optimize.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distn.c -o distn.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zeroin.c -o zeroin.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcont.c -o rcont.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c influence.c -o influence.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c bsplvd.f -o bsplvd.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c bvalue.f -o bvalue.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c bvalus.f -o bvalus.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c loessf.f -o loessf.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c ppr.f -o ppr.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c qsbart.f -o qsbart.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c sgram.f -o sgram.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c sinerp.f -o sinerp.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c sslvrg.f -o sslvrg.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c stxwx.f -o stxwx.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c hclust.f -o hclust.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c kmns.f -o kmns.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c eureka.f -o eureka.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c stl.f -o stl.o gfortran -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c portsrc.f -o portsrc.o gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -c lminfl.f -o lminfl.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lblas -lgfortran -lm -L../../../../lib -lR make[7]: Entering directory '/build/r-base-3.5.2/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[7]: Leaving directory '/build/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' byte-compiling package 'stats' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/build/r-base-3.5.2/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[5]: Entering directory '/build/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[4]: Leaving directory '/build/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/build/r-base-3.5.2/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' mkdir -p -- ../../../library/methods/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/build/r-base-3.5.2/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c making init.d from init.c making methods_list_dispatch.d from methods_list_dispatch.c making slot.d from slot.c making class_support.d from class_support.c making tests.d from tests.c making utils.d from utils.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c do_substitute_direct.c -o do_substitute_direct.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c slot.c -o slot.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c class_support.c -o class_support.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tests.c -o tests.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[7]: Entering directory '/build/r-base-3.5.2/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[7]: Leaving directory '/build/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' mkdir -p -- ../../../library/grid/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grid/src' making gpar.d from gpar.c making grid.d from grid.c making just.d from just.c making layout.d from layout.c making matrix.d from matrix.c making register.d from register.c making state.d from state.c making unit.d from unit.c making util.d from util.c making viewport.d from viewport.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gpar.c -o gpar.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grid.c -o grid.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c just.c -o just.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c layout.c -o layout.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matrix.c -o matrix.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c register.c -o register.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c state.c -o state.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unit.c -o unit.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c viewport.c -o viewport.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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/r-base-3.5.2/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[7]: Leaving directory '/build/r-base-3.5.2/src/library/grid/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/grid/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' byte-compiling package 'grid' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[4]: Entering directory '/build/r-base-3.5.2/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' mkdir -p -- ../../../library/splines/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' make[6]: Entering directory '/build/r-base-3.5.2/src/library/splines/src' making splines.d from splines.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR make[7]: Entering directory '/build/r-base-3.5.2/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[7]: Leaving directory '/build/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' byte-compiling package 'splines' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/build/r-base-3.5.2/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats4' byte-compiling package 'stats4' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/build/r-base-3.5.2/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 -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk.c -o tcltk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk_unix.c -o tcltk_unix.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib/aarch64-linux-gnu -ltcl8.6 -L/usr/lib/aarch64-linux-gnu -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR make[6]: Entering directory '/build/r-base-3.5.2/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[6]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' byte-compiling package 'tcltk' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/build/r-base-3.5.2/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/build/r-base-3.5.2/src/library/parallel/src' making init.d from init.c making rngstream.d from rngstream.c making fork.d from fork.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rngstream.c -o rngstream.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fork.c -o fork.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[7]: Entering directory '/build/r-base-3.5.2/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[7]: Leaving directory '/build/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' byte-compiling package 'parallel' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[2]: Leaving directory '/build/r-base-3.5.2/src' make[2]: Entering directory '/build/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/tests' you should 'make docs' now ... make[1]: Leaving directory '/build/r-base-3.5.2' (cd src/nmath/standalone; \ /usr/bin/make CFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ R_GZIPCMD="/bin/gzip -n" \ libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.1 \ shared static ) make[1]: Entering directory '/build/r-base-3.5.2/src/nmath/standalone' (cd ../../include; /usr/bin/make Rmath.h) make[2]: Entering directory '/build/r-base-3.5.2/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/build/r-base-3.5.2/src/include' Copying source files make[2]: Entering directory '/build/r-base-3.5.2/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 lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_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/r-base-3.5.2/src/nmath/standalone' make[2]: Entering directory '/build/r-base-3.5.2/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.lo gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro -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 lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.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 -lm make[2]: Leaving directory '/build/r-base-3.5.2/src/nmath/standalone' make[2]: Entering directory '/build/r-base-3.5.2/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o ranlib libRmath.a make[2]: Leaving directory '/build/r-base-3.5.2/src/nmath/standalone' make[1]: Leaving directory '/build/r-base-3.5.2/src/nmath/standalone' R_GZIPCMD="/bin/gzip -n" \ /usr/bin/make docs R_CMD_BUILD_HELP_OPTS="--txt --example" make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/m4' make[2]: Entering directory '/build/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/tools' make[2]: Entering directory '/build/r-base-3.5.2/doc' make[3]: Entering directory '/build/r-base-3.5.2/doc/html' make[3]: Leaving directory '/build/r-base-3.5.2/doc/html' make[3]: Entering directory '/build/r-base-3.5.2/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/build/r-base-3.5.2/doc' make[2]: Entering directory '/build/r-base-3.5.2/etc' make[2]: Leaving directory '/build/r-base-3.5.2/etc' make[2]: Entering directory '/build/r-base-3.5.2/share' make[2]: Leaving directory '/build/r-base-3.5.2/share' make[2]: Entering directory '/build/r-base-3.5.2/src' make[3]: Entering directory '/build/r-base-3.5.2/src/scripts' make[4]: Entering directory '/build/r-base-3.5.2/src/scripts' make[4]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Entering directory '/build/r-base-3.5.2/src/include' make[4]: Entering directory '/build/r-base-3.5.2/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/build/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/build/r-base-3.5.2/src/include' make[3]: Entering directory '/build/r-base-3.5.2/src/extra' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/build/r-base-3.5.2/src/extra' make[3]: Entering directory '/build/r-base-3.5.2/src/appl' make[4]: Entering directory '/build/r-base-3.5.2/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Entering directory '/build/r-base-3.5.2/src/nmath' make[4]: Entering directory '/build/r-base-3.5.2/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Entering directory '/build/r-base-3.5.2/src/unix' make[4]: Entering directory '/build/r-base-3.5.2/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[4]: Entering directory '/build/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/build/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Entering directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Entering directory '/build/r-base-3.5.2/src/main' /build/r-base-3.5.2/lib/libR.so is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Entering directory '/build/r-base-3.5.2/src/main' /build/r-base-3.5.2/bin/exec/R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Entering directory '/build/r-base-3.5.2/src/modules' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/internet' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/X11' /build/r-base-3.5.2/modules/R_X11.so is unchanged /build/r-base-3.5.2/modules/R_de.so is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/build/r-base-3.5.2/src/modules' make[3]: Entering directory '/build/r-base-3.5.2/src/library' make[4]: Entering directory '/build/r-base-3.5.2/src/library/profile' building system startup profile make[4]: Leaving directory '/build/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/build/r-base-3.5.2/src/library/translations' building package 'translations' make[5]: Entering directory '/build/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/build/r-base-3.5.2/src/library/base' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tools' building package 'tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/build/r-base-3.5.2/src/library/tools/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/build/r-base-3.5.2/src/library/compiler' building package 'compiler' make[5]: Entering directory '/build/r-base-3.5.2/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/build/r-base-3.5.2/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/build/r-base-3.5.2/src/library/utils' building package 'utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/build/r-base-3.5.2/src/library/utils/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/build/r-base-3.5.2/src/library/graphics' building package 'graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/build/r-base-3.5.2/src/library/graphics/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/build/r-base-3.5.2/src/library/stats' building package 'stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/build/r-base-3.5.2/src/library/stats/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/build/r-base-3.5.2/src/library/datasets' building package 'datasets' make[5]: Entering directory '/build/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/datasets' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/build/r-base-3.5.2/src/library/methods' building package 'methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/build/r-base-3.5.2/src/library/methods/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grid' building package 'grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grid/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/grid/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/grid/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[4]: Entering directory '/build/r-base-3.5.2/src/library/splines' building package 'splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' make[6]: Entering directory '/build/r-base-3.5.2/src/library/splines/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/build/r-base-3.5.2/src/library/stats4' building package 'stats4' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk/src' make[6]: Entering directory '/build/r-base-3.5.2/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/build/r-base-3.5.2/src/library/parallel' building package 'parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/build/r-base-3.5.2/src/library/parallel/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[2]: Leaving directory '/build/r-base-3.5.2/src' make[2]: Entering directory '/build/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/tests' you should 'make docs' now ... make[2]: Entering directory '/build/r-base-3.5.2/doc' creating doc/NEWS creating doc/NEWS.pdf make[3]: Entering directory '/build/r-base-3.5.2/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-admin.html 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/r-base-3.5.2/doc/html' make[4]: Leaving directory '/build/r-base-3.5.2/doc/html' make[3]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/build/r-base-3.5.2/doc' make[2]: Entering directory '/build/r-base-3.5.2/src/library' make[3]: Entering directory '/build/r-base-3.5.2/src/library' installing parsed Rd make[4]: Entering directory '/build/r-base-3.5.2/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/build/r-base-3.5.2/src/library' make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[3]: Entering directory '/build/r-base-3.5.2/src/library' building/updating package metadata ... make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[3]: Entering directory '/build/r-base-3.5.2/src/library' writing package indices make[4]: Entering directory '/build/r-base-3.5.2/src/library' make[4]: Leaving directory '/build/r-base-3.5.2/src/library' make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[2]: Leaving directory '/build/r-base-3.5.2/src/library' make[1]: Leaving directory '/build/r-base-3.5.2' /usr/bin/make javaconf