I: pbuilder: network access will be disabled during build I: Current time: Fri Jan 26 01:27:08 -12 2024 I: pbuilder-time-stamp: 1706275628 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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_4.2.2.20221110-2.dsc] I: copying [./r-base_4.2.2.20221110.orig.tar.gz] I: copying [./r-base_4.2.2.20221110-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jan 20 17:47:53 2023 gpgv: using RSA key A1489FE2AB99A21A gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./r-base_4.2.2.20221110-2.dsc: no acceptable signature found dpkg-source: info: extracting r-base in r-base-4.2.2.20221110 dpkg-source: info: unpacking r-base_4.2.2.20221110.orig.tar.gz dpkg-source: info: unpacking r-base_4.2.2.20221110-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying set_R_LIBS_USER_and_SITE_in_Renviron.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/478551/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='72737c98d69f493d87c8a7f60814cc7c' 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='478551' 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/r-b-build.AQRjbPCD/pbuilderrc_t3S0 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AQRjbPCD/b1 --logfile b1/build.log r-base_4.2.2.20221110-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/478551/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: amd64 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 (>= 4:4.9.2-2), g++ (>= 4:4.9.2-2), gfortran (>= 4:4.9.2-2), libblas-dev, liblapack-dev, tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper-compat (= 12), texinfo, libbz2-dev, liblzma-dev, libpcre2-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-plain-generic, 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 ... 18148 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 (>= 4:4.9.2-2); 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; 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-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on texinfo; 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 libpcre2-dev; however: Package libpcre2-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-plain-generic; however: Package texlive-plain-generic 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: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bison{a} bsdextrautils{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-12{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} gtk-update-icon-cache{a} hicolor-icon-theme{a} icu-devtools{a} intltool-debian{a} java-common{a} libapache-pom-java{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas-dev{a} libblas3{a} libblkid-dev{a} libbrotli-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2{a} libcurl4{a} libcurl4-openssl-dev{a} libdatrie-dev{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{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} libfontbox-java{a} libfontconfig-dev{a} libfontconfig1{a} libfontconfig1-dev{a} libfontenc1{a} libfreetype-dev{a} libfreetype6{a} libfribidi-dev{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran-12-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} libgtk2.0-0{a} libgtk2.0-common{a} libharfbuzz-dev{a} libharfbuzz-gobject0{a} libharfbuzz-icu0{a} libharfbuzz-subset0{a} libharfbuzz0b{a} libice-dev{a} libice6{a} libicu-dev{a} libicu72{a} libjbig-dev{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libkpathsea6{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc-dev{a} liblerc4{a} libllvm15{a} liblzma-dev{a} liblzo2-2{a} libmagic-mgc{a} libmagic1{a} libmime-charset-perl{a} libmount-dev{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{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} libpciaccess0{a} libpcre16-3{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpcre3{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpcsclite1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16{a} libpsl5{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline-dev{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsensors-config{a} libsensors5{a} libsepol-dev{a} libsm-dev{a} libsm6{a} libsombok3{a} libssh2-1{a} libsub-override-perl{a} libsynctex2{a} libtcl8.6{a} libteckit0{a} libtexlua53-5{a} libtexluajit2{a} libtext-unidecode-perl{a} libthai-data{a} libthai-dev{a} libthai0{a} libtiff-dev{a} libtiff5-dev{a} libtiff6{a} libtiffxx6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{a} libunwind8{a} libwebp-dev{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{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-randr0{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes3{a} libxfont2{a} libxft-dev{a} libxft2{a} libxi6{a} libxinerama1{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} libxrandr2{a} libxrender-dev{a} libxrender1{a} libxshmfence1{a} libxss-dev{a} libxss1{a} libxt-dev{a} libxt6{a} libxtst6{a} libxxf86vm1{a} libz3-4{a} libzstd-dev{a} libzzip-0-13{a} lmodern{a} m4{a} man-db{a} media-types{a} mpack{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} pango1.0-tools{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} preview-latex-style{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} shared-mime-info{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-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-luatex{a} texlive-pictures{a} texlive-plain-generic{a} tk8.6{a} tk8.6-dev{a} tzdata{a} ucf{a} uuid-dev{a} x11-common{a} x11-xkb-utils{a} x11proto-core-dev{a} x11proto-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: alsa-topology-conf alsa-ucm-conf bzip2-doc cm-super curl dbus dvisvgm fonts-adf-accanthis fonts-adf-berenis fonts-adf-gillius fonts-adf-universalis fonts-cabin fonts-cantarell fonts-clear-sans fonts-comfortaa fonts-comic-neue fonts-croscore fonts-crosextra-caladea fonts-crosextra-carlito fonts-dejavu-extra 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-inter fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobstertwo fonts-noto-color-emoji fonts-noto-core fonts-noto-mono fonts-oflb-asana-math fonts-open-sans fonts-paratype fonts-roboto-slab fonts-roboto-unhinted fonts-sil-andika fonts-sil-charis fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix ghostscript javascript-common libarchive-cpio-perl libatk-wrapper-java-jni libfile-homedir-perl libfile-mimeinfo-perl libgail-common libgdk-pixbuf2.0-bin libgpm2 libgtk2.0-bin libldap-common liblog-log4perl-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools librsvg2-common libsasl2-modules libspreadsheet-parseexcel-perl libwww-perl libx11-protocol-perl libxml-sax-expat-perl libyaml-tiny-perl lynx publicsuffix ruby tex-gyre texlive-fonts-extra-links tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 328 newly installed, 0 to remove and 0 not upgraded. Need to get 1012 MB of archives. After unpacking 2913 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2023c-5+deb12u1 [296 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 bash-completion all 1:2.11-6 [234 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.38-2~deb12u1 [44.0 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 bison amd64 2:3.8.2+dfsg-1+b1 [1175 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230710~deb12u1 [11.9 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.10-1~deb12u1 [201 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u5 [245 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.9+9-1~deb12u1 [43.7 MB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2+deb12u2 [192 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.9+9-1~deb12u1 [184 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get: 148 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk-headless amd64 17.0.9+9-1~deb12u1 [71.3 MB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 default-jdk-headless amd64 2:1.17-74 [1108 B] Get: 150 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk amd64 17.0.9+9-1~deb12u1 [2777 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 default-jdk amd64 2:1.17-74 [1068 B] Get: 152 http://deb.debian.org/debian bookworm/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 gfortran amd64 4:12.2.0-3 [1428 B] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libgirepository-1.0-1 amd64 1.74.0-3 [101 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 gir1.2-glib-2.0 amd64 1.74.0-3 [159 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 gir1.2-freedesktop amd64 1.74.0-3 [37.2 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 gir1.2-harfbuzz-0.0 amd64 6.0.0+dfsg-3 [1579 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libpangoxft-1.0-0 amd64 1.50.12+ds-1 [26.7 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 gir1.2-pango-1.0 amd64 1.50.12+ds-1 [37.4 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libblas-dev amd64 3.11.0-2 [158 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 uuid-dev amd64 2.38.1-5+b1 [39.9 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libblkid-dev amd64 2.38.1-5+b1 [179 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libbrotli-dev amd64 1.0.9-2+b6 [287 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libcairo-gobject2 amd64 1.16.0-7 [112 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libcairo-script-interpreter2 amd64 1.16.0-7 [149 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libpng-dev amd64 1.6.39-2 [359 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libfreetype-dev amd64 2.12.1+dfsg-5 [567 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libfontconfig-dev amd64 2.14.1-4 [409 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libffi-dev amd64 3.4.4-1 [59.4 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-data all 2.74.6-2 [1207 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-bin amd64 2.74.6-2 [110 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-dev-bin amd64 2.74.6-2 [151 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libsepol-dev amd64 3.4-2.1 [351 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libpcre2-16-0 amd64 10.42-1 [245 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libpcre2-32-0 amd64 10.42-1 [234 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libpcre2-posix3 amd64 10.42-1 [55.4 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libpcre2-dev amd64 10.42-1 [753 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libselinux1-dev amd64 3.4-1+b6 [157 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libmount-dev amd64 2.38.1-5+b1 [22.5 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-dev amd64 2.74.6-2 [1601 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-dev amd64 0.42.2-1 [564 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 x11proto-dev all 2022.1-1 [599 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 x11proto-core-dev all 2022.1-1 [3528 B] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libice-dev amd64 2:1.0.10-1 [67.1 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libx11-dev amd64 2:1.8.4-2+deb12u2 [837 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0-dev amd64 1.15-1 [118 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0-dev amd64 1.15-1 [107 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 libxrender-dev amd64 1:0.9.10-1.1 [41.1 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libcairo2-dev amd64 1.16.0-7 [727 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u4 [390 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 libcurl4-openssl-dev amd64 7.88.1-10+deb12u4 [491 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 libdatrie-dev amd64 0.2.13-2+b1 [18.2 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1-dev amd64 2.14.1-4 [268 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libfribidi-dev amd64 1.0.8-2.1 [105 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-dev amd64 1.3.14-1 [24.0 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz-icu0 amd64 6.0.0+dfsg-3 [1557 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz-gobject0 amd64 6.0.0+dfsg-3 [1572 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz-subset0 amd64 6.0.0+dfsg-3 [1931 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz-dev amd64 6.0.0+dfsg-3 [1668 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libjbig-dev amd64 2.1-6.1 [31.0 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2 [290 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libjpeg-dev amd64 1:2.1.5-2 [71.8 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libkpathsea6 amd64 2022.20220321.62855-5.1+deb12u1 [152 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 liblapack-dev amd64 3.11.0-2 [4631 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 liblerc-dev amd64 4.0.0+ds-2 [175 kB] Get: 248 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 249 http://deb.debian.org/debian bookworm/main amd64 libmime-charset-perl all 1.013.1-2 [34.0 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 libncurses-dev amd64 6.4-4 [349 kB] Get: 252 http://deb.debian.org/debian bookworm/main amd64 libncurses5-dev amd64 6.4-4 [932 B] Get: 253 http://deb.debian.org/debian bookworm/main amd64 libthai-dev amd64 0.1.29-1 [24.0 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 libxft-dev amd64 2.3.6-1 [80.3 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 pango1.0-tools amd64 1.50.12+ds-1 [40.8 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 libpango1.0-dev amd64 1.50.12+ds-1 [152 kB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get: 258 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get: 259 http://deb.debian.org/debian bookworm/main amd64 libpcre16-3 amd64 2:8.39-15 [257 kB] Get: 260 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 libpcre32-3 amd64 2:8.39-15 [248 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 libpcrecpp0v5 amd64 2:8.39-15 [143 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 libpcre3-dev amd64 2:8.39-15 [653 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 libptexenc1 amd64 2022.20220321.62855-5.1+deb12u1 [43.7 kB] Get: 266 http://deb.debian.org/debian bookworm/main amd64 libreadline-dev amd64 8.2-1.3 [151 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 libsombok3 amd64 2.4.0-2+b1 [31.4 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 libsynctex2 amd64 2022.20220321.62855-5.1+deb12u1 [59.8 kB] Get: 269 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get: 270 http://deb.debian.org/debian bookworm/main amd64 libteckit0 amd64 2.5.11+ds1-1+b1 [335 kB] Get: 271 http://deb.debian.org/debian bookworm/main amd64 libtexlua53-5 amd64 2022.20220321.62855-5.1+deb12u1 [111 kB] Get: 272 http://deb.debian.org/debian bookworm/main amd64 libtexluajit2 amd64 2022.20220321.62855-5.1+deb12u1 [246 kB] Get: 273 http://deb.debian.org/debian bookworm/main amd64 libtext-unidecode-perl all 1.30-3 [101 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 libzstd-dev amd64 1.5.4+dfsg2-5 [354 kB] Get: 275 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get: 276 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get: 277 http://deb.debian.org/debian bookworm/main amd64 libwebp-dev amd64 1.2.4-0.2+deb12u1 [400 kB] Get: 278 http://deb.debian.org/debian bookworm/main amd64 libtiffxx6 amd64 4.5.0-6+deb12u1 [144 kB] Get: 