make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/m4' make[2]: Entering directory '/build/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/tools' make[2]: Entering directory '/build/r-base-3.5.2/doc' make[3]: Entering directory '/build/r-base-3.5.2/doc/html' make[3]: Leaving directory '/build/r-base-3.5.2/doc/html' make[3]: Entering directory '/build/r-base-3.5.2/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/build/r-base-3.5.2/doc' make[2]: Entering directory '/build/r-base-3.5.2/etc' make[2]: Leaving directory '/build/r-base-3.5.2/etc' make[2]: Entering directory '/build/r-base-3.5.2/share' make[2]: Leaving directory '/build/r-base-3.5.2/share' make[2]: Entering directory '/build/r-base-3.5.2/src' make[3]: Entering directory '/build/r-base-3.5.2/src/scripts' make[4]: Entering directory '/build/r-base-3.5.2/src/scripts' make[4]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Entering directory '/build/r-base-3.5.2/src/include' make[4]: Entering directory '/build/r-base-3.5.2/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/build/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/build/r-base-3.5.2/src/include' make[3]: Entering directory '/build/r-base-3.5.2/src/extra' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/build/r-base-3.5.2/src/extra' make[3]: Entering directory '/build/r-base-3.5.2/src/appl' make[4]: Entering directory '/build/r-base-3.5.2/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Entering directory '/build/r-base-3.5.2/src/nmath' make[4]: Entering directory '/build/r-base-3.5.2/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Entering directory '/build/r-base-3.5.2/src/unix' make[4]: Entering directory '/build/r-base-3.5.2/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[4]: Entering directory '/build/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/build/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Entering directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Entering directory '/build/r-base-3.5.2/src/main' /build/r-base-3.5.2/lib/libR.so is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Entering directory '/build/r-base-3.5.2/src/main' /build/r-base-3.5.2/bin/exec/R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Entering directory '/build/r-base-3.5.2/src/modules' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/internet' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/X11' /build/r-base-3.5.2/modules/R_X11.so is unchanged /build/r-base-3.5.2/modules/R_de.so is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/build/r-base-3.5.2/src/modules' make[3]: Entering directory '/build/r-base-3.5.2/src/library' make[4]: Entering directory '/build/r-base-3.5.2/src/library/profile' building system startup profile make[4]: Leaving directory '/build/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/build/r-base-3.5.2/src/library/translations' building package 'translations' make[5]: Entering directory '/build/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/build/r-base-3.5.2/src/library/base' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tools' building package 'tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/build/r-base-3.5.2/src/library/tools/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/build/r-base-3.5.2/src/library/compiler' building package 'compiler' make[5]: Entering directory '/build/r-base-3.5.2/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/build/r-base-3.5.2/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/build/r-base-3.5.2/src/library/utils' building package 'utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/build/r-base-3.5.2/src/library/utils/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/build/r-base-3.5.2/src/library/graphics' building package 'graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/build/r-base-3.5.2/src/library/graphics/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/build/r-base-3.5.2/src/library/stats' building package 'stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/build/r-base-3.5.2/src/library/stats/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/build/r-base-3.5.2/src/library/datasets' building package 'datasets' make[5]: Entering directory '/build/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/datasets' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/build/r-base-3.5.2/src/library/methods' building package 'methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/build/r-base-3.5.2/src/library/methods/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grid' building package 'grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grid/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/grid/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/grid/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[4]: Entering directory '/build/r-base-3.5.2/src/library/splines' building package 'splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' make[6]: Entering directory '/build/r-base-3.5.2/src/library/splines/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/build/r-base-3.5.2/src/library/stats4' building package 'stats4' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk/src' make[6]: Entering directory '/build/r-base-3.5.2/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/build/r-base-3.5.2/src/library/parallel' building package 'parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/build/r-base-3.5.2/src/library/parallel/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[2]: Leaving directory '/build/r-base-3.5.2/src' make[2]: Entering directory '/build/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/tests' make[2]: Entering directory '/build/r-base-3.5.2' configuring Java ... Java interpreter : /usr/lib/jvm/default-java/bin/java Java version : 11.0.9.1 Java home path : /usr/lib/jvm/default-java Java compiler : /usr/lib/jvm/default-java/bin/javac Java headers gen.: Java archive tool: /usr/lib/jvm/default-java/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm make[3]: Entering directory '/tmp/Rjavareconf.uG88v9' gcc -std=gnu99 -I"/build/r-base-3.5.2/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o gcc -std=gnu99 -shared -L/build/r-base-3.5.2/lib -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/build/r-base-3.5.2/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.uG88v9' JAVA_HOME : /usr/lib/jvm/default-java Java library path: $(JAVA_HOME)/lib/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm Updating Java configuration in /build/r-base-3.5.2 Done. make[2]: Leaving directory '/build/r-base-3.5.2' make[1]: Leaving directory '/build/r-base-3.5.2' touch make-arch-stamp *** make-indep *** /usr/bin/make -k docs make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/m4' make[2]: Entering directory '/build/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/tools' make[2]: Entering directory '/build/r-base-3.5.2/doc' make[3]: Entering directory '/build/r-base-3.5.2/doc/html' make[3]: Leaving directory '/build/r-base-3.5.2/doc/html' make[3]: Entering directory '/build/r-base-3.5.2/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/build/r-base-3.5.2/doc' make[2]: Entering directory '/build/r-base-3.5.2/etc' make[2]: Leaving directory '/build/r-base-3.5.2/etc' make[2]: Entering directory '/build/r-base-3.5.2/share' make[2]: Leaving directory '/build/r-base-3.5.2/share' make[2]: Entering directory '/build/r-base-3.5.2/src' make[3]: Entering directory '/build/r-base-3.5.2/src/scripts' make[4]: Entering directory '/build/r-base-3.5.2/src/scripts' make[4]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Entering directory '/build/r-base-3.5.2/src/include' make[4]: Entering directory '/build/r-base-3.5.2/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/build/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/build/r-base-3.5.2/src/include' make[3]: Entering directory '/build/r-base-3.5.2/src/extra' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/build/r-base-3.5.2/src/extra' make[3]: Entering directory '/build/r-base-3.5.2/src/appl' make[4]: Entering directory '/build/r-base-3.5.2/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Entering directory '/build/r-base-3.5.2/src/nmath' make[4]: Entering directory '/build/r-base-3.5.2/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Entering directory '/build/r-base-3.5.2/src/unix' make[4]: Entering directory '/build/r-base-3.5.2/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[4]: Entering directory '/build/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/build/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Entering directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Entering directory '/build/r-base-3.5.2/src/main' /build/r-base-3.5.2/lib/libR.so is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Entering directory '/build/r-base-3.5.2/src/main' /build/r-base-3.5.2/bin/exec/R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Entering directory '/build/r-base-3.5.2/src/modules' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/internet' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/X11' /build/r-base-3.5.2/modules/R_X11.so is unchanged /build/r-base-3.5.2/modules/R_de.so is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/build/r-base-3.5.2/src/modules' make[3]: Entering directory '/build/r-base-3.5.2/src/library' make[4]: Entering directory '/build/r-base-3.5.2/src/library/profile' building system startup profile make[4]: Leaving directory '/build/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/build/r-base-3.5.2/src/library/translations' building package 'translations' make[5]: Entering directory '/build/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/build/r-base-3.5.2/src/library/base' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tools' building package 'tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/build/r-base-3.5.2/src/library/tools/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/build/r-base-3.5.2/src/library/compiler' building package 'compiler' make[5]: Entering directory '/build/r-base-3.5.2/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/build/r-base-3.5.2/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/build/r-base-3.5.2/src/library/utils' building package 'utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/build/r-base-3.5.2/src/library/utils/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/build/r-base-3.5.2/src/library/graphics' building package 'graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/build/r-base-3.5.2/src/library/graphics/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/build/r-base-3.5.2/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/build/r-base-3.5.2/src/library/stats' building package 'stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/build/r-base-3.5.2/src/library/stats/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/build/r-base-3.5.2/src/library/datasets' building package 'datasets' make[5]: Entering directory '/build/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/datasets' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/build/r-base-3.5.2/src/library/methods' building package 'methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/build/r-base-3.5.2/src/library/methods/src' 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Converting parsed Rd's to LaTeX ...... collecting LaTeX docs for package 'utils' ... 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 'stats' ... Converting parsed Rd's to LaTeX .............................. collecting LaTeX docs for package 'datasets' ... Converting parsed Rd's to LaTeX ........ collecting LaTeX docs for package 'methods' ... Converting parsed Rd's to LaTeX ........ collecting LaTeX docs for package 'grid' ... Converting parsed Rd's to LaTeX ......... collecting LaTeX docs for package 'splines' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'stats4' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'tcltk' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'compiler' ... Converting parsed Rd's to LaTeX collecting LaTeX docs for package 'parallel' ... Converting parsed Rd's to LaTeX . PDF/LaTeX documentation: reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. 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(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [201] [202] [203] [204] [205] [206] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\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-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\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 32188--32195 \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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [793] [794] [795] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\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 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [935] [936] [937] [938] [939] [940] [941] [942] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1090] [1091] [1092] [1093] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1207] [1208] [1209] [1210] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1230] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1356] [1357] [1358] [1359] [1360] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] [1494] [1495] [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18450--18453 []\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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1790] [1791] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1873] [1874] Underfull \hbox (badness 1308) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1888] Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1889] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\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 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4380 ...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.4380 ...mat Unordered and Ordered Lists}{format} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\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 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2034] [2035] [2036] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2037] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2038] [2039] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2040] Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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If [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and Underfull \hbox (badness 1052) in paragraph at lines 13296--13298 []\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 13326--13331 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] Underfull \hbox (badness 1454) in paragraph at lines 13748--13752 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). 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LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (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.lmList} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.