279 http://deb.debian.org/debian bookworm/main amd64 libtiff-dev amd64 4.5.0-6+deb12u1 [456 kB] Get: 280 http://deb.debian.org/debian bookworm/main amd64 libtiff5-dev amd64 4.5.0-6+deb12u1 [141 kB] Get: 281 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 282 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get: 283 http://deb.debian.org/debian bookworm/main amd64 libunicode-linebreak-perl amd64 0.0.20190101-1+b5 [97.8 kB] Get: 284 http://deb.debian.org/debian bookworm/main amd64 libunwind8 amd64 1.6.2-3 [51.2 kB] Get: 285 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get: 286 http://deb.debian.org/debian bookworm/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB] Get: 287 http://deb.debian.org/debian bookworm/main amd64 libxpm4 amd64 1:3.5.12-1.1+deb12u1 [48.6 kB] Get: 288 http://deb.debian.org/debian bookworm/main amd64 libxaw7 amd64 2:1.0.14-1 [201 kB] Get: 289 http://deb.debian.org/debian bookworm/main amd64 libxfont2 amd64 1:2.0.6-1 [136 kB] Get: 290 http://deb.debian.org/debian bookworm/main amd64 libxkbfile1 amd64 1:1.1.0-1 [75.2 kB] Get: 291 http://deb.debian.org/debian bookworm/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get: 292 http://deb.debian.org/debian bookworm/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get: 293 http://deb.debian.org/debian bookworm/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get: 294 http://deb.debian.org/debian bookworm/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get: 295 http://deb.debian.org/debian bookworm/main amd64 libxmuu1 amd64 2:1.1.3-3 [23.9 kB] Get: 296 http://deb.debian.org/debian bookworm/main amd64 libxss-dev amd64 1:1.2.3-1 [23.5 kB] Get: 297 http://deb.debian.org/debian bookworm/main amd64 libxt-dev amd64 1:1.2.1-1.1 [405 kB] Get: 298 http://deb.debian.org/debian bookworm/main amd64 libzzip-0-13 amd64 0.13.72+dfsg.1-1.1 [58.3 kB] Get: 299 http://deb.debian.org/debian bookworm/main amd64 tex-common all 6.18 [32.5 kB] Get: 300 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 301 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 302 http://deb.debian.org/debian bookworm/main amd64 lmodern all 2.005-1 [9480 kB] Get: 303 http://deb.debian.org/debian bookworm/main amd64 mpack amd64 1.6-18+b1 [39.7 kB] Get: 304 http://deb.debian.org/debian bookworm/main amd64 preview-latex-style all 12.2-1 [201 kB] Get: 305 http://deb.debian.org/debian bookworm/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 306 http://deb.debian.org/debian bookworm/main amd64 tcl8.6 amd64 8.6.13+dfsg-2 [120 kB] Get: 307 http://deb.debian.org/debian bookworm/main amd64 tcl8.6-dev amd64 8.6.13+dfsg-2 [1023 kB] Get: 308 http://deb.debian.org/debian bookworm/main amd64 texinfo amd64 6.8-6+b1 [1816 kB] Get: 309 http://deb.debian.org/debian bookworm/main amd64 texlive-binaries amd64 2022.20220321.62855-5.1+deb12u1 [10.5 MB] Get: 310 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 311 http://deb.debian.org/debian bookworm/main amd64 texlive-base all 2022.20230122-3 [21.9 MB] Get: 312 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 313 http://deb.debian.org/debian bookworm/main amd64 texlive-luatex all 2022.20230122-3 [22.7 MB] Get: 314 http://deb.debian.org/debian bookworm/main amd64 texlive-plain-generic all 2022.20230122-4 [28.9 MB] Get: 315 http://deb.debian.org/debian bookworm/main amd64 texlive-extra-utils all 2022.20230122-4 [59.0 MB] Get: 316 http://deb.debian.org/debian bookworm/main amd64 texlive-fonts-extra all 2022.20230122-4 [509 MB] Get: 317 http://deb.debian.org/debian bookworm/main amd64 texlive-fonts-recommended all 2022.20230122-3 [4988 kB] Get: 318 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 319 http://deb.debian.org/debian bookworm/main amd64 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 320 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-extra all 2022.20230122-4 [19.2 MB] Get: 321 http://deb.debian.org/debian bookworm/main amd64 tk8.6 amd64 8.6.13-2 [69.4 kB] Get: 322 http://deb.debian.org/debian bookworm/main amd64 tk8.6-dev amd64 8.6.13-2 [781 kB] Get: 323 http://deb.debian.org/debian bookworm/main amd64 x11-xkb-utils amd64 7.7+7 [165 kB] Get: 324 http://deb.debian.org/debian bookworm/main amd64 xauth amd64 1:1.1.2-1 [36.0 kB] Get: 325 http://deb.debian.org/debian bookworm/main amd64 xfonts-base all 1:1.0.5+nmu1 [5895 kB] Get: 326 http://deb.debian.org/debian bookworm/main amd64 xkb-data all 2.35.1-1 [764 kB] Get: 327 http://deb.debian.org/debian bookworm/main amd64 xserver-common all 2:21.1.7-3+deb12u2 [2382 kB] Get: 328 http://deb.debian.org/debian bookworm/main amd64 xvfb amd64 2:21.1.7-3+deb12u2 [3151 kB] Fetched 1012 MB in 19s (53.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 18148 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 18464 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 18898 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package tzdata. Preparing to unpack .../001-tzdata_2023c-5+deb12u1_all.deb ... 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Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up xkb-data (2.35.1-1) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libzzip-0-13:amd64 (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.44-3) ... Setting up libffi-dev:amd64 (3.4.4-1) ... Setting up libunwind8:amd64 (1.6.2-3) ... Setting up libpthread-stubs0-dev:amd64 (0.4-1) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libpcre2-16-0:amd64 (10.42-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 26 13:31:35 UTC 2024. Universal Time is now: Fri Jan 26 13:31:35 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.8-1) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up xtrans-dev (1.4.0-1) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up libgraphite2-dev:amd64 (1.3.14-1) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libpcre2-32-0:amd64 (10.42-1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libglib2.0-data (2.74.6-2) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2) ... Setting up libnspr4:amd64 (2:4.35-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libteckit0:amd64 (2.5.11+ds1-1+b1) ... Setting up bash-completion (1:2.11-6) ... Setting up uuid-dev:amd64 (2.38.1-5+b1) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up libdbus-1-3:amd64 (1.14.10-1~deb12u1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2022.20220321.62855-5.1+deb12u1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libpcre32-3:amd64 (2:8.39-15) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up icu-devtools (72.1-3) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsepol-dev:amd64 (3.4-2.1) ... Setting up libpcsclite1:amd64 (1.9.9-2) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up liblerc-dev:amd64 (4.0.0+ds-2) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up libkpathsea6:amd64 (2022.20220321.62855-5.1+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up libgif7:amd64 (5.2.1-2.5) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libpcre2-posix3:amd64 (10.42-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up at-spi2-common (2.46.0-5) ... Setting up libmime-charset-perl (1.013.1-2) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libasound2:amd64 (1.2.8-1+b1) ... Setting up bison (2:3.8.2+dfsg-1+b1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up fonts-lmodern (2.005-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libthai-data (0.1.29-1) ... Setting up libgirepository-1.0-1:amd64 (1.74.0-3) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up libgtk2.0-common (2.24.33-2) ... Setting up libatk1.0-0:amd64 (2.46.0-5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtext-unidecode-perl (1.30-3) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libtiffxx6:amd64 (4.5.0-6+deb12u1) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:amd64 (72.1-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libbrotli-dev:amd64 (1.0.9-2+b6) ... Setting up libblas-dev:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsynctex2:amd64 (2022.20220321.62855-5.1+deb12u1) ... Setting up libbz2-dev:amd64 (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2022.1-1) ... Setting up libpcrecpp0v5:amd64 (2:8.39-15) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libblkid-dev:amd64 (2.38.1-5+b1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up tcl8.6 (8.6.13+dfsg-2) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libncurses-dev:amd64 (6.4-4) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libxau-dev:amd64 (1:1.0.9-1) ... Setting up libpcre2-dev:amd64 (10.42-1) ... Setting up libice-dev:amd64 (2:1.0.10-1) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libselinux1-dev:amd64 (3.4-1+b6) ... Setting up libpcre3-dev:amd64 (2:8.39-15) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libfribidi-dev:amd64 (1.0.8-2.1) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up tcl8.6-dev:amd64 (8.6.13+dfsg-2) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libpng-dev:amd64 (1.6.39-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libjpeg-dev:amd64 (1:2.1.5-2) ... Setting up libjbig-dev:amd64 (2.1-6.1) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libglib2.0-bin (2.74.6-2) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libgfortran-12-dev:amd64 (12.2.0-14) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libreadline-dev:amd64 (8.2-1.3) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up pkgconf:amd64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libwebp-dev:amd64 (1.2.4-0.2+deb12u1) ... Setting up libptexenc1:amd64 (2022.20220321.62855-5.1+deb12u1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libtiff-dev:amd64 (4.5.0-6+deb12u1) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up x11proto-core-dev (2022.1-1) ... Setting up shared-mime-info (2.2-1) ... Setting up liblapack-dev:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up pkg-config:amd64 (1.8.1-1) ... Setting up ucf (3.0043+nmu1) ... Setting up gir1.2-glib-2.0:amd64 (1.74.0-3) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libdatrie-dev:amd64 (0.2.13-2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libncurses5-dev:amd64 (6.4-4) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u4) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libxkbfile1:amd64 (1:1.1.0-1) ... Setting up ca-certificates-java (20230710~deb12u1) ... No JRE found. Skipping Java certificates setup. Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libxfont2:amd64 (1:2.0.6-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libmount-dev:amd64 (2.38.1-5+b1) ... Setting up libxmuu1:amd64 (2:1.1.3-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.38-2~deb12u1) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2+deb12u2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up gir1.2-freedesktop:amd64 (1.74.0-3) ... Setting up libharfbuzz-icu0:amd64 (6.0.0+dfsg-3) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libxpm4:amd64 (1:3.5.12-1.1+deb12u1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libsombok3:amd64 (2.4.0-2+b1) ... Setting up libsm-dev:amd64 (2:1.2.3-1) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libx11-dev:amd64 (2:1.8.4-2+deb12u2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libtiff5-dev:amd64 (4.5.0-6+deb12u1) ... Setting up libharfbuzz-gobject0:amd64 (6.0.0+dfsg-3) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... 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:amd64 (6.0.0+dfsg-3) ... Setting up gfortran (4:12.2.0-3) ... 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 libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libfreetype-dev:amd64 (2.12.1+dfsg-5) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxcb-shm0-dev:amd64 (1.15-1) ... Setting up xfonts-base (1:1.0.5+nmu1) ... Setting up adwaita-icon-theme (43-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libcurl4-openssl-dev:amd64 (7.88.1-10+deb12u4) ... Setting up libunicode-linebreak-perl (0.0.20190101-1+b5) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up libxcb-render0-dev:amd64 (1.15-1) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b1) ... Setting up libthai-dev:amd64 (0.1.29-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... 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:amd64 (2.4.2-3+deb12u5) ... Setting up xauth (1:1.1.2-1) ... Setting up lmodern (2.005-1) ... Setting up libharfbuzz-subset0:amd64 (6.0.0+dfsg-3) ... Setting up libcairo-gobject2:amd64 (1.16.0-7) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up libcairo-script-interpreter2:amd64 (1.16.0-7) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libxmu6:amd64 (2:1.1.3-3) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libpangoxft-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libfontconfig-dev:amd64 (2.14.1-4) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up preview-latex-style (12.2-1) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up pango1.0-tools (1.50.12+ds-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libxaw7:amd64 (2:1.0.14-1) ... Setting up libxss-dev:amd64 (1:1.2.3-1) ... Setting up gir1.2-pango-1.0:amd64 (1.50.12+ds-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libxt-dev:amd64 (1:1.2.1-1.1) ... Setting up texinfo (6.8-6+b1) ... Running mktexlsr. This may take some time. ... done. Setting up openjdk-17-jre-headless:amd64 (17.0.9+9-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up texlive-binaries (2022.20220321.62855-5.1+deb12u1) ... 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 python3-lib2to3 (3.11.2-3) ... Setting up texlive-base (2022.20230122-3) ... 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/tex-ini-files/pdftexconfig.tex Setting up libxft-dev:amd64 (2.3.6-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up tk8.6 (8.6.13-2) ... Setting up libglib2.0-dev-bin (2.74.6-2) ... Setting up libfontconfig1-dev:amd64 (2.14.1-4) ... Setting up texlive-luatex (2022.20230122-3) ... Setting up x11-xkb-utils (7.7+7) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up texlive-plain-generic (2022.20230122-4) ... Setting up libglib2.0-dev:amd64 (2.74.6-2) ... Setting up texlive-latex-base (2022.20230122-3) ... Setting up texlive-extra-utils (2022.20230122-4) ... Setting up texlive-fonts-extra (2022.20230122-4) ... Setting up texlive-latex-recommended (2022.20230122-3) ... Setting up texlive-pictures (2022.20230122-3) ... Setting up tk8.6-dev:amd64 (8.6.13-2) ... Setting up texlive-fonts-recommended (2022.20230122-3) ... Setting up libcairo2-dev:amd64 (1.16.0-7) ... Setting up xserver-common (2:21.1.7-3+deb12u2) ... Setting up libharfbuzz-dev:amd64 (6.0.0+dfsg-3) ... Setting up xvfb (2:21.1.7-3+deb12u2) ... Setting up texlive-latex-extra (2022.20230122-4) ... Setting up libpango1.0-dev:amd64 (1.50.12+ds-1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for ca-certificates-java (20230710~deb12u1) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_FÅ‘tanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-17-jdk-headless:amd64 (17.0.9+9-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre:amd64 (17.0.9+9-1~deb12u1) ... Setting up default-jre (2:1.17-74) ... Setting up openjdk-17-jdk:amd64 (17.0.9+9-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.17-74) ... Setting up default-jdk (2:1.17-74) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... 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. Processing triggers for ca-certificates-java (20230710~deb12u1) ... 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 (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/r-base-4.2.2.20221110/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../r-base_4.2.2.20221110-2_source.changes dpkg-buildpackage: info: source package r-base dpkg-buildpackage: info: source version 4.2.2.20221110-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dirk Eddelbuettel dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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 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 \ CXX=g++ \ F77=gfortran \ FC=gfortran \ CFLAGS="`DEB_BUILD_MAINT_OPTIONS=optimize=-lto dpkg-buildflags --get CFLAGS` -Wdate-time -D_FORTIFY_SOURCE=2" \ CXXFLAGS="`DEB_BUILD_MAINT_OPTIONS=optimize=-lto dpkg-buildflags --get CFLAGS` -Wdate-time -D_FORTIFY_SOURCE=2" \ FFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong" \ FCFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -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 \ --mandir=/usr/share/man \ --infodir=/usr/share/info \ --datadir=/usr/share/R/share \ --includedir=/usr/share/R/include \ --with-blas \ --with-lapack \ --enable-long-double \ --enable-R-profiling \ --enable-R-shlib \ --enable-memory-profiling \ --without-recommended-packages \ --build x86_64-linux-gnu checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking 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 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether gcc needs -traditional... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking for sys/time.h... yes checking for sys/param.h... yes checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking how to run the C preprocessor... gcc -E looking for a modern Fortran compiler checking whether the compiler supports GNU Fortran... yes checking whether gfortran accepts -g... yes checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 can compile C++ code... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc accepts -fvisibility... yes checking whether g++ accepts -fvisibility... yes checking whether gfortran accepts -fvisibility... yes checking for gcc... gcc checking whether the compiler supports GNU Objective C... no checking whether gcc accepts -g... no checking whether g++ can compile ObjC++... no checking whether can compile ObjC++... no checking for Objective C++ compiler... 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... /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 x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-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 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 supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking for readline/history.h... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking for tilde_expand_word... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking for fcntl.h... yes checking for glob.h... yes checking for grp.h... yes checking for pwd.h... yes checking for sched.h... yes checking for strings.h... (cached) yes checking for sys/resource.h... yes checking for sys/select.h... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking for sys/time.h... (cached) yes checking for sys/times.h... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking for utime.h... yes checking for arpa/inet.h... yes checking for elf.h... yes checking for features.h... yes checking for floatingpoint.h... no checking for langinfo.h... yes checking for netdb.h... yes checking for netinet/in.h... yes checking for sys/param.h... (cached) yes checking for stdalign.h... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking for limits.h... yes checking for locale.h... yes checking for stdarg.h... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking for gcc options needed to detect all undeclared functions... none needed checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of double... 8 checking size of size_t... 8 checking for C stack direction... down checking size of long double... 16 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether gcc supports -c -o FILE.lo... yes checking for gcc option to support OpenMP... -fopenmp checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gcc... -v checking for C libraries of gcc... -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking whether gfortran appends underscores to external names... yes checking whether gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether gfortran and gcc agree on int and double... yes checking whether gfortran and gcc agree on double complex... yes checking for gfortran option to support OpenMP... -fopenmp checking whether g++ accepts -M for generating dependencies... yes checking whether we can compute ObjC Make dependencies... no checking if need -fno-optimize-sibling-calls for gfortran... yes checking for type of 'hidden' Fortran character lengths... size_t checking for xmkmf... no checking whether g++ supports C++11 features with -std=gnu++11... yes checking whether g++ supports C++14 features with -std=gnu++14... yes checking whether g++ supports C++17 features with 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checking for isblank... yes checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for __tanpi... no checking for fseeko... yes checking for ftello... yes checking for matherr... no checking whether fcntl exists and is declared... yes checking whether getgrgid exists and is declared... yes checking whether getpwnam exists and is declared... yes checking whether getpwuid exists and is declared... yes checking whether kill exists and is declared... yes checking whether sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether getline exists and is declared... yes checking whether select exists and is declared... yes checking whether setenv exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether setrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether getpriority exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking for thread.h... no checking whether thr_stksegment exists and is declared... no checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for mkdtemp... yes checking for strdup... yes checking for strncasecmp... yes checking whether mkdtemp is declared... yes checking whether strdup is declared... yes checking whether strncasecmp is declared... yes checking for library containing connect... none required checking for library containing gethostbyname... none required checking for library containing xdr_string... -ltirpc checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking whether mktime sets errno... no checking whether mktime works correctly after 2037... checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes configure: searching for an external BLAS configure: searching for BLAS in default libraries checking for dgemm_... no configure: searching for OpenBLAS checking for sgemm_ in -lopenblas... no configure: searching for BLIS checking for sgemm_ in -lblis... no configure: searching for ATLAS checking for ATL_xerbla in -latlas... no configure: searching for PhiPACK checking for dgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no configure: searching for IBM ESSL checking for dgemm_ in -lblas... (cached) yes checking for dgemm_ in -lessl... no configure: searching for generic BLAS library checking for dgemm_ in -lblas... (cached) yes checking whether double complex BLAS can be used... yes checking whether the BLAS is complete... yes checking for dpstrf_... no checking for dpstrf_ in -llapack... yes checking for iconv.h... yes checking for iconv... yes checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes checking whether iconv accepts "CP1252"... yes checking for iconvlist... no checking for iconv... yes checking for iconv declaration... extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for wchar.h... (cached) yes checking for wctype.h... yes checking whether mbrtowc exists and is declared... yes checking whether wcrtomb exists and is declared... yes checking whether wcscoll exists and is declared... yes checking whether wcsftime exists and is declared... yes checking whether wcstod exists and is declared... yes checking whether mbstowcs exists and is declared... yes checking whether wcstombs exists and is declared... yes checking whether wctrans exists and is declared... yes checking whether wctype exists and is declared... yes checking whether iswctype exists and is declared... yes checking whether wcwidth exists and is declared... yes checking whether wcswidth exists and is declared... yes checking for wctrans_t... yes checking for mbstate_t... yes checking for ICU... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for X11/Intrinsic.h... yes checking for XtToolkitInitialize in -lXt... yes using X11 ... yes checking for KeySym... yes checking for X11/Xmu/Atoms.h... no checking whether pkg-config knows about cairo and pango... yes checking whether cairo including pango is >= 1.2 and works... yes checking for tclConfig.sh... no checking for tclConfig.sh in library (sub)directories... /usr/lib/tcl8.6/tclConfig.sh checking for tkConfig.sh... no checking for tkConfig.sh in library (sub)directories... /usr/lib/tk8.6/tkConfig.sh checking for tcl.h... yes checking for tk.h... yes checking whether compiling/linking Tcl/Tk code works... yes checking for BSD networking... yes checking for rpc/types.h... no checking for tirpc/rpc/types.h... yes checking for tirpc/rpc/xdr.h... yes checking for XDR support... yes checking for inflateInit2_ in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.2.5... yes checking whether zlib support suffices... yes checking for BZ2_bzlibVersion in -lbz2... yes checking for bzlib.h... yes checking if bzip2 version >= 1.0.6... yes checking whether bzip2 support suffices... yes checking for lzma_version_number in -llzma... yes checking for lzma.h... yes checking if lzma version >= 5.0.3... yes checking for pcre2.h... yes checking for pcre2_compile_8 in -lpcre2-8... yes checking if PCRE2 has Unicode support... yes checking whether PCRE support suffices... yes checking for curl-config... /usr/bin/curl-config checking libcurl version ... 7.88.1 checking for curl/curl.h... yes checking if libcurl is version 7 and >= 7.28.0... yes checking if libcurl supports https... yes checking if pkg-config knows about libjpeg... yes checking if jpeglib version >= 6b... yes checking for jpeg_destroy_compress in -ljpeg... yes checking if pkg-config knows about libpng... yes checking if libpng version >= 1.2.7... yes checking for png_create_write_struct in -lpng... yes checking if pkg-config knows about libtiff... yes checking for tiffio.h... yes checking for TIFFOpen in -ltiff... yes checking whether leap seconds are treated according to POSIX... yes checking for inline... inline checking for struct stat.st_atim.tv_nsec... yes checking whether struct stat.st_atim is of type struct timespec... yes checking for setitimer... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking whether KERN_USRSTACK sysctl is supported... no checking for visible __lib_stack_end... yes checking for paperconf... /usr/bin/paperconf checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking for gfortran option to support OpenMP... (cached) -fopenmp checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a race-free mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for ranlib... (cached) ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... no checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking for ld used by gcc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.8.2, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking 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/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 R is now configured for x86_64-pc-linux-gnu Source directory: . Installation directory: /usr C compiler: gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 Fortran fixed-form compiler: gfortran -fno-optimize-sibling-calls -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong Default C++ compiler: g++ -std=gnu++14 -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 C++11 compiler: g++ -std=gnu++11 -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 C++14 compiler: g++ -std=gnu++14 -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 C++17 compiler: g++ -std=gnu++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 C++20 compiler: g++ -std=gnu++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 Fortran free-form compiler: gfortran -fno-optimize-sibling-calls -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong Obj-C compiler: Interfaces supported: X11, tcltk External libraries: pcre2, 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="`DEB_BUILD_MAINT_OPTIONS=optimize=-lto dpkg-buildflags --get CFLAGS` -Wdate-time -D_FORTIFY_SOURCE=2" \ CXXFLAGS="`DEB_BUILD_MAINT_OPTIONS=optimize=-lto dpkg-buildflags --get CFLAGS` -Wdate-time -D_FORTIFY_SOURCE=2" \ FFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong" \ FCFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong" \ CC=gcc \ CXX=g++ \ F77=gfortran \ LDFLAGS="-Wl,-z,relro" \ PKG_BUILT_STAMP="""" \ R_GZIPCMD="/bin/gzip -n" \ R make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' creating src/scripts/R.fe make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' mkdir -p -- ../../bin make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' mkdir -p -- ../../include make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c regerror.c -o regerror.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c regexec.c -o regexec.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c tre-stack.c -o tre-stack.o gcc -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/src/appl' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c integrate.c -o integrate.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c interv.c -o interv.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c maxcol.c -o maxcol.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c optim.c -o optim.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pretty.c -o pretty.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c uncmin.c -o uncmin.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dchdc.f -o dchdc.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dpbfa.f -o dpbfa.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dpbsl.f -o dpbsl.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dpoco.f -o dpoco.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dpodi.f -o dpodi.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dpofa.f -o dpofa.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dposl.f -o dposl.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dqrdc.f -o dqrdc.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dqrls.f -o dqrls.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dqrsl.f -o dqrsl.