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 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Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2019/dev] (kpathsea + Thai support). Scanning input file refman.idx.................done (13579 entries accepted, 34 rejected). Sorting entries....................................................................................................................................................done (217268 comparisons). Generating output file refman.ind................done (13394 lines written, 50 warnings). Output written in refman.ind. Transcript written in refman.ilg. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [201] [202] [203] [204] [205] [206] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\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-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\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 32188--32195 \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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [793] [794] [795] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\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 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [935] [936] [937] [938] [939] [940] [941] [942] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1090] [1091] [1092] [1093] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1207] [1208] [1209] [1210] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1230] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1356] [1357] [1358] [1359] [1360] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] [1494] [1495] [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18450--18453 []\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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1790] [1791] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1873] [1874] Underfull \hbox (badness 1308) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1888] Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1889] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\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 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4380 ...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.4380 ...mat Unordered and Ordered Lists}{format} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\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 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2034] [2035] [2036] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2037] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2038] [2039] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2040] Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2115] [2116] [2117] Underfull \hbox (badness 2150) in paragraph at lines 10813--10815 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2118] [2119] [2120] [2121] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 11063--11069 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2122] [2123] Underfull \hbox (badness 2096) in paragraph at lines 11181--11184 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2124] Underfull \hbox (badness 1009) in paragraph at lines 11257--11268 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and Underfull \hbox (badness 1052) in paragraph at lines 13296--13298 []\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 13326--13331 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] Underfull \hbox (badness 1454) in paragraph at lines 13748--13752 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2164] Underfull \hbox (badness 10000) in paragraph at lines 13818--13820 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2165] [2166] [2167] [2168]) (./refman.ind [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] Overfull \hbox (33.3567pt too wide) in paragraph at lines 8658--8660 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [2218] [2219] [2220] [2221] [2222] [2223] Overfull \hbox (20.8567pt too wide) in paragraph at lines 9958--9960 []\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [2224] [2225] [2226] [2227] [2228] [2229] [2230] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11665--11667 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11667--11669 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results [2231] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11669--11671 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240]) (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (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.lmList} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.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 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [201] [202] [203] [204] [205] [206] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\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-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\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 32188--32195 \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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [793] [794] [795] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\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 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [935] [936] [937] [938] [939] [940] [941] [942] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1090] [1091] [1092] [1093] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1207] [1208] [1209] [1210] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1230] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1356] [1357] [1358] [1359] [1360] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] [1494] [1495] [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18450--18453 []\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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1790] [1791] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1873] [1874] Underfull \hbox (badness 1308) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1888] Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1889] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\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 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4380 ...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.4380 ...mat Unordered and Ordered Lists}{format} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\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 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2034] [2035] [2036] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2037] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2038] [2039] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2040] Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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If [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. 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Transcript written on refman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2035--2035 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2229--2240 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2702--2702 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2722--2722 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2723--2723 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3626--3626 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6 4/jre[] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [67] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [68] Overfull \hbox (106.92076pt too wide) in paragraph at lines 5172--5172 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5206--5206 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 5311--5316 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5335--5335 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [71] [72] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5504--5504 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 5613--5619 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5628--5628 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] Underfull \hbox (badness 10000) in paragraph at lines 5680--5684 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [75] [76] [77] [78] Appendix D [79] [80] [81] (Function and variable index) [82] No file R-admin.vrs. (Concept index) [83] No file R-admin.cps. (Environment variable index) [84] No file R-admin.ens. [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (88 pages, 483652 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-admin.toc [-1] [-2]) [-3] (/build/r-base-3.5.2/doc/manual/R-admin.toc) (/build/r-base-3.5.2/doc/manual/R-admin.toc) Chapter 1 (/build/r-base-3.5.2/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2035--2035 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2229--2240 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2702--2702 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2722--2722 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2723--2723 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3626--3626 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6 4/jre[] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [67] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [68] Overfull \hbox (106.92076pt too wide) in paragraph at lines 5172--5172 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5206--5206 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 5311--5316 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5335--5335 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [71] [72] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5504--5504 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 5613--5619 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5628--5628 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] Underfull \hbox (badness 10000) in paragraph at lines 5680--5684 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [75] [76] [77] [78] Appendix D [79] [80] [81] (Function and variable index) [82] (Concept index) [83] (Environment variable index) [84] [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (90 pages, 529160 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-admin.toc [-1] [-2]) [-3] (/build/r-base-3.5.2/doc/manual/R-admin.toc) (/build/r-base-3.5.2/doc/manual/R-admin.toc) Chapter 1 (/build/r-base-3.5.2/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2035--2035 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2229--2240 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2702--2702 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2722--2722 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2723--2723 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3626--3626 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6 4/jre[] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [67] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [68] Overfull \hbox (106.92076pt too wide) in paragraph at lines 5172--5172 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5206--5206 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 5311--5316 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5335--5335 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [71] [72] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5504--5504 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 5613--5619 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5628--5628 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] Underfull \hbox (badness 10000) in paragraph at lines 5680--5684 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [75] [76] [77] [78] Appendix D [79] [80] [81] (Function and variable index) [82] (Concept index) [83] (Environment variable index) [84] [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (90 pages, 529164 bytes). Transcript written on R-admin.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] No file R-data.vrs. (Concept index) [35] No file R-data.cps. [36] ) (see the transcript file for additional information) Output written on R-data.pdf (39 pages, 272437 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-data.toc [-1]) [-2] (/build/r-base-3.5.2/doc/manual/R-data.toc) (/build/r-base-3.5.2/doc/manual/R-data.toc) (Acknowledgements) (/build/r-base-3.5.2/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . 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Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35] (Concept index) [36] [37] Overfull \vbox (1.73251pt too high) has occurred while \output is active [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 312471 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-data.toc [-1]) [-2] (/build/r-base-3.5.2/doc/manual/R-data.toc) (/build/r-base-3.5.2/doc/manual/R-data.toc) (Acknowledgements) (/build/r-base-3.5.2/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35] (Concept index) [36] [37] Overfull \vbox (1.73251pt too high) has occurred while \output is active [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 312472 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1917--1917 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] [29] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2415--2415 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [33] [34] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [35] [36] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2799--2801 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 4638--4638 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4951--4951 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [64] [65] [66] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5157--5157 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5158--5158 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [67] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5252--5252 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [68] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5318--5318 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [69] [70] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5546--5546 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [72] [73] [74] Chapter 2 [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] Underfull \hbox (badness 10000) in paragraph at lines 6806--6813 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [89] [90] [91] [92] Underfull \hbox (badness 10000) in paragraph at lines 7125--7129 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [93] [94] Chapter 3 [95] [96] [97] [98] [99] [100] [101] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7726--7726 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [102] [103] [104] Chapter 4 [105] [106] [107] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8103--8103 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [108] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8144--8144 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [109] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8248--8248 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [110] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [111] [112] [113] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [114] [115] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8729--8729 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8730--8730 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [116] Underfull \hbox (badness 8151) in paragraph at lines 8777--8781 []@textrm From GCC 8 @texttt signed-integer-overflow[] @textrm is no longer a d e-fault part of Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 @texttt -fsanitize=undefined[]@textrm , but can be spec-i-fied sep-a-rately. It adds op-tions [117] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8847--8847 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [118] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8899--8899 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [119] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8978--8978 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [120] [121] Chapter 5 [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9946--9946 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [133] [134] [135] [136] [137] [138] [139] [140] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11346--11346 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [151] Underfull \hbox (badness 10000) in paragraph at lines 11407--11409 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [152] [153] [154] [155] [156] [157] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11929--11929 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12052--12052 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12057--12057 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12112--12112 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12124--12124 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [162] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12223--12223 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [163] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12359--12359 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [165] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [166] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12528--12528 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 13688--13692 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [180] [181] Warning: unbalanced parentheses in @def... [182] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13899--13899 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [183] [184] [185] [186] [187] Chapter 7 [188] [189] Chapter 8 [190] [191] [192] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [193] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14690--14690 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [198] [199] [200] [201] [202] Underfull \hbox (badness 10000) in paragraph at lines 15332--15336 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [203] No file R-exts.vrs. (Concept index) [204] No file R-exts.cps. [205] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (208 pages, 900129 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/build/r-base-3.5.2/doc/manual/R-exts.toc) (/build/r-base-3.5.2/doc/manual/R-exts.toc) (Acknowledgements) (/build/r-base-3.5.2/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1917--1917 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] [29] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2415--2415 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [33] [34] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [35] [36] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2799--2801 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 4638--4638 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4951--4951 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [64] [65] [66] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5157--5157 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5158--5158 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [67] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5252--5252 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [68] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5318--5318 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [69] [70] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5546--5546 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [72] [73] [74] Chapter 2 [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] Underfull \hbox (badness 10000) in paragraph at lines 6806--6813 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [89] [90] [91] [92] Underfull \hbox (badness 10000) in paragraph at lines 7125--7129 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [93] [94] Chapter 3 [95] [96] [97] [98] [99] [100] [101] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7726--7726 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [102] [103] [104] Chapter 4 [105] [106] [107] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8103--8103 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [108] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8144--8144 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [109] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8248--8248 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [110] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [111] [112] [113] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [114] [115] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8729--8729 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8730--8730 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [116] Underfull \hbox (badness 8151) in paragraph at lines 8777--8781 []@textrm From GCC 8 @texttt signed-integer-overflow[] @textrm is no longer a d e-fault part of Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 @texttt -fsanitize=undefined[]@textrm , but can be spec-i-fied sep-a-rately. It adds op-tions [117] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8847--8847 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [118] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8899--8899 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [119] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8978--8978 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [120] [121] Chapter 5 [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9946--9946 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [133] [134] [135] [136] [137] [138] [139] [140] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11346--11346 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [151] Underfull \hbox (badness 10000) in paragraph at lines 11407--11409 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [152] [153] [154] [155] [156] [157] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11929--11929 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12052--12052 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12057--12057 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12112--12112 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12124--12124 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [162] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12223--12223 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [163] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12359--12359 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [165] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [166] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12528--12528 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 13688--13692 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [180] Warning: unbalanced parentheses in @def... [181] [182] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13899--13899 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [183] [184] [185] [186] [187] Chapter 7 [188] [189] Chapter 8 [190] [191] [192] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [193] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14690--14690 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [198] [199] [200] [201] [202] Underfull \hbox (badness 10000) in paragraph at lines 15332--15336 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [203] [204] [205] [206] (Concept index) [207] [208] [209] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (216 pages, 964236 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/build/r-base-3.5.2/doc/manual/R-exts.toc) (/build/r-base-3.5.2/doc/manual/R-exts.toc) (Acknowledgements) (/build/r-base-3.5.2/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1917--1917 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] [29] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2415--2415 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [33] [34] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [35] [36] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2799--2801 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 4638--4638 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4951--4951 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [64] [65] [66] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5157--5157 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5158--5158 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [67] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5252--5252 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [68] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5318--5318 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [69] [70] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5546--5546 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [72] [73] [74] Chapter 2 [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] Underfull \hbox (badness 10000) in paragraph at lines 6806--6813 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [89] [90] [91] [92] Underfull \hbox (badness 10000) in paragraph at lines 7125--7129 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [93] [94] Chapter 3 [95] [96] [97] [98] [99] [100] [101] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7726--7726 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [102] [103] [104] Chapter 4 [105] [106] [107] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8103--8103 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [108] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8144--8144 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [109] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8248--8248 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [110] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [111] [112] [113] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [114] [115] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8729--8729 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8730--8730 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [116] Underfull \hbox (badness 8151) in paragraph at lines 8777--8781 []@textrm From GCC 8 @texttt signed-integer-overflow[] @textrm is no longer a d e-fault part of Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 @texttt -fsanitize=undefined[]@textrm , but can be spec-i-fied sep-a-rately. It adds op-tions [117] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8847--8847 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [118] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8899--8899 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [119] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8978--8978 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [120] [121] Chapter 5 [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9946--9946 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [133] [134] [135] [136] [137] [138] [139] [140] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11346--11346 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [151] Underfull \hbox (badness 10000) in paragraph at lines 11407--11409 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [152] [153] [154] [155] [156] [157] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11929--11929 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12052--12052 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12057--12057 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12112--12112 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12124--12124 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [162] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12223--12223 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [163] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12359--12359 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [165] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [166] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12528--12528 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 13688--13692 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [180] Warning: unbalanced parentheses in @def... [181] [182] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13899--13899 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [183] [184] [185] [186] [187] Chapter 7 [188] [189] Chapter 8 [190] [191] [192] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [193] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14690--14690 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [198] [199] [200] [201] [202] Underfull \hbox (badness 10000) in paragraph at lines 15332--15336 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [203] [204] [205] [206] (Concept index) [207] [208] [209] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (216 pages, 964283 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) 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. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] 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] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 365574 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) 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}] (/build/r-base-3.5.2/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/build/r-base-3.5.2/doc/manual/R-FAQ.toc) (/build/r-base-3.5.2/doc/manual/R-FAQ.toc) Chapter 1 (/build/r-base-3.5.2/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] 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] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 382056 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) 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}] (/build/r-base-3.5.2/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/build/r-base-3.5.2/doc/manual/R-FAQ.toc) (/build/r-base-3.5.2/doc/manual/R-FAQ.toc) Chapter 1 (/build/r-base-3.5.2/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] 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] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 382058 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] No file R-intro.vrs. Appendix E [102] No file R-intro.cps. Appendix F [103] [104] ) (see the transcript file for additional information) Output written on R-intro.pdf (107 pages, 575876 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/build/r-base-3.5.2/doc/manual/R-intro.toc) (/build/r-base-3.5.2/doc/manual/R-intro.toc) (Preface) (/build/r-base-3.5.2/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E [104] [105] Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 625538 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/build/r-base-3.5.2/doc/manual/R-intro.toc) (/build/r-base-3.5.2/doc/manual/R-intro.toc) (Preface) (/build/r-base-3.5.2/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E [104] [105] Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 625607 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 4031--4039 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11 [63] Chapter 12 [64] [65] (Function and variable index) [66] [67] No file R-ints.vrs. (Concept index) [68] No file R-ints.cps. [69] ) (see the transcript file for additional information) Output written on R-ints.pdf (72 pages, 397180 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-ints.toc [-1] [-2]) [-3] (/build/r-base-3.5.2/doc/manual/R-ints.toc) (/build/r-base-3.5.2/doc/manual/R-ints.toc) Chapter 1 (/build/r-base-3.5.2/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 4031--4039 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11 [63] Chapter 12 [64] [65] (Function and variable index) [66] [67] [68] (Concept index) [69] [70] ) (see the transcript file for additional information) Output written on R-ints.pdf (75 pages, 446907 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-ints.toc [-1] [-2]) [-3] (/build/r-base-3.5.2/doc/manual/R-ints.toc) (/build/r-base-3.5.2/doc/manual/R-ints.toc) Chapter 1 (/build/r-base-3.5.2/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 4031--4039 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11 [63] Chapter 12 [64] [65] (Function and variable index) [66] [67] [68] (Concept index) [69] [70] ) (see the transcript file for additional information) Output written on R-ints.pdf (75 pages, 446907 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @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] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] No file R-lang.vrs. (Concept Index) [60] No file R-lang.cps. Appendix A [61] [62] ) (see the transcript file for additional information) Output written on R-lang.pdf (65 pages, 329878 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-lang.toc [-1] [-2]) [-3] (/build/r-base-3.5.2/doc/manual/R-lang.toc) (/build/r-base-3.5.2/doc/manual/R-lang.toc) Chapter 1 (/build/r-base-3.5.2/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @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] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] [60] (Concept Index) [61] [62] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 378955 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/r-base-3.5.