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dqrutl.f -o dqrutl.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dsvdc.f -o dsvdc.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c dtrco.f -o dtrco.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -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/reproducible-path/r-base-4.2.2.20221110/src/appl' #@/usr/bin/make install-Linpack make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 qnbinom_mu.d from qnbinom_mu.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/reproducible-path/r-base-4.2.2.20221110/src/nmath' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mlutils.c -o mlutils.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c d1mach.c -o d1mach.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c i1mach.c -o i1mach.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fmax2.c -o fmax2.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fmin2.c -o fmin2.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fprec.c -o fprec.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fround.c -o fround.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ftrunc.c -o ftrunc.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sign.c -o sign.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fsign.c -o fsign.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c imax2.c -o imax2.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c imin2.c -o imin2.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c chebyshev.c -o chebyshev.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c log1p.c -o log1p.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lgammacor.c -o lgammacor.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gammalims.c -o gammalims.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c stirlerr.c -o stirlerr.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bd0.c -o bd0.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gamma.c -o gamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lgamma.c -o lgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gamma_cody.c -o gamma_cody.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c beta.c -o beta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lbeta.c -o lbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c polygamma.c -o polygamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cospi.c -o cospi.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bessel_i.c -o bessel_i.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bessel_j.c -o bessel_j.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bessel_k.c -o bessel_k.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bessel_y.c -o bessel_y.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c choose.c -o choose.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c snorm.c -o snorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sexp.c -o sexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dgamma.c -o dgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pgamma.c -o pgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qgamma.c -o qgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgamma.c -o rgamma.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dbeta.c -o dbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pbeta.c -o pbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qbeta.c -o qbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rbeta.c -o rbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dunif.c -o dunif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c punif.c -o punif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qunif.c -o qunif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c runif.c -o runif.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dnorm.c -o dnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pnorm.c -o pnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qnorm.c -o qnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rnorm.c -o rnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dlnorm.c -o dlnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plnorm.c -o plnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qlnorm.c -o qlnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rlnorm.c -o rlnorm.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c df.c -o df.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pf.c -o pf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qf.c -o qf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rf.c -o rf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dnf.c -o dnf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dt.c -o dt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pt.c -o pt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qt.c -o qt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rt.c -o rt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dnt.c -o dnt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dchisq.c -o dchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pchisq.c -o pchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qchisq.c -o qchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rchisq.c -o rchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rnchisq.c -o rnchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dbinom.c -o dbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pbinom.c -o pbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qbinom.c -o qbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rbinom.c -o rbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rmultinom.c -o rmultinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dcauchy.c -o dcauchy.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pcauchy.c -o pcauchy.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qcauchy.c -o qcauchy.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rcauchy.c -o rcauchy.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dexp.c -o dexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pexp.c -o pexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qexp.c -o qexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rexp.c -o rexp.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dgeom.c -o dgeom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pgeom.c -o pgeom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qgeom.c -o qgeom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeom.c -o rgeom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dhyper.c -o dhyper.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c phyper.c -o phyper.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qhyper.c -o qhyper.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rhyper.c -o rhyper.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dnbinom.c -o dnbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pnbinom.c -o pnbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qnbinom.c -o qnbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qnbinom_mu.c -o qnbinom_mu.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rnbinom.c -o rnbinom.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dpois.c -o dpois.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ppois.c -o ppois.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qpois.c -o qpois.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rpois.c -o rpois.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dweibull.c -o dweibull.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pweibull.c -o pweibull.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qweibull.c -o qweibull.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rweibull.c -o rweibull.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dlogis.c -o dlogis.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plogis.c -o plogis.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qlogis.c -o qlogis.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rlogis.c -o rlogis.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dnchisq.c -o dnchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pnchisq.c -o pnchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qnchisq.c -o qnchisq.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dnbeta.c -o dnbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pnbeta.c -o pnbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qnbeta.c -o qnbeta.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pnf.c -o pnf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pnt.c -o pnt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qnf.c -o qnf.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qnt.c -o qnt.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ptukey.c -o ptukey.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qtukey.c -o qtukey.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c toms708.c -o toms708.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c wilcox.c -o wilcox.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 qnbinom_mu.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/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rembedded.c -o Rembedded.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dynload.c -o dynload.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c system.c -o system.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sys-unix.c -o sys-unix.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sys-std.c -o sys-std.o gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DR_HOME='"/build/reproducible-path/r-base-4.2.2.20221110"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 altclasses.d from altclasses.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 clippath.d from clippath.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 mask.d from mask.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 patterns.d from patterns.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/reproducible-path/r-base-4.2.2.20221110/src/main' gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c CommandLineArgs.c -o CommandLineArgs.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rdynload.c -o Rdynload.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Renviron.c -o Renviron.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RNG.c -o RNG.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agrep.c -o agrep.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c altclasses.c -o altclasses.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep.c -o altrep.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c apply.c -o apply.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c arithmetic.c -o arithmetic.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c array.c -o array.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c attrib.c -o attrib.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bind.c -o bind.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c builtin.c -o builtin.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c character.c -o character.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c clippath.c -o clippath.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c coerce.c -o coerce.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c colors.c -o colors.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c complex.c -o complex.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c connections.c -o connections.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c context.c -o context.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cum.c -o cum.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dcf.c -o dcf.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c datetime.c -o datetime.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c debug.c -o debug.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c deparse.c -o deparse.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c devices.c -o devices.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dotcode.c -o dotcode.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dounzip.c -o dounzip.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dstruct.c -o dstruct.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c duplicate.c -o duplicate.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c edit.c -o edit.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c engine.c -o engine.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c envir.c -o envir.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c errors.c -o errors.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c eval.c -o eval.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c format.c -o format.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gevents.c -o gevents.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gram.c -o gram.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gram-ex.c -o gram-ex.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c graphics.c -o graphics.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c grep.c -o grep.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c identical.c -o identical.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c inlined.c -o inlined.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c inspect.c -o inspect.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c internet.c -o internet.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c iosupport.c -o iosupport.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lapack.c -o lapack.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c list.c -o list.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c localecharset.c -o localecharset.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c logic.c -o logic.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c main.c -o main.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mapply.c -o mapply.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mask.c -o mask.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match.c -o match.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c memory.c -o memory.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c names.c -o names.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c objects.c -o objects.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c options.c -o options.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c paste.c -o paste.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c patterns.c -o patterns.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c platform.c -o platform.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plot.c -o plot.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plot3d.c -o plot3d.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plotmath.c -o plotmath.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c print.c -o print.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printarray.c -o printarray.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printvector.c -o printvector.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printutils.c -o printutils.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qsort.c -o qsort.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c radixsort.c -o radixsort.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c random.c -o random.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c raw.c -o raw.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c registration.c -o registration.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c relop.c -o relop.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rlocale.c -o rlocale.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c saveload.c -o saveload.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c scan.c -o scan.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c seq.c -o seq.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c serialize.c -o serialize.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sort.c -o sort.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c source.c -o source.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c split.c -o split.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sprintf.c -o sprintf.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c startup.c -o startup.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c subassign.c -o subassign.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c subscript.c -o subscript.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c subset.c -o subset.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c summary.c -o summary.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sysutils.c -o sysutils.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c times.c -o times.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c unique.c -o unique.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c util.c -o util.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c g_alab_her.c -o g_alab_her.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c g_cntrlify.c -o g_cntrlify.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c g_fontdb.c -o g_fontdb.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c g_her_glyph.c -o g_her_glyph.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c xxxpr.f -o xxxpr.o gcc -shared -fopenmp -Wl,-z,relro -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o clippath.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 mask.o match.o memory.o names.o objects.o options.o paste.o patterns.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 -lquadmath -lreadline -lpcre2-8 -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/bin/exec mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/lib make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rmain.c -o Rmain.o gcc -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,-z,relro -o R.bin Rmain.o -lR make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 sock.d from sock.c making sockconn.d from sockconn.c make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c internet.c -o internet.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c libcurl.c -o libcurl.o libcurl.c: In function 'in_do_curlDownload': libcurl.c:637:13: warning: 'CURLOPT_PROGRESSFUNCTION' is deprecated: since 7.32.0. Use CURLOPT_XFERINFOFUNCTION [-Wdeprecated-declarations] 637 | curl_easy_setopt(hnd[i], CURLOPT_PROGRESSFUNCTION, progress); | ^~~~~~~~~~~~~~~~ In file included from libcurl.c:38: /usr/include/x86_64-linux-gnu/curl/curl.h:1295:3: note: declared here 1295 | CURLOPTDEPRECATED(CURLOPT_PROGRESSFUNCTION, CURLOPTTYPE_FUNCTIONPOINT, 56, | ^~~~~~~~~~~~~~~~~ libcurl.c:693:9: warning: 'CURLINFO_SIZE_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_SIZE_DOWNLOAD_T [-Wdeprecated-declarations] 693 | curl_easy_getinfo(hnd[0], CURLINFO_SIZE_DOWNLOAD, &dl); | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/curl/curl.h:2841:3: note: declared here 2841 | CURLINFO_SIZE_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~ libcurl.c:702:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 702 | curl_easy_getinfo(hnd[0], CURLINFO_CONTENT_LENGTH_DOWNLOAD, &cl); | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/curl/curl.h:2858:3: note: declared here 2858 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libcurl.c:714:13: warning: 'CURLINFO_SIZE_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_SIZE_DOWNLOAD_T [-Wdeprecated-declarations] 714 | curl_easy_getinfo(hnd[i], CURLINFO_SIZE_DOWNLOAD, &dl); | ^~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/curl/curl.h:2841:3: note: declared here 2841 | CURLINFO_SIZE_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c sock.c -o sock.o gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -shared -L"../../../lib" -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o sock.o sockconn.o -lcurl -lR make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/modules make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' making Lapack.d from Lapack.c make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' gcc -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lapack.c -o Lapack.o gcc -shared -L"../../../lib" -Wl,-z,relro -o lapack.so Lapack.o -lR -llapack -lblas -lgfortran -lm -lquadmath make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' gcc -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c devX11.c -o devX11.o gcc -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rotated.c -o rotated.o gcc -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rbitmap.c -o rbitmap.o gcc -shared -L"../../../lib" -Wl,-z,relro -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm gcc -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dataentry.c -o dataentry.o gcc -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 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' mkdir -p -- ../../library make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/profile' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' building package 'base' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' mkdir -p -- ../../../library/base/demo make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' mkdir -p -- ../../../library/tools/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 making pdscan.d from pdscan.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c text.c -o text.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rmd5.c -o Rmd5.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c md5.c -o md5.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c signals.c -o signals.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c install.c -o install.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getfmts.c -o getfmts.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c http.c -o http.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gramLatex.c -o gramLatex.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gramRd.c -o gramRd.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pdscan.c -o pdscan.o gcc -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 pdscan.o -L../../../../lib -lR make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' byte-compiling package 'compiler' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' byte-compiling package 'base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' byte-compiling package 'tools' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 making hashtab.d from hashtab.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c -o io.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c size.c -o size.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sock.c -o sock.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c stubs.c -o stubs.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hashtab.c -o hashtab.o gcc -shared -L../../../../lib -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o hashtab.o -L../../../../lib -lR make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' byte-compiling package 'utils' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 clippath.d from clippath.c making patterns.d from patterns.c making mask.d from mask.c making group.d from group.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 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c axis_scales.c -o axis_scales.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c chull.c -o chull.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c devices.c -o devices.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c stubs.c -o stubs.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c colors.c -o colors.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c clippath.c -o clippath.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c patterns.c -o patterns.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mask.c -o mask.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c group.c -o group.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c devCairo.c -o devCairo.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c devPicTeX.c -o devPicTeX.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c devPS.c -o devPS.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c devQuartz.c -o devQuartz.o gcc -shared -L../../../../lib -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o clippath.o patterns.o mask.o group.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[8]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[9]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -pthread -I../../../../../src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cairoBM.c -o cairoBM.o gcc -shared -L"../../../../../lib" -Wl,-z,relro -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm make[10]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' byte-compiling package 'grDevices' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c base.c -o base.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c graphics.c -o graphics.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c par.c -o par.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plot.c -o plot.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plot3d.c -o plot3d.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c stem.c -o stem.o gcc -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/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' byte-compiling package 'graphics' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' mkdir -p -- ../../../library/stats/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c kmeans.c -o kmeans.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ansari.c -o ansari.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bandwidths.c -o bandwidths.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c chisqsim.c -o chisqsim.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c d2x2xk.c -o d2x2xk.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fexact.c -o fexact.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c kendall.c -o kendall.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ks.c -o ks.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c line.c -o line.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c smooth.c -o smooth.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c prho.c -o prho.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c swilk.c -o swilk.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ksmooth.c -o ksmooth.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c loessc.c -o loessc.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c monoSpl.c -o monoSpl.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c isoreg.c -o isoreg.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Srunmed.c -o Srunmed.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dblcen.c -o dblcen.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c distance.c -o distance.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hclust-utils.c -o hclust-utils.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nls.c -o nls.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rWishart.c -o rWishart.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c HoltWinters.c -o HoltWinters.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c PPsum.c -o PPsum.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c arima.c -o arima.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c burg.c -o burg.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filter.c -o filter.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mAR.c -o mAR.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pacf.c -o pacf.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c starma.c -o starma.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c port.c -o port.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c family.c -o family.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sbart.c -o sbart.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c approx.c -o approx.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c loglin.c -o loglin.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lowess.c -o lowess.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c massdist.c -o massdist.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splines.c -o splines.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lm.c -o lm.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c complete_cases.c -o complete_cases.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cov.c -o cov.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c deriv.c -o deriv.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c -o fft.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fourier.c -o fourier.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c model.c -o model.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c optim.c -o optim.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c optimize.c -o optimize.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c integrate.c -o integrate.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c random.c -o random.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c distn.c -o distn.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c zeroin.c -o zeroin.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rcont.c -o rcont.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c influence.c -o influence.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c bsplvd.f -o bsplvd.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c bvalue.f -o bvalue.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c bvalus.f -o bvalus.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c loessf.f -o loessf.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c ppr.f -o ppr.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c qsbart.f -o qsbart.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c sgram.f -o sgram.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c sinerp.f -o sinerp.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c sslvrg.f -o sslvrg.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c stxwx.f -o stxwx.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c hclust.f -o hclust.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c kmns.f -o kmns.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c eureka.f -o eureka.