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/r-base-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/build/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/r-base-3.5.2/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte x/updmap/pdftex.map}] [2] (/build/r-base-3.5.2/doc/manual/R-lang.toc [-1] [-2]) [-3] (/build/r-base-3.5.2/doc/manual/R-lang.toc) (/build/r-base-3.5.2/doc/manual/R-lang.toc) Chapter 1 (/build/r-base-3.5.2/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @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] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] [60] (Concept Index) [61] [62] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 378941 bytes). Transcript written on R-lang.log. make[1]: Leaving directory '/build/r-base-3.5.2/doc/manual' /usr/bin/make -k pdf make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/doc' make[3]: Entering directory '/build/r-base-3.5.2/doc/manual' PDF/LaTeX documentation: full reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. 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(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [201] [202] [203] [204] [205] [206] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\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-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\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 32188--32195 \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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [793] [794] [795] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\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 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [935] [936] [937] [938] [939] [940] [941] [942] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1090] [1091] [1092] [1093] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1207] [1208] [1209] [1210] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1230] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1356] [1357] [1358] [1359] [1360] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] [1494] [1495] [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18450--18453 []\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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1790] [1791] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1873] [1874] Underfull \hbox (badness 1308) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1888] Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1889] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\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 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4380 ...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.4380 ...mat Unordered and Ordered Lists}{format} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\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 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2034] [2035] [2036] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2037] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2038] [2039] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2040] Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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If [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and Underfull \hbox (badness 1052) in paragraph at lines 13296--13298 []\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 13326--13331 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] Underfull \hbox (badness 1454) in paragraph at lines 13748--13752 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). 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LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (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.lmList} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.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 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2019/dev] (kpathsea + Thai support). Scanning input file fullrefman.idx.................done (13579 entries accepted, 34 rejected). Sorting entries....................................................................................................................................................done (217268 comparisons). Generating output file fullrefman.ind................done (13394 lines written, 50 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [201] [202] [203] [204] [205] [206] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\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-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\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 32188--32195 \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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [793] [794] [795] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\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 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [935] [936] [937] [938] [939] [940] [941] [942] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1090] [1091] [1092] [1093] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1207] [1208] [1209] [1210] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1230] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1356] [1357] [1358] [1359] [1360] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] [1494] [1495] [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18450--18453 []\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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1790] [1791] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1873] [1874] Underfull \hbox (badness 1308) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1888] Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1889] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\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 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4380 ...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.4380 ...mat Unordered and Ordered Lists}{format} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\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 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2034] [2035] [2036] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2037] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2038] [2039] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2040] Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2115] [2116] [2117] Underfull \hbox (badness 2150) in paragraph at lines 10813--10815 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2118] [2119] [2120] [2121] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 11063--11069 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2122] [2123] Underfull \hbox (badness 2096) in paragraph at lines 11181--11184 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2124] Underfull \hbox (badness 1009) in paragraph at lines 11257--11268 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and Underfull \hbox (badness 1052) in paragraph at lines 13296--13298 []\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 13326--13331 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] Underfull \hbox (badness 1454) in paragraph at lines 13748--13752 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2164] Underfull \hbox (badness 10000) in paragraph at lines 13818--13820 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2165] [2166] [2167] [2168]) (./fullrefman.ind [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] Overfull \hbox (33.3567pt too wide) in paragraph at lines 8658--8660 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [2218] [2219] [2220] [2221] [2222] [2223] Overfull \hbox (20.8567pt too wide) in paragraph at lines 9958--9960 []\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [2224] [2225] [2226] [2227] [2228] [2229] [2230] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11665--11667 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11667--11669 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results [2231] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11669--11671 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240]) (./fullrefman.aux) Package rerunfilecheck Warning: File `fullrefman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (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.lmList} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.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 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [201] [202] [203] [204] [205] [206] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\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-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\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 32188--32195 \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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [793] [794] [795] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\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 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [935] [936] [937] [938] [939] [940] [941] [942] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1090] [1091] [1092] [1093] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1207] [1208] [1209] [1210] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1230] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1356] [1357] [1358] [1359] [1360] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] [1494] [1495] [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18450--18453 []\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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1790] [1791] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1873] [1874] Underfull \hbox (badness 1308) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1888] Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1889] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\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 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4380 ...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.4380 ...mat Unordered and Ordered Lists}{format} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\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 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2034] [2035] [2036] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2037] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2038] [2039] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2040] Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2124] Underfull \hbox (badness 1009) in paragraph at lines 11257--11268 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and Underfull \hbox (badness 1052) in paragraph at lines 13296--13298 []\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 13326--13331 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] Underfull \hbox (badness 1454) in paragraph at lines 13748--13752 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). 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11665--11667 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11667--11669 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results [2231] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11669--11671 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240]) (./fullrefman.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (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.lmList} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): 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'/build/r-base-3.5.2/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[4]: Entering directory '/build/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/build/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Entering directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Entering directory '/build/r-base-3.5.2/src/main' /build/r-base-3.5.2/lib/libR.so is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[5]: Entering directory '/build/r-base-3.5.2/src/main' /build/r-base-3.5.2/bin/exec/R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Entering directory '/build/r-base-3.5.2/src/modules' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/internet' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory 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'/build/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/build/r-base-3.5.2/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grDevices' make[5]: Nothing to be done for 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Leaving directory '/build/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/build/r-base-3.5.2/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/build/r-base-3.5.2/src/library/grid' building package 'grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/build/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/build/r-base-3.5.2/src/library/grid/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory 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'/build/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/build/r-base-3.5.2/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/build/r-base-3.5.2/src/library/stats4' building package 'stats4' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/build/r-base-3.5.2/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk/src' make[6]: Entering directory '/build/r-base-3.5.2/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/build/r-base-3.5.2/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/build/r-base-3.5.2/src/library/parallel' building package 'parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/build/r-base-3.5.2/src/library/parallel/src' make[7]: Entering directory '/build/r-base-3.5.2/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/build/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/build/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/build/r-base-3.5.2/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/build/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/build/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[2]: Leaving directory '/build/r-base-3.5.2/src' make[2]: Entering directory '/build/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/r-base-3.5.2/tests' make[2]: Entering directory '/build/r-base-3.5.2/doc' make[3]: Entering directory '/build/r-base-3.5.2/doc/manual' make[4]: Entering directory '/build/r-base-3.5.2/doc/html' make[4]: Leaving directory '/build/r-base-3.5.2/doc/html' make[3]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/build/r-base-3.5.2/doc' make[2]: Entering directory '/build/r-base-3.5.2/src/library' make[3]: Entering directory '/build/r-base-3.5.2/src/library' installing parsed Rd make[4]: Entering directory '/build/r-base-3.5.2/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/build/r-base-3.5.2/src/library' make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[3]: Entering directory '/build/r-base-3.5.2/src/library' building/updating package metadata ... make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[3]: Entering directory '/build/r-base-3.5.2/src/library' writing package indices make[4]: Entering directory '/build/r-base-3.5.2/src/library' make[4]: Leaving directory '/build/r-base-3.5.2/src/library' make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[2]: Leaving directory '/build/r-base-3.5.2/src/library' make[2]: Entering directory '/build/r-base-3.5.2/src/library/Recommended' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/r-base-3.5.2/src/library/Recommended' make[2]: Entering directory '/build/r-base-3.5.2/src/library' building/updating vignettes for package 'grid' ... processing 'grid.Rnw' building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... make[2]: Leaving directory '/build/r-base-3.5.2/src/library' make[1]: Leaving directory '/build/r-base-3.5.2' touch make-indep-stamp *** check *** xvfb-run make check-all make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' make[4]: Entering directory '/build/r-base-3.5.2/tests/Examples' Testing examples for package 'base' Testing examples for package 'tools' comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK Testing examples for package 'utils' Testing examples for package 'grDevices' comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK Testing examples for package 'graphics' comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK Testing examples for package 'stats' comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE 17463c17463 < assertCondition: caught "error" --- > assertCondition: caught 'error' Testing examples for package 'datasets' comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK Testing examples for package 'methods' Testing examples for package 'grid' comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK Testing examples for package 'splines' comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK Testing examples for package 'stats4' comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK Testing examples for package 'tcltk' Testing examples for package 'compiler' Testing examples for package 'parallel' make[4]: Leaving directory '/build/r-base-3.5.2/tests/Examples' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running strict specific tests make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'any-all.R' ... OK comparing 'any-all.Rout' to './any-all.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ... OK comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' running sloppy specific tests make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'eval-etc-2.R' ... OK comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ...67,69c67,231 < Warning message: < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : < there is no package called 'Matrix' --- > > cat("Trying some Matrix objects, too\n") > Trying some Matrix objects, too > > D5. <- Diagonal(x = 5:1) > > D5N <- D5. > > D5N[5, 5] <- NA > > example(Matrix) > > Matrix> Matrix(0, 3, 2) # 3 by 2 matrix of zeros -> sparse > 3 x 2 sparse Matrix of class "dgCMatrix" > > [1,] . . > [2,] . . > [3,] . . > > Matrix> Matrix(0, 3, 2, sparse=FALSE)# -> 'dense' > 3 x 2 Matrix of class "dgeMatrix" > [,1] [,2] > [1,] 0 0 > [2,] 0 0 > [3,] 0 0 > > Matrix> Matrix(0, 2, 2, sparse=FALSE)# diagonal ! > 2 x 2 diagonal matrix of class "ddiMatrix" > [,1] [,2] > [1,] 0 . > [2,] . 0 > > Matrix> Matrix(0, 2, 2, sparse=FALSE, doDiag=FALSE)# -> dense > 2 x 2 Matrix of class "dsyMatrix" > [,1] [,2] > [1,] 0 0 > [2,] 0 0 > > Matrix> Matrix(1:6, 3, 2) # a 3 by 2 matrix (+ integer warning) > 3 x 2 Matrix of class "dgeMatrix" > [,1] [,2] > [1,] 1 4 > [2,] 2 5 > [3,] 3 6 > > Matrix> Matrix(1:6 + 1, nrow=3) > 3 x 2 Matrix of class "dgeMatrix" > [,1] [,2] > [1,] 2 5 > [2,] 3 6 > [3,] 4 7 > > Matrix> ## logical ones: > Matrix> Matrix(diag(4) > 0)# -> "ldiMatrix" with diag = "U" > 4 x 4 diagonal matrix of class "ldiMatrix" > [,1] [,2] [,3] [,4] > [1,] TRUE . . . > [2,] . TRUE . . > [3,] . . TRUE . > [4,] . . . TRUE > > Matrix> Matrix(diag(4) > 0, sparse=TRUE)# -> sparse... > 4 x 4 sparse Matrix of class "lsCMatrix" > > [1,] | . . . > [2,] . | . . > [3,] . . | . > [4,] . . . | > > Matrix> Matrix(diag(4) >= 0)# -> "lsyMatrix" (of all 'TRUE') > 4 x 4 Matrix of class "lsyMatrix" > [,1] [,2] [,3] [,4] > [1,] TRUE TRUE TRUE TRUE > [2,] TRUE TRUE TRUE TRUE > [3,] TRUE TRUE TRUE TRUE > [4,] TRUE TRUE TRUE TRUE > > Matrix> ## triangular > Matrix> l3 <- upper.tri(matrix(,3,3)) > > Matrix> (M <- Matrix(l3)) # -> "ltCMatrix" > 3 x 3 sparse Matrix of class "ltCMatrix" > > [1,] . | | > [2,] . . | > [3,] . . . > > Matrix> Matrix(! l3)# -> "ltrMatrix" > 3 x 3 Matrix of class "ltrMatrix" > [,1] [,2] [,3] > [1,] TRUE . . > [2,] TRUE TRUE . > [3,] TRUE TRUE TRUE > > Matrix> as(l3, "CsparseMatrix") > 3 x 3 sparse Matrix of class "lgCMatrix" > > [1,] . | | > [2,] . . | > [3,] . . . > > Matrix> Matrix(1:9, nrow=3, > Matrix+ dimnames = list(c("a", "b", "c"), c("A", "B", "C"))) > 3 x 3 Matrix of class "dgeMatrix" > A B C > a 1 4 7 > b 2 5 8 > c 3 6 9 > > Matrix> (I3 <- Matrix(diag(3)))# identity, i.e., unit "diagonalMatrix" > 3 x 3 diagonal matrix of class "ddiMatrix" > [,1] [,2] [,3] > [1,] 1 . . > [2,] . 1 . > [3,] . . 1 > > Matrix> str(I3) # note the empty 'x' slot > Formal class 'ddiMatrix' [package "Matrix"] with 4 slots > ..@ diag : chr "U" > ..@ Dim : int [1:2] 3 3 > ..@ Dimnames:List of 2 > .. ..$ : NULL > .. ..$ : NULL > ..@ x : num(0) > > Matrix> (A <- cbind(a=c(2,1), b=1:2))# symmetric *apart* from dimnames > a b > [1,] 2 1 > [2,] 1 2 > > Matrix> Matrix(A) # hence 'dgeMatrix' > 2 x 2 Matrix of class "dgeMatrix" > a b > [1,] 2 1 > [2,] 1 2 > > Matrix> (As <- Matrix(A, dimnames = list(NULL,NULL)))# -> symmetric > 2 x 2 Matrix of class "dsyMatrix" > [,1] [,2] > [1,] 2 1 > [2,] 1 2 > > Matrix> stopifnot(is(As, "symmetricMatrix"), > Matrix+ is(Matrix(0, 3,3), "sparseMatrix"), > Matrix+ is(Matrix(FALSE, 1,1), "sparseMatrix")) > > i <- c(1, 3:8) > > j <- c(2, 9, 6:10) > > x <- 7 * (1:7) > > A <- sparseMatrix(i, j, x = x) > > sA <- sparseMatrix(i, j, x = x, symmetric = TRUE) > > tA <- sparseMatrix(i, j, x = x, triangular = TRUE) > > AA <- sparseMatrix(c(1, 3:8), c(2, 9, 6:10), x = 7 * (1:7), dims = c(10, > + 20)) > > set.seed(1) > > (perm <- sample(1:7)) > [1] 2 3 6 4 1 7 5 > > A1 <- sparseMatrix(i[perm], j[perm], x = x[perm]) > > args <- data.frame(i = c(i, 1), j = c(j, 2), x = c(x, 2)) > > Aa <- do.call(sparseMatrix, args) > > A. <- do.call(sparseMatrix, c(args, list(use.last.ij = TRUE))) > > nA <- do.call(sparseMatrix, args[c("i", "j")]) > > dn <- list(LETTERS[1:3], letters[1:5]) > > m <- sparseMatrix(i = c(3, 1, 3:2, 2:1), p = c(0:2, 4, 4, 6), x = 1:6, > + dimnames = dn) > > n <- sparseMatrix(i = 1:6, j = rev(2:7)) > > e <- sparseMatrix(dims = c(4, 6), i = { > + }, j = { > + }) > > sy <- sparseMatrix(i = c(2, 4, 3:5), j = c(4, 7:5, 5), x = 1:5, dims = c(7, > + 7), symmetric = TRUE) 83a246,297 > A: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > A.: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), x = c(2, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > A1: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > AA: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, > 7L, 7L, 7L, 7L), Dim = c(10L, 20L), Dimnames = list(NULL, NULL), > x = c(7, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > Aa: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), x = c(9, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > As: new("dsyMatrix", x = c(2, 1, 1, 2), Dim = c(2L, 2L), Dimnames = list( > NULL, NULL), uplo = "U", factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > D5.: new("ddiMatrix", diag = "N", Dim = c(5L, 5L), Dimnames = list( > NULL, NULL), x = c(5, 4, 3, 2, 1)) > --> checking list(*): Ok > --=--=--=--=-- > D5N: new("ddiMatrix", diag = "N", Dim = c(5L, 5L), Dimnames = list( > NULL, NULL), x = c(5, 4, 3, 2, NA)) > --> checking list(*): Ok > --=--=--=--=-- > I3: new("ddiMatrix", diag = "U", Dim = c(3L, 3L), Dimnames = list( > NULL, NULL), x = numeric(0)) > --> checking list(*): Ok > --=--=--=--=-- > M: new("ltCMatrix", i = c(0L, 0L, 1L), p = c(0L, 0L, 1L, 3L), Dim = c(3L, > 3L), Dimnames = list(NULL, NULL), x = c(TRUE, TRUE, TRUE), uplo = "U", > diag = "N") > --> checking list(*): Ok > --=--=--=--=-- > args: structure(list(i = c(1, 3, 4, 5, 6, 7, 8, 1), j = c(2, 9, 6, > 7, 8, 9, 10, 2), x = c(7, 14, 21, 28, 35, 42, 49, 2)), class = "data.frame", row.names = c(NA, > -8L)) > --> checking list(*): Ok > --=--=--=--=-- 183a398,404 > dn: list(c("A", "B", "C"), c("a", "b", "c", "d", "e")) > --> checking list(*): Ok > --=--=--=--=-- > e: new("ngCMatrix", i = integer(0), p = c(0L, 0L, 0L, 0L, 0L, 0L, > 0L), Dim = c(4L, 6L), Dimnames = list(NULL, NULL), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- 245a467,469 > i: c(1, 3, 4, 5, 6, 7, 8) > --> checking list(*): Ok > --=--=--=--=-- 265a490,510 > j: c(2, 9, 6, 7, 8, 9, 10) > --> checking list(*): Ok > --=--=--=--=-- > l3: structure(c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, > FALSE), .Dim = c(3L, 3L)) > --> checking list(*): Ok > --=--=--=--=-- > m: new("dgCMatrix", i = c(2L, 0L, 1L, 2L, 0L, 1L), p = c(0L, 1L, > 2L, 4L, 4L, 6L), Dim = c(3L, 5L), Dimnames = list(c("A", "B", > "C"), c("a", "b", "c", "d", "e")), x = c(1, 2, 4, 3, 6, 5), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > n: new("ngCMatrix", i = 5:0, p = c(0L, 0L, 1L, 2L, 3L, 4L, 5L, 6L > ), Dim = 6:7, Dimnames = list(NULL, NULL), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > nA: new("ngCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- 275a521,546 > perm: c(2L, 3L, 6L, 4L, 1L, 7L, 5L) > --> checking list(*): Ok > --=--=--=--=-- > sA: new("dsCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", > factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > sy: new("dsCMatrix", i = c(1L, 3L, 4L, 2L, 3L), p = c(0L, 0L, 0L, > 0L, 1L, 3L, 4L, 5L), Dim = c(7L, 7L), Dimnames = list(NULL, NULL), > x = c(1, 4, 5, 3, 2), uplo = "U", factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > tA: new("dtCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", > diag = "N") > --> checking list(*): Ok > --=--=--=--=-- > x: new("dtCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", > diag = "N") > --> checking list(*): Ok > --=--=--=--=-- 277,279c548,549 < 1 identical warnings: < In library(package, lib.loc = lib.loc, character.only = TRUE, ... : < there is no package called 'Matrix' --- > Length Class Mode > 0 NULL NULL OK running code in 'print-tests.R' ... OK comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK running code in 'lapack.R' ... OK comparing 'lapack.Rout' to './lapack.Rout.save' ... OK running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK running code in 'datetime.R' ... OK comparing 'datetime.Rout' to './datetime.Rout.save' ... OK running code in 'iec60559.R' ... OK comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[4]: Entering directory '/build/r-base-3.5.2/tests' checking Sys.timezone ... make[5]: Entering directory '/build/r-base-3.5.2/tests' running code in 'timezone.R' ... OK make[5]: Leaving directory '/build/r-base-3.5.2/tests' make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running regression tests ... make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'array-subset.R' ... OK running code in 'reg-tests-1a.R' ... OK running code in 'reg-tests-1b.R' ... OK running code in 'reg-tests-1c.R' ... OK running code in 'reg-tests-1d.R' ... OK running code in 'reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ... OK running code in 'p-qbeta-strict-tst.R' ... OK running code in 'r-strict-tst.R' ... OK running code in 'reg-IO.R' ... OK comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK running code in 'reg-IO2.R' ... OK comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK running code in 'reg-plot.R' ... OK comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK running code in 'reg-S4-examples.R' ... OK running code in 'reg-BLAS.R' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[4]: Entering directory '/build/r-base-3.5.2/tests' running tests of plotting Latin-1 expect failure or some differences if not in a Latin-1 or UTF-8 locale running code in 'reg-plot-latin1.R' ... FAILED running code in 'reg-S4.R' ... OK comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ...610,612c610 < Warning message: < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : < there is no package called 'Matrix' --- > [ ] : .M.sub.i.logical() maybe inefficient 1250,1252c1248,1270 < Warning message: < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : < there is no package called 'Matrix' --- > > setClass("Z", representation(zz = "list")) > > setClass("C", contains = c("Z", "dgCMatrix")) > > setClass("C2", contains = "C") > > setClass("C3", contains = "C2") > > m <- matrix(c(0, 0, 2:0), 3, 5, dimnames = list(NULL, NULL)) > > (mC <- as(m, "dgCMatrix")) > 3 x 5 sparse Matrix of class "dgCMatrix" > > [1,] . 1 . . 2 > [2,] . . 2 . 1 > [3,] 2 . 1 . . > > (cc <- as(mC, "C")) > 3 x 5 sparse Matrix of class "C" > > [1,] . 1 . . 2 > [2,] . . 2 . 1 > [3,] 2 . 