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c stl.f -o stl.o gfortran -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -c lminfl.f -o lminfl.o gcc -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 -lquadmath -L../../../../lib -lR make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' byte-compiling package 'stats' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' mkdir -p -- ../../../library/methods/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c do_substitute_direct.c -o do_substitute_direct.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c slot.c -o slot.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c class_support.c -o class_support.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tests.c -o tests.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -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/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' byte-compiling package 'methods' initializing class and method definitions ... done make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' mkdir -p -- ../../../library/grid/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' making clippath.d from clippath.c 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 mask.d from mask.c making matrix.d from matrix.c making path.d from path.c making register.d from register.c making state.d from state.c making unit.d from unit.c making util.d from util.c making viewport.d from viewport.c gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c clippath.c -o clippath.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gpar.c -o gpar.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c grid.c -o grid.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c just.c -o just.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c layout.c -o layout.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mask.c -o mask.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c matrix.c -o matrix.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c path.c -o path.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c register.c -o register.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c state.c -o state.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c unit.c -o unit.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c util.c -o util.o gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c viewport.c -o viewport.o gcc -shared -L../../../../lib -Wl,-z,relro -o grid.so clippath.o gpar.o grid.o just.o layout.o mask.o matrix.o path.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' byte-compiling package 'grid' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' mkdir -p -- ../../../library/splines/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' making splines.d from splines.c gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splines.c -o splines.o gcc -shared -L../../../../lib -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' byte-compiling package 'splines' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' byte-compiling package 'stats4' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' making init.d from init.c making tcltk.d from tcltk.c making tcltk_unix.d from tcltk_unix.c gcc -I"../../../../include" -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/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -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/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tcltk.c -o tcltk.o gcc -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/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tcltk_unix.c -o tcltk_unix.o gcc -shared -L../../../../lib -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -L/usr/lib/x86_64-linux-gnu -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' byte-compiling package 'tcltk' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' making init.d from init.c making rngstream.d from rngstream.c making fork.d from fork.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rngstream.c -o rngstream.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fork.c -o fork.o gcc -shared -L../../../../lib -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' byte-compiling package 'parallel' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' you should 'make docs' now ... make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' (cd src/nmath/standalone; \ /usr/bin/make CFLAGS="`DEB_BUILD_MAINT_OPTIONS=optimize=-lto dpkg-buildflags --get CFLAGS` -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT" \ CXXFLAGS="`DEB_BUILD_MAINT_OPTIONS=optimize=-lto dpkg-buildflags --get CFLAGS` -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT" \ FFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -D_REENTRANT" \ CC=gcc \ CXX=g++ \ F77=gfortran \ R_GZIPCMD="/bin/gzip -n" \ libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.1 \ shared static ) make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' (cd ../../include; /usr/bin/make Rmath.h) make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' Copying source files make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 qnbinom_mu.d from qnbinom_mu.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/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c mlutils.c -o mlutils.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c d1mach.c -o d1mach.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c i1mach.c -o i1mach.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fmax2.c -o fmax2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fmin2.c -o fmin2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fprec.c -o fprec.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fround.c -o fround.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c ftrunc.c -o ftrunc.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c sign.c -o sign.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fsign.c -o fsign.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c imax2.c -o imax2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c imin2.c -o imin2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c chebyshev.c -o chebyshev.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c log1p.c -o log1p.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c lgammacor.c -o lgammacor.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c gammalims.c -o gammalims.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c stirlerr.c -o stirlerr.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bd0.c -o bd0.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c gamma.c -o gamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c lgamma.c -o lgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c gamma_cody.c -o gamma_cody.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c beta.c -o beta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c lbeta.c -o lbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c polygamma.c -o polygamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c cospi.c -o cospi.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bessel_i.c -o bessel_i.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bessel_j.c -o bessel_j.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bessel_k.c -o bessel_k.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bessel_y.c -o bessel_y.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c choose.c -o choose.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c snorm.c -o snorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c sexp.c -o sexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dgamma.c -o dgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pgamma.c -o pgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qgamma.c -o qgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rgamma.c -o rgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dbeta.c -o dbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pbeta.c -o pbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qbeta.c -o qbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rbeta.c -o rbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dunif.c -o dunif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c punif.c -o punif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qunif.c -o qunif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c runif.c -o runif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnorm.c -o dnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnorm.c -o pnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnorm.c -o qnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rnorm.c -o rnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dlnorm.c -o dlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c plnorm.c -o plnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qlnorm.c -o qlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rlnorm.c -o rlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c df.c -o df.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pf.c -o pf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qf.c -o qf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rf.c -o rf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnf.c -o dnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dt.c -o dt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pt.c -o pt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qt.c -o qt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rt.c -o rt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnt.c -o dnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dchisq.c -o dchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pchisq.c -o pchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qchisq.c -o qchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rchisq.c -o rchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rnchisq.c -o rnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dbinom.c -o dbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pbinom.c -o pbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qbinom.c -o qbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rbinom.c -o rbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rmultinom.c -o rmultinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dcauchy.c -o dcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pcauchy.c -o pcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qcauchy.c -o qcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rcauchy.c -o rcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dexp.c -o dexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pexp.c -o pexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qexp.c -o qexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rexp.c -o rexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dgeom.c -o dgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pgeom.c -o pgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qgeom.c -o qgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rgeom.c -o rgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dhyper.c -o dhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c phyper.c -o phyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qhyper.c -o qhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rhyper.c -o rhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnbinom.c -o dnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnbinom.c -o pnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnbinom.c -o qnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnbinom_mu.c -o qnbinom_mu.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rnbinom.c -o rnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dpois.c -o dpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c ppois.c -o ppois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qpois.c -o qpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rpois.c -o rpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dweibull.c -o dweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pweibull.c -o pweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qweibull.c -o qweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rweibull.c -o rweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dlogis.c -o dlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c plogis.c -o plogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qlogis.c -o qlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rlogis.c -o rlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnchisq.c -o dnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnchisq.c -o pnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnchisq.c -o qnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnbeta.c -o dnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnbeta.c -o pnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnbeta.c -o qnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnf.c -o pnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnt.c -o pnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnf.c -o qnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnt.c -o qnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c ptukey.c -o ptukey.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qtukey.c -o qtukey.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c toms708.c -o toms708.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c wilcox.c -o wilcox.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c signrank.c -o signrank.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c std_unif.c -o std_unif.lo gcc -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 qnbinom_mu.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/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c mlutils.c -o mlutils.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c d1mach.c -o d1mach.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c i1mach.c -o i1mach.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fmax2.c -o fmax2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fmin2.c -o fmin2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fprec.c -o fprec.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fround.c -o fround.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c ftrunc.c -o ftrunc.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c sign.c -o sign.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c fsign.c -o fsign.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c imax2.c -o imax2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c imin2.c -o imin2.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c chebyshev.c -o chebyshev.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c log1p.c -o log1p.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c lgammacor.c -o lgammacor.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c gammalims.c -o gammalims.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c stirlerr.c -o stirlerr.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bd0.c -o bd0.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c gamma.c -o gamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c lgamma.c -o lgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c gamma_cody.c -o gamma_cody.