1 . . > > c2 <- as(mC, "C2") > > c3 <- as(mC, "C3") > > stopifnot(identical(capture.output(c2), sub("C3", "C2", capture.output(c3))), > + identical(as(cc, "matrix"), m), identical(as(c2, "matrix"), m), identical(as(c3, > + "matrix"), m)) > > invisible(lapply(c("Z", "C", "C2", "C3"), removeClass)) OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running tests of Internet functions make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247 < Warning message: < In nsl("cran.r-project.org") : < nsl() was unable to resolve host 'cran.r-project.org' --- > > > > # test do_download (and "record" #{packages}): > > ap <- available.packages(contrib.url("http://cran.r-project.org")) > > ## IGNORE_RDIFF_END > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "" > [2] "" > [3] "" > [4] "The Comprehensive R Archive Network" > [5] "" > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > [11] "" > [12] "" > [13] "" > [14] "" > [15] "" > [16] "" > [17] "" > [18] "<h1>The Comprehensive R Archive Network</h1>" > [19] "" > [20] "Your browser seems not to support frames," > [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN." > [22] "" > [23] "" > > close(zz) > > > > # and via read.table, test http and ftp. > > > > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running tests of date-time printing expect platform-specific differences make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'datetime2.R' ... OK comparing 'datetime2.Rout' to './datetime2.Rout.save' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running tests of documentation examples make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'R-intro.R' ... OK comparing 'R-intro.Rout' to './R-intro.Rout.save' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[4]: Entering directory '/build/r-base-3.5.2/tests' gcc -std=gnu99 -I"/build/r-base-3.5.2/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R-exts.c -o R-exts.o gcc -std=gnu99 -shared -L/build/r-base-3.5.2/lib -Wl,-z,relro -o R-exts.so R-exts.o -L/build/r-base-3.5.2/lib -lR make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'R-exts.R' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running tests of consistency of as/is.* make[4]: Entering directory '/build/r-base-3.5.2/tests' creating 'isas-tests.R' running code in 'isas-tests.R' ... OK comparing 'isas-tests.Rout' to './isas-tests.Rout.save' ... OK rm isas-tests.R make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running tests of random deviate generation make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'p-r-random-tests.R' ... OK comparing 'p-r-random-tests.Rout' to './p-r-random-tests.Rout.save' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running demos from base and stats make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'demos.R' ... OK comparing 'demos.Rout' to './demos.Rout.save' ... OK running code in 'demos2.R' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running tests of primitives make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'primitives.R' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running regexp regression tests make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running more Internet and socket tests make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'internet2.R' ... OK running code in 'libcurl.R' ... OK make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: Entering directory '/build/r-base-3.5.2/tests' running tests of CRAN tools (can be slow unless mirror is local) make[4]: Entering directory '/build/r-base-3.5.2/tests' running code in 'CRANtools.R' ...make[4]: *** [Makefile.common:105: CRANtools.Rout] Error 1 make[4]: Leaving directory '/build/r-base-3.5.2/tests' make[3]: *** [Makefile.common:275: test-CRANtools] Error 2 make[3]: Leaving directory '/build/r-base-3.5.2/tests' make[2]: *** [Makefile.common:179: test-all-devel] Error 1 make[2]: Leaving directory '/build/r-base-3.5.2/tests' make[1]: *** [Makefile:241: check-all] Error 2 make[1]: Leaving directory '/build/r-base-3.5.2' make: [debian/rules:387: check-stamp] Error 2 (ignored) touch check-stamp fakeroot debian/rules binary *** install-arch *** dh_testdir dh_testroot dh_prep -a dh_installdirs -A /build/r-base-3.5.2/debian/r-base-core /usr/bin/make DESTDIR=/build/r-base-3.5.2/debian/r-base-core install make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/m4' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/r-base-3.5.2/m4' make[2]: Entering directory '/build/r-base-3.5.2/tools' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/r-base-3.5.2/tools' make[2]: Entering directory '/build/r-base-3.5.2/doc' installing doc ... mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/doc mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/man/man1 make[3]: Entering directory '/build/r-base-3.5.2/doc/html' installing doc/html ... mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/html make[3]: Leaving directory '/build/r-base-3.5.2/doc/html' make[3]: Entering directory '/build/r-base-3.5.2/doc/manual' installing doc/manual ... mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/manual mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/manual/images make[3]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/build/r-base-3.5.2/doc' make[2]: Entering directory '/build/r-base-3.5.2/etc' mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/etc installing etc ... make[2]: Leaving directory '/build/r-base-3.5.2/etc' make[2]: Entering directory '/build/r-base-3.5.2/share' installing share ... mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/R mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/dictionaries mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/encodings mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/java mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/licenses mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/make mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/Rd mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/Rd/macros mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/sh mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/texmf mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/texmf/tex/latex make[2]: Leaving directory '/build/r-base-3.5.2/share' make[2]: Entering directory '/build/r-base-3.5.2/src' make[3]: Entering directory '/build/r-base-3.5.2/src/scripts' mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/bin make[3]: Leaving directory '/build/r-base-3.5.2/src/scripts' make[3]: Entering directory '/build/r-base-3.5.2/src/include' make[4]: Entering directory '/build/r-base-3.5.2/src/include/R_ext' mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/R/include/R_ext make[4]: Leaving directory '/build/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/build/r-base-3.5.2/src/include' make[3]: Entering directory '/build/r-base-3.5.2/src/extra' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/blas' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/blas' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/tre' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/tre' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/tzone' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/tzone' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/xdr' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/xdr' make[4]: Entering directory '/build/r-base-3.5.2/src/extra/intl' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/r-base-3.5.2/src/extra/intl' make[3]: Leaving directory '/build/r-base-3.5.2/src/extra' make[3]: Entering directory '/build/r-base-3.5.2/src/appl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/build/r-base-3.5.2/src/appl' make[3]: Entering directory '/build/r-base-3.5.2/src/nmath' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/build/r-base-3.5.2/src/nmath' make[3]: Entering directory '/build/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/lib/pkgconfig make[3]: Leaving directory '/build/r-base-3.5.2/src/unix' make[3]: Entering directory '/build/r-base-3.5.2/src/main' mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/bin/exec make[4]: Entering directory '/build/r-base-3.5.2/src/main' make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[4]: Entering directory '/build/r-base-3.5.2/src/main' mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/lib make[4]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Leaving directory '/build/r-base-3.5.2/src/main' make[3]: Entering directory '/build/r-base-3.5.2/src/modules' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/internet' mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/modules make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/build/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/build/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/build/r-base-3.5.2/src/modules' make[3]: Entering directory '/build/r-base-3.5.2/src/library' mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/library installing packages ... building HTML index ... make[3]: Leaving directory '/build/r-base-3.5.2/src/library' make[2]: Leaving directory '/build/r-base-3.5.2/src' make[2]: Entering directory '/build/r-base-3.5.2/tests' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/r-base-3.5.2/tests' make[1]: Leaving directory '/build/r-base-3.5.2' (cd src/unix; \ rm -vf Rscript /build/r-base-3.5.2/debian/r-base-core/usr/bin/Rscript; \ /usr/bin/make CFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ RHOME=/usr/lib/R \ DESTDIR=/build/r-base-3.5.2/debian/r-base-core \ install-Rscript ) removed 'Rscript' removed '/build/r-base-3.5.2/debian/r-base-core/usr/bin/Rscript' make[1]: Entering directory '/build/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c make[1]: Leaving directory '/build/r-base-3.5.2/src/unix' #ls -ltr /build/r-base-3.5.2/debian/r-base-core/usr/bin/ #strings src/unix/Rscript cp -vax src/unix/Rscript /build/r-base-3.5.2/debian/r-base-core/usr/bin/ 'src/unix/Rscript' -> '/build/r-base-3.5.2/debian/r-base-core/usr/bin/Rscript' #ls -ltr /build/r-base-3.5.2/debian/r-base-core/usr/bin/ #strings /build/r-base-3.5.2/debian/r-base-core/usr/bin/Rscript (cd src/nmath/standalone; \ /usr/bin/make DESTDIR=/build/r-base-3.5.2/debian/r-base-core install ) make[1]: Entering directory '/build/r-base-3.5.2/src/nmath/standalone' make[2]: Entering directory '/build/r-base-3.5.2/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/build/r-base-3.5.2/src/include' /build/r-base-3.5.2/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged make[1]: Leaving directory '/build/r-base-3.5.2/src/nmath/standalone' chmod a+x /build/r-base-3.5.2/debian/r-base-core/usr/share/R/share/sh/echo.sh rm -v /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/COPYING removed '/build/r-base-3.5.2/debian/r-base-core/usr/lib/R/COPYING' (cd /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/; \ ln -s ../../share/common-licenses/GPL-2 COPYING) rm -v /build/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/COPYING removed '/build/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/COPYING' (cd /build/r-base-3.5.2/debian/r-base-core/usr/share/R/doc; \ ln -s ../../../share/common-licenses/GPL-2 COPYING) (cd /build/r-base-3.5.2/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 make prefix=/build/r-base-3.5.2/debian/r-base-core/usr \ rdocdir=/build/r-base-3.5.2/debian/r-base-core/usr/share/R/doc \ install-pdf make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/doc/manual' installing R manuals in PDF format ... make[2]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[1]: Leaving directory '/build/r-base-3.5.2' make prefix=/build/r-base-3.5.2/debian/r-base-core/usr \ infodir=/build/r-base-3.5.2/debian/r-base-core/usr/share/info install-info make[1]: Entering directory '/build/r-base-3.5.2' make[2]: Entering directory '/build/r-base-3.5.2/doc/manual' mkdir -p -- /build/r-base-3.5.2/debian/r-base-core/usr/share/info /usr/bin/install -c -m 644 "./dir" "/build/r-base-3.5.2/debian/r-base-core/usr/share/info" installing R info pages ... updating '/build/r-base-3.5.2/debian/r-base-core/usr/share/info/dir' ... you need to adjust /build/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually make[2]: Leaving directory '/build/r-base-3.5.2/doc/manual' make[1]: Leaving directory '/build/r-base-3.5.2' 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/r-base-3.5.2/debian/r-base-core/usr/share/info/*.gz /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-FAQ.info.gz: 67.0% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-FAQ.info /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-admin.info.gz: 68.1% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-admin.info /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-data.info.gz: 70.6% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-data.info /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-1.gz: 66.7% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-1 /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-2.gz: 69.8% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-2 /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-3.gz: 83.3% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-3 /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info.gz: 69.7% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-intro.info.gz: 70.0% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-intro.info /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-ints.info.gz: 67.9% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-ints.info /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-lang.info.gz: 71.6% -- replaced with /build/r-base-3.5.2/debian/r-base-core/usr/share/info/R-lang.info dh_movefiles --sourcedir=debian/r-base-core -pr-doc-info rm -vf /build/r-base-3.5.2/debian/r-doc-info/usr/share/info/dir \ /build/r-base-3.5.2/debian/r-doc-info/usr/share/info/dir.old removed '/build/r-base-3.5.2/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/r-base-3.5.2/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 2804 -rw-r--r-- 1 root root 1872858 Feb 19 14:55 libRmath.a -rwxr-xr-x 1 root root 993088 Feb 19 14:55 libRmath.so drwxr-xr-x 2 root root 60 Feb 19 14:55 pkgconfig renamed '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/r-base-3.5.2/debian/r-mathlib/usr/include install -m 0644 debian/Rprofile.site /build/r-base-3.5.2/debian/r-base-core/etc/R install -m 0644 debian/Renviron.site /build/r-base-3.5.2/debian/r-base-core/etc/R (cd /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/etc; \ cat /build/r-base-3.5.2/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 42 with fuzz 2 (offset 9 lines). done dh_bash-completion # edd 12 Jan 2016 new location #install -m 0644 debian/R.bash-completion \ # debian/r-base-core/usr/share/bash-completion/completions/R (cd /build/r-base-3.5.2/debian/r-base-core/usr/lib/; \ ln -sv R/lib/libR.so . ) './libR.so' -> 'R/lib/libR.so' (cd debian/icon-class-patch && munpack rlogo_icon.png.mpack) rlogo_icon.png (application/octet-stream) install -m 0644 debian/icon-class-patch/rlogo_icon.png \ debian/r-base-core/usr/share/icons/hicolor/48x48/apps install -m 0644 debian/icon-class-patch/R.desktop \ debian/r-base-core/usr/share/applications rm debian/icon-class-patch/rlogo_icon.png touch install-arch-stamp *** binary-arch *** dh_testdir -a dh_testroot -a dh_installdocs -pr-base-core doc/NEWS.* README \ debian/README.Atlas \ debian/README.mathlib dh_installdocs -pr-mathlib doc/NEWS.