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c beta.c -o beta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c lbeta.c -o lbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c polygamma.c -o polygamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c cospi.c -o cospi.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bessel_i.c -o bessel_i.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bessel_j.c -o bessel_j.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bessel_k.c -o bessel_k.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c bessel_y.c -o bessel_y.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c choose.c -o choose.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c snorm.c -o snorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c sexp.c -o sexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dgamma.c -o dgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pgamma.c -o pgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qgamma.c -o qgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rgamma.c -o rgamma.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dbeta.c -o dbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pbeta.c -o pbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qbeta.c -o qbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rbeta.c -o rbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dunif.c -o dunif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c punif.c -o punif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qunif.c -o qunif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c runif.c -o runif.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnorm.c -o dnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnorm.c -o pnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnorm.c -o qnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rnorm.c -o rnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dlnorm.c -o dlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c plnorm.c -o plnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qlnorm.c -o qlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rlnorm.c -o rlnorm.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c df.c -o df.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pf.c -o pf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qf.c -o qf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rf.c -o rf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnf.c -o dnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dt.c -o dt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pt.c -o pt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qt.c -o qt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rt.c -o rt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnt.c -o dnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dchisq.c -o dchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pchisq.c -o pchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qchisq.c -o qchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rchisq.c -o rchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rnchisq.c -o rnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dbinom.c -o dbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pbinom.c -o pbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qbinom.c -o qbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rbinom.c -o rbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rmultinom.c -o rmultinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dcauchy.c -o dcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pcauchy.c -o pcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qcauchy.c -o qcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rcauchy.c -o rcauchy.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dexp.c -o dexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pexp.c -o pexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qexp.c -o qexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rexp.c -o rexp.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dgeom.c -o dgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pgeom.c -o pgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qgeom.c -o qgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rgeom.c -o rgeom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dhyper.c -o dhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c phyper.c -o phyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qhyper.c -o qhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rhyper.c -o rhyper.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnbinom.c -o dnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnbinom.c -o pnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnbinom.c -o qnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnbinom_mu.c -o qnbinom_mu.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rnbinom.c -o rnbinom.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dpois.c -o dpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c ppois.c -o ppois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qpois.c -o qpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rpois.c -o rpois.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dweibull.c -o dweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pweibull.c -o pweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qweibull.c -o qweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rweibull.c -o rweibull.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dlogis.c -o dlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c plogis.c -o plogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qlogis.c -o qlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c rlogis.c -o rlogis.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnchisq.c -o dnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnchisq.c -o pnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnchisq.c -o qnchisq.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c dnbeta.c -o dnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnbeta.c -o pnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnbeta.c -o qnbeta.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnf.c -o pnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c pnt.c -o pnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnf.c -o qnf.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qnt.c -o qnt.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c ptukey.c -o ptukey.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c qtukey.c -o qtukey.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c toms708.c -o toms708.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c wilcox.c -o wilcox.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -c signrank.c -o signrank.o gcc -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 qnbinom_mu.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/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' R_GZIPCMD="/bin/gzip -n" \ /usr/bin/make docs R_CMD_BUILD_HELP_OPTS="--txt --example" make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' #@/usr/bin/make install-Linpack make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DR_HOME='"/build/reproducible-path/r-base-4.2.2.20221110"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' /build/reproducible-path/r-base-4.2.2.20221110/lib/libR.so is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' /build/reproducible-path/r-base-4.2.2.20221110/bin/exec/R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' /build/reproducible-path/r-base-4.2.2.20221110/modules/R_X11.so is unchanged /build/reproducible-path/r-base-4.2.2.20221110/modules/R_de.so is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/profile' building system startup profile make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/profile' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' building package 'translations' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' building package 'base' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' building package 'tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' building package 'compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' building package 'utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' building package 'graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' building package 'stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' building package 'datasets' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' building package 'methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' building package 'grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' building package 'splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' building package 'stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' building package 'parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' you should 'make docs' now ... make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' creating doc/NEWS creating doc/NEWS.pdf make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/html' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' installing parsed Rd make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' building/updating package metadata ... make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' writing package indices make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' /usr/bin/make javaconf make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' #@/usr/bin/make install-Linpack make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DR_HOME='"/build/reproducible-path/r-base-4.2.2.20221110"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' /build/reproducible-path/r-base-4.2.2.20221110/lib/libR.so is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' /build/reproducible-path/r-base-4.2.2.20221110/bin/exec/R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' /build/reproducible-path/r-base-4.2.2.20221110/modules/R_X11.so is unchanged /build/reproducible-path/r-base-4.2.2.20221110/modules/R_de.so is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/profile' building system startup profile make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/profile' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' building package 'translations' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' building package 'base' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' building package 'tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' building package 'compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' building package 'utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' building package 'graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' building package 'stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' building package 'datasets' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' building package 'methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' building package 'grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' building package 'splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' building package 'stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' building package 'parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' configuring Java ... Java interpreter : /usr/lib/jvm/default-java/bin/java Java version : 17.0.9 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.FqhcVm' gcc -I"/build/reproducible-path/r-base-4.2.2.20221110/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c conftest.c -o conftest.o gcc -shared -L/build/reproducible-path/r-base-4.2.2.20221110/lib -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/build/reproducible-path/r-base-4.2.2.20221110/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.FqhcVm' 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/reproducible-path/r-base-4.2.2.20221110 Done. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' touch make-arch-stamp *** make-indep *** /usr/bin/make -k docs make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' #@/usr/bin/make install-Linpack make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DR_HOME='"/build/reproducible-path/r-base-4.2.2.20221110"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' /build/reproducible-path/r-base-4.2.2.20221110/lib/libR.so is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' /build/reproducible-path/r-base-4.2.2.20221110/bin/exec/R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' /build/reproducible-path/r-base-4.2.2.20221110/modules/R_X11.so is unchanged /build/reproducible-path/r-base-4.2.2.20221110/modules/R_de.so is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/profile' building system startup profile make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/profile' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' building package 'translations' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/translations' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' building package 'base' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' building package 'tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' building package 'compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' building package 'utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' building package 'graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' building package 'stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' building package 'datasets' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' building package 'methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' building package 'grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' building package 'splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' building package 'stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' building package 'parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' installing parsed Rd make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' building/updating package metadata ... make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' writing package indices make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' (cd doc/manual && /usr/bin/make html) make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' /usr/bin/make info make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-exts.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-intro.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-ints.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-lang.texi make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' (cd doc/manual && \ /usr/bin/make refman.pdf R-admin.pdf R-data.pdf R-exts.pdf \ R-FAQ.pdf R-intro.pdf R-ints.pdf R-lang.pdf) make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' creating doc/manual/version.tex collecting LaTeX docs for package 'base' ... Converting parsed Rd's to LaTeX ........................................... collecting LaTeX docs for package 'tools' ... Converting parsed Rd's to LaTeX ...... collecting LaTeX docs for package 'utils' ... Converting parsed Rd's to LaTeX ............... 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 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2022/07/02 v1.4n 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/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty) (/usr/share/texlive/texmf-dist/tex/latex/jknapltx/mathrsfs.