* README \ debian/README.mathlib dh_installdocs -pr-base-core-dbg dh_installexamples -pr-mathlib src/nmath/standalone/test.c #dh_installmenu -a # (cd /build/r-base-3.5.2/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .) (cd /build/r-base-3.5.2/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .) (cd /build/r-base-3.5.2/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/r-base-3.5.2/debian/r-base-core/usr/share/lintian/overrides/r-base-core install -p -m 0644 debian/r-recommended.lintian \ /build/r-base-3.5.2/debian/r-recommended/usr/share/lintian/overrides/r-recommended install -p -m 0644 debian/r-mathlib.lintian \ /build/r-base-3.5.2/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib dh_installchangelogs -a -k doc/NEWS dh_strip --dbg-package=r-base-core-dbg dh_compress -a dh_fixperms -a dh_link -a dh_makeshlibs -a dh_installdeb -a dh_perl -a dh_shlibdeps -a -l /build/r-base-3.5.2/debian/r-base-core/usr/lib/R/lib dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-mathlib/usr/lib/libRmath.so.1.0.0 was not linked against libgomp.so.1 (it uses none of the library's symbols) 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 'libtcl8.6.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtk8.6.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: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/library/stats/libs/stats.so debian/r-base-core/usr/lib/R/lib/libR.so debian/r-base-core/usr/lib/R/modules/lapack.so were not linked against libgfortran.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/library/tcltk/libs/tcltk.so was not linked against libXss.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_de.so debian/r-base-core/usr/lib/R/library/tcltk/libs/tcltk.so debian/r-base-core/usr/lib/R/modules/R_X11.so were not linked against libXext.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_de.so debian/r-base-core/usr/lib/R/modules/R_X11.so were not linked against libSM.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_de.so debian/r-base-core/usr/lib/R/modules/R_X11.so were not linked against libICE.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_de.so debian/r-base-core/usr/lib/R/library/grDevices/libs/cairo.so debian/r-base-core/usr/lib/R/modules/R_X11.so were not linked against libglib-2.0.so.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/lib/libR.so was not linked against librt.so.1 (it uses none of the library's symbols) dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package r-base-core: substitution variable ${perl:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'r-base-core' in '../r-base-core_3.5.2-1_arm64.deb'. dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.5.2-1_arm64.deb'. dpkg-deb: building package 'r-base-core-dbg' in '../r-base-core-dbg_3.5.2-1_arm64.deb'. *** binary-indep *** dh_testdir -i dh_testroot -i dh_link -i dh_installdocs -i dh_installdocs -v -pr-doc-html install -p -m0644 debian/copyright debian/r-doc-html/usr/share/doc/r-doc-html/copyright install -p -m0644 debian/r-doc-html.doc-base.lang debian/r-doc-html/usr/share/doc-base/r-language install -p -m0644 debian/r-doc-html.doc-base.exts debian/r-doc-html/usr/share/doc-base/r-extensions install -p -m0644 debian/r-doc-html.doc-base.admin debian/r-doc-html/usr/share/doc-base/r-admin install -p -m0644 debian/r-doc-html.doc-base.data debian/r-doc-html/usr/share/doc-base/r-data install -p -m0644 debian/r-doc-html.doc-base.ints debian/r-doc-html/usr/share/doc-base/r-ints install -p -m0644 debian/r-doc-html.doc-base.intro debian/r-doc-html/usr/share/doc-base/r-intro install -p -m0644 debian/r-doc-html.doc-base.faq debian/r-doc-html/usr/share/doc-base/r-faq dh_installchangelogs -i dh_installdirs -pr-base-dev usr/share/R/debian install -p -m 0755 debian/r-cran.mk \ /build/r-base-3.5.2/debian/r-base-dev/usr/share/R/debian dh_compress -i dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'r-base-dev' in '../r-base-dev_3.5.2-1_all.deb'. dpkg-deb: building package 'r-base' in '../r-base_3.5.2-1_all.deb'. dpkg-deb: building package 'r-base-html' in '../r-base-html_3.5.2-1_all.deb'. dpkg-deb: building package 'r-doc-pdf' in '../r-doc-pdf_3.5.2-1_all.deb'. dpkg-deb: building package 'r-doc-info' in '../r-doc-info_3.5.2-1_all.deb'. dpkg-deb: building package 'r-doc-html' in '../r-doc-html_3.5.2-1_all.deb'. dpkg-deb: building package 'r-recommended' in '../r-recommended_3.5.2-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../r-base_3.5.2-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/14484 and its subdirectories I: Current time: Sat Feb 19 14:57:01 -12 2022 I: pbuilder-time-stamp: 1645325821 Sun Jan 17 20:34:09 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Sun Jan 17 20:34:09 UTC 2021 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Sun Jan 17 21:04:50 UTC 2021 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Sun Jan 17 21:04:51 UTC 2021 I: r-base_3.5.2-1_arm64.changes: Format: 1.8 Date: Thu, 20 Dec 2018 05:35:13 -0600 Source: r-base Binary: r-base r-base-core r-base-core-dbg r-base-dev r-base-html r-doc-html r-doc-info r-doc-pdf r-mathlib r-recommended Architecture: arm64 all Version: 3.5.2-1 Distribution: unstable Urgency: medium Maintainer: Dirk Eddelbuettel Changed-By: Dirk Eddelbuettel 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 (3.5.2-1) unstable; urgency=medium . * New upstream version released this morning Checksums-Sha1: 5ec2af4efff397175574bbefec01c00538470c05 6522912 r-base-core-dbg_3.5.2-1_arm64.deb 28ecf01803bfc494706fb01b2be91ac03abeb2c9 23739948 r-base-core_3.5.2-1_arm64.deb eaa13c306a0eb1214bff4d29573666947c10f18c 4480 r-base-dev_3.5.2-1_all.deb 3a12492cdee30edb53580991da74508558c7834d 87912 r-base-html_3.5.2-1_all.deb b7ead9a10959c4f99040016797b983572783792b 42144 r-base_3.5.2-1_all.deb accd6601a12e3d39da3e3f1e752629dcba68b1dc 15921 r-base_3.5.2-1_arm64.buildinfo c9452b5a2fb9557abbe8f6e5e749b149876b81bd 562724 r-doc-html_3.5.2-1_all.deb 145722d7789afe2b41b86caf1c62e69e0ed0d4d0 625568 r-doc-info_3.5.2-1_all.deb bebdd51b456e6812974cc460925e2fd0295f17e7 9370020 r-doc-pdf_3.5.2-1_all.deb 0783d1a9a724444c342d23b81d6b20e4914191b2 1836820 r-mathlib_3.5.2-1_arm64.deb 9906e8c487c987cdba9a2592c86a3a8e47a03fe9 2772 r-recommended_3.5.2-1_all.deb Checksums-Sha256: 35cdaf2dea15dd0716a8d2983e033eb10e151e0db5ae7028e327efb30544734c 6522912 r-base-core-dbg_3.5.2-1_arm64.deb f131f7318c41e15dfc5ded57eba774a6c4cd7ef4971ec6112a5598336d7ea588 23739948 r-base-core_3.5.2-1_arm64.deb 97b6f94f2db0ca449320109391d5088f83bb600d1c4293c9d38e391e912b6e16 4480 r-base-dev_3.5.2-1_all.deb c38301f55dee4bd877a38650670e37a598b57a2753fa9d7b2edf5f20607a388c 87912 r-base-html_3.5.2-1_all.deb 68a013797777cb1875a7570491a276cf6270aaa82307b4f070281332786337cb 42144 r-base_3.5.2-1_all.deb 35160ec1449ed6a0fa6c447a15a2656eb0246144d2cd1c07f2d4c93aada73fa4 15921 r-base_3.5.2-1_arm64.buildinfo d7fb87b675ae631b31609335cfb16efc0d331fdf0ee52187d20e7f0facdaa8c3 562724 r-doc-html_3.5.2-1_all.deb 7639f5832b6f1ea78884da1d3fb3fbbb0f69405c05786b2cb08f905732803210 625568 r-doc-info_3.5.2-1_all.deb 84758f8a366e05ffae76913198731a99e2aaf872aa09b8d67994337a34f11df1 9370020 r-doc-pdf_3.5.2-1_all.deb 8501897cfa3a62697f7fe72958a6104229c59e76d9c7562549d0f57bfd0caf91 1836820 r-mathlib_3.5.2-1_arm64.deb 244be2117948480bfb2d3715a1cc9b3a21cbc45a94d3af6ddf7e1e8bf2e5fb4e 2772 r-recommended_3.5.2-1_all.deb Files: e70c3a50cce75644e2c28bef247c8e54 6522912 debug optional r-base-core-dbg_3.5.2-1_arm64.deb ed5809d07b96d00a0dc8de4a1f675eae 23739948 gnu-r optional r-base-core_3.5.2-1_arm64.deb 1041a66eb24fc518dda1641528b94f2f 4480 gnu-r optional r-base-dev_3.5.2-1_all.deb 2ff434f8433f2956bfc2cdb5c93281d3 87912 doc optional r-base-html_3.5.2-1_all.deb 18283f45c5afa10ada525a8e0faf3a65 42144 gnu-r optional r-base_3.5.2-1_all.deb 54f2386ea8eaea2f29181c24f50351c7 15921 gnu-r optional r-base_3.5.2-1_arm64.buildinfo 92838b4a6dcac9f7e5af2da2faafdeaf 562724 doc optional r-doc-html_3.5.2-1_all.deb 4dc3701b5c9d52c6119dbd3d4b5e9889 625568 doc optional r-doc-info_3.5.2-1_all.deb 5342280d108ce2c9e824a40ba9a34fec 9370020 doc optional r-doc-pdf_3.5.2-1_all.deb a08d1eb89d699205d53b418fb5b7450f 1836820 gnu-r optional r-mathlib_3.5.2-1_arm64.deb da7da3533e49d316c9f54ad069d8b607 2772 gnu-r optional r-recommended_3.5.2-1_all.deb Sun Jan 17 21:05:07 UTC 2021 I: diffoscope 163 will be used to compare the two builds: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/diffoscope/main.py", line 763, in main sys.exit(run_diffoscope(parsed_args)) File "/usr/lib/python3/dist-packages/diffoscope/main.py", line 717, in run_diffoscope difference = compare_root_paths(path1, path2) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/compare.py", line 69, in compare_root_paths difference = compare_files(file1, file2) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/compare.py", line 125, in compare_files return file1.compare(file2, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/debian.py", line 236, in compare differences = super().compare(other, *args, **kwargs) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 478, in compare difference = self._compare_using_details(other, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 425, in _compare_using_details other.as_container, no_recurse=no_recurse File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/container.py", line 194, in compare_pair file1, file2, source=None, diff_content_only=no_recurse File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/compare.py", line 125, in compare_files return file1.compare(file2, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 478, in compare difference = self._compare_using_details(other, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 425, in _compare_using_details other.as_container, no_recurse=no_recurse File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/container.py", line 194, in compare_pair file1, file2, source=None, diff_content_only=no_recurse File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/compare.py", line 125, in compare_files return file1.compare(file2, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 478, in compare difference = self._compare_using_details(other, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 425, in _compare_using_details other.as_container, no_recurse=no_recurse File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/container.py", line 194, in compare_pair file1, file2, source=None, diff_content_only=no_recurse File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/compare.py", line 125, in compare_files return file1.compare(file2, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 478, in compare difference = self._compare_using_details(other, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 425, in _compare_using_details other.as_container, no_recurse=no_recurse File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/container.py", line 194, in compare_pair file1, file2, source=None, diff_content_only=no_recurse File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/compare.py", line 125, in compare_files return file1.compare(file2, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 478, in compare difference = self._compare_using_details(other, source) File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/file.py", line 395, in _compare_using_details details.extend(self.compare_details(other, source)) File "/usr/lib/python3/dist-packages/diffoscope/comparators/rdata.py", line 171, in compare_details return [Difference.from_operation(RdbReader, a, b)] File "/usr/lib/python3/dist-packages/diffoscope/difference.py", line 255, in from_operation klass, path1, path2, *args, **kwargs File "/usr/lib/python3/dist-packages/diffoscope/difference.py", line 275, in from_operation_exc feeder1, operation1, excluded1 = operation_and_feeder(path1) File "/usr/lib/python3/dist-packages/diffoscope/difference.py", line 272, in operation_and_feeder operation.start() File "/usr/lib/python3/dist-packages/diffoscope/comparators/utils/command.py", line 52, in start stderr=subprocess.PIPE, File "/usr/lib/python3.7/subprocess.py", line 462, in run raise ValueError('stdin and input arguments may not both be used.') ValueError: stdin and input arguments may not both be used. # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.cCDsfdUQXN/r-base_3.5.2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.cCDsfdUQXN/r-base_3.5.2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.cCDsfdUQXN/r-base_3.5.2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.cCDsfdUQXN/b1/r-base_3.5.2-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.cCDsfdUQXN/b2/r-base_3.5.2-1_arm64.changes ## close_archive (total time: 0.000s) 0.000s 4 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer ## command (total time: 8.556s) 5.154s 6 calls xz 2.242s 62 calls diff 0.610s 16 calls cmp 0.300s 80 calls Rscript 0.216s 14 calls gzip 0.033s 11 calls pdftotext 0.002s 29 calls cmp (internal) ## compare_files (cumulative) (total time: 34.620s) 15.257s 7 calls abc.GzipFile 14.593s 7 calls abc.RdsFile 3.084s 1 call abc.PdfFile 0.859s 8 calls abc.TextFile 0.500s 1 call abc.XzFile 0.243s 1 call abc.TarFile 0.082s 1 call abc.Md5sumsFile ## container_extract (total time: 14.134s) 5.155s 6 calls diffoscope.comparators.xz.XzContainer 5.010s 1878 calls diffoscope.comparators.deb.DebTarContainer 3.720s 8 calls diffoscope.comparators.deb.DebContainer 0.241s 14 calls diffoscope.comparators.gzip.GzipContainer 0.008s 16 calls diffoscope.comparators.tar.TarContainer ## has_same_content_as (total time: 0.620s) 0.335s 2 calls abc.DebFile 0.089s 7 calls abc.GzipFile 0.078s 20 calls abc.TextFile 0.038s 2 calls abc.XzFile 0.037s 2 calls abc.Md5sumsFile 0.012s 1 call abc.PdfFile 0.011s 1 call abc.DebDataTarFile 0.009s 1 call abc.TarFile 0.008s 1 call abc.RdbFile 0.001s 7 calls abc.RdsFile 0.000s 1 call abc.DotChangesFile ## main (total time: 0.331s) 0.331s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 14 calls diffoscope.comparators.gzip.GzipContainer 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## recognizes (total time: 3.406s) 2.363s 10 calls diffoscope.comparators.binary.FilesystemFile 0.809s 1834 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.144s 88 calls diffoscope.comparators.debian.DebControlMember 0.089s 916 calls diffoscope.comparators.utils.archive.ArchiveMember 0.001s 8 calls abc.DotChangesFile 0.000s 14 calls abc.Md5sumsFile Sun Jan 17 21:13:26 UTC 2021 E: r-base failed to build reproducibly in buster on arm64. Sun Jan 17 21:13:27 UTC 2021 W: diffoscope 163 produced no output (which is strange). Sun Jan 17 21:13:30 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Jan 17 21:13:30 UTC 2021 I: Submitting 20K b1/r-base_3.5.2-1_arm64.buildinfo.asc Sun Jan 17 21:13:32 UTC 2021 I: Submitting 20K b2/r-base_3.5.2-1_arm64.buildinfo.asc Sun Jan 17 21:13:33 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jan 17 21:13:33 UTC 2021 I: Done submitting .buildinfo files. Sun Jan 17 21:13:33 UTC 2021 I: Removing signed r-base_3.5.2-1_arm64.buildinfo.asc files: removed './b1/r-base_3.5.2-1_arm64.buildinfo.asc' removed './b2/r-base_3.5.2-1_arm64.buildinfo.asc' Sun Jan 17 21:13:44 UTC 2021 I: Artifacts from this build have been preserved. They will be available for 24h only, so download them now. WARNING: You shouldn't trust packages downloaded from this host, they can contain malware or the worst of your fears, packaged nicely in debian format. If you are aware of this and just want to use these artifacts to investigate why diffoscope 163 had issues, you can download the artifacts from the following location: https://tests.reproducible-builds.org/debian/artifacts/r00t-me/r-base_buster_arm64_tmp-Aen9Q/