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 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/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 394. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 394. ) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) Writing index file refman.idx (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file refman.aux. (/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/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/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}] No file refman.toc. (./base-pkg.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/share/texlive/texmf-dist/tex/latex/jknapltx/ursfs.fd) [1] [2] Underfull \hbox (badness 6252) in paragraph at lines 143--151 []\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 . It Underfull \hbox (badness 10000) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/zi4/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 143--151 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/z i4/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 143--151 []\T1/zi4/m/n/10 double.neg.ulp.digits []\T1/ptm/m/n/10 is bounded be-low by [] \T1/zi4/m/n/10 -(double.digits + 3)[]\T1/ptm/m/n/10 , [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 335--338 []\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] [7] [8] [9] Underfull \hbox (badness 2556) in paragraph at lines 574--580 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/zi4/m/n/10 insertions[]\T1/ptm/m/n/10 ', [10] [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1586--1592 [26] [27] [28] [29] [30] [31] [32] Overfull \hbox (26.27782pt too wide) in paragraph at lines 2064--2064 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] Underfull \hbox (badness 1721) in paragraph at lines 2721--2725 [][][]\T1/zi4/m/n/10 assign[][][] []\T1/ptm/m/n/10 (and its in-verse [][][]\T1/ zi4/m/n/10 get[][][][]\T1/ptm/m/n/10 ), for ``sub-assign-ment'' such as []\T1/z i4/m/n/10 x[i] <- v[]\T1/ptm/m/n/10 , see [][][]\T1/zi4/m/n/10 [<-[][][][]\T1/p tm/m/n/10 ; fur-ther, [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 2521) in paragraph at lines 5197--5199 []\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 [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6388--6388 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] Underfull \hbox (badness 1303) in paragraph at lines 7281--7288 []\T1/zi4/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/zi4/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/zi4/m/n/10 "r" []\T1/ptm/m/n /10 only. This reads the Underfull \hbox (badness 2111) in paragraph at lines 7292--7297 []\T1/ptm/m/n/10 Unix users wish-ing to \T1/ptm/m/it/10 write \T1/ptm/m/n/10 to one of the X11 se-lec-tions may be able to do so via [113] [114] Underfull \vbox (badness 3803) has occurred while \output is active [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] [117] [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 2096) in paragraph at lines 7962--7966 \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 . [124] [125] Underfull \hbox (badness 2351) in paragraph at lines 8076--8079 [][][]\T1/zi4/m/n/10 split[][][] []\T1/ptm/m/n/10 for split-ting a vari-able ac -cord-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 t able[][][][]\T1/ptm/m/n/10 , [126] [127] [128] [129] [130] Underfull \hbox (badness 4479) in paragraph at lines 8393--8404 [][][]\T1/zi4/m/n/10 I[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 plot.data.f rame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 print.data.frame[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 row.names[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 names[][][] []\T1/ptm/m/n/10 (for the col-umn names), [131] [132] [133] [134] [135] [136] [137] Underfull \hbox (badness 1629) in paragraph at lines 8861--8873 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 2875) in paragraph at lines 8861--8873 []\T1/zi4/m/n/10 NA[]\T1/ptm/m/n/10 , and hence []\T1/zi4/m/n/10 as.POSIXct("19 69-12-31 23:59:59", tz = "UTC") []\T1/ptm/m/n/10 will give []\T1/zi4/m/n/10 "19 69-12-31 [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] Underfull \hbox (badness 1178) in paragraph at lines 9629--9633 []\T1/ptm/m/n/10 If true, [][][]\T1/zi4/m/n/10 list[][][][]\T1/ptm/m/n/10 s and atomic vec-tors with non-[][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 names (see [][][]\T1/zi4/m/n/10 names[][][][]\T1/ptm/m/n/10 ) are de- [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 2744) in paragraph at lines 11938--11940 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] Underfull \hbox (badness 2253) in paragraph at lines 14134--14136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [217] Underfull \hbox (badness 1490) in paragraph at lines 14169--14172 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [218] Underfull \hbox (badness 1565) in paragraph at lines 14251--14255 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] []\T1/ptm/m/n/10 to find out about sym- bolic links, [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 file.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.files[][][] []\T1/ptm/m/n/10 , and [219] Underfull \hbox (badness 4927) in paragraph at lines 14302--14304 []\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 []\T1/zi4/m/n/10 fsep = [220] Underfull \hbox (badness 3148) in paragraph at lines 14404--14409 [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.fi les[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 help[][][][]\T1/ptm/m/n/10 ; [ ][][]\T1/zi4/m/n/10 RShowDoc[][][] []\T1/ptm/m/n/10 call []\T1/zi4/m/n/10 file. show() []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 type = "text"[]\T1/ptm/m/n/10 . Co n-sider [221] Underfull \hbox (badness 1466) in paragraph at lines 14451--14454 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [222] [223] Underfull \hbox (badness 10000) in paragraph at lines 14582--14586 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\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 14593--14596 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [224] [225] [226] [227] [228] Underfull \hbox (badness 3965) in paragraph at lines 14890--14894 []\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, [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 4429) in paragraph at lines 15679--15682 []\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 [241] [242] Underfull \hbox (badness 10000) in paragraph at lines 15785--15787 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [243] Underfull \hbox (badness 2035) in paragraph at lines 15858--15862 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 2452) in paragraph at lines 16471--16475 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment 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 16471--16475 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s 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 [254] [255] Underfull \hbox (badness 1092) in paragraph at lines 16644--16649 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [256] [257] [258] [259] Underfull \hbox (badness 6741) in paragraph at lines 16897--16901 \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/pt m/m/n/10 , [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \vbox (badness 10000) has occurred while \output is active [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1478) in paragraph at lines 18349--18352 []\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 [282] [283] [284] [285] Underfull \hbox (badness 10000) in paragraph at lines 18621--18623 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 18627--18636 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1442) in paragraph at lines 19235--19237 []\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 [296] [297] [298] [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 19566--19572 [301] [302] [303] [304] Underfull \hbox (badness 1248) in paragraph at lines 19811--19814 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\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 , [305] [306] [307] [308] Underfull \hbox (badness 4739) in paragraph at lines 20074--20076 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] Underfull \hbox (badness 2469) in paragraph at lines 21158--21163 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [326] [327] Underfull \hbox (badness 1675) in paragraph at lines 21246--21255 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21256--21271 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the Underfull \hbox (badness 10000) in paragraph at lines 21306--21309 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21306--21309 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [328] [329] Underfull \hbox (badness 1014) in paragraph at lines 21440--21445 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 1264) in paragraph at lines 22289--22297 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [343] Underfull \hbox (badness 4441) in paragraph at lines 22323--22326 []\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/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 5231) in paragraph at lines 23120--23122 []\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 []\T1/zi4/m/n/10 make.unique(c(A, B)) == [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / zlib . net/$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m /n/10 https : / / en . wikipedia . org / wiki / Gzip$[][]\T1/ptm/m/n/10 , [][]$ \T1/zi4/m/n/10 http : / / www . bzip . org/$[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , [][]$\T1/zi4/m/n/10 https : / / tukaani . org / xz/$[][] \T1/ptm/m/n/ 10 and [][]$\T1/zi4/m/n/10 https : [373] [374] [375] [376] [377] [378] [379] [380] Underfull \hbox (badness 2790) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [381] [382] [383] [384] [385] Underfull \hbox (badness 1194) in paragraph at lines 25033--25036 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [386] [387] [388] Underfull \hbox (badness 2368) in paragraph at lines 25240--25246 []\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-r e-spond-ing list, i.e., [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 25630--25633 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [395] [396] [397] [398] [399] [400] [401] [402] [403] [404] Underfull \hbox (badness 10000) in paragraph at lines 26251--26253 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 1881) in paragraph at lines 27146--27149 []\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 27171--27173 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [418] [419] Underfull \hbox (badness 2142) in paragraph at lines 27312--27316 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 27369--27374 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [420] [421] [422] [423] Underfull \hbox (badness 10000) in paragraph at lines 27663--27669 []\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 27663--27669 \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 27663--27669 \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 27676--27679 []\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/pt m/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 27702--27704 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [424] Underfull \hbox (badness 10000) in paragraph at lines 27744--27749 []\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 2529) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 27762--27765 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [425] [426] [427] [428] [429] Underfull \vbox (badness 3803) has occurred while \output is active [430] Underfull \hbox (badness 10000) in paragraph at lines 28162--28166 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [431] [432] Underfull \hbox (badness 10000) in paragraph at lines 28309--28312 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [433] Underfull \hbox (badness 7925) in paragraph at lines 28390--28394 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 28390--28394 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 28395--28404 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] Underfull \hbox (badness 2726) in paragraph at lines 29391--29394 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 1533) in paragraph at lines 31181--31184 []\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 [477] [478] [479] Underfull \hbox (badness 1163) in paragraph at lines 31344--31355 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 10000) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33029--33031 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33032--33036 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [506] [507] Underfull \vbox (badness 10000) has occurred while \output is active [508] [509] [510] [511] [512] [513] [514] [515] Underfull \hbox (badness 1655) in paragraph at lines 33626--33628 []\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 [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] Underfull \hbox (badness 2261) in paragraph at lines 34832--34837 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 10000) in paragraph at lines 35952--35963 \T1/zi4/m/n/10 / / docs . microsoft . com / en-[]us / cpp / c-[]language / pars ing-[]c-[]command-[]line-[]arguments ? [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 10000) in paragraph at lines 37483--37485 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [576] Underfull \vbox (badness 10000) has occurred while \output is active [577] [578] [579] [580] [581] [582] Underfull \hbox (badness 2913) in paragraph at lines 37903--37907 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [583] [584] [585] Underfull \hbox (badness 1072) in paragraph at lines 38149--38153 []\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 38154--38158 []\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/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', [586] Underfull \hbox (badness 10000) in paragraph at lines 38194--38200 []\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 38194--38200 \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 38194--38200 \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 Underfull \hbox (badness 3009) in paragraph at lines 38209--38216 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38209--38216 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38209--38216 \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 38209--38216 \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 [587] [588] [589] Underfull \hbox (badness 2644) in paragraph at lines 38444--38448 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [590] [591] [592] Underfull \hbox (badness 1142) in paragraph at lines 38597--38603 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] Underfull \hbox (badness 1158) in paragraph at lines 39914--39916 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 1137) in paragraph at lines 40505--40511 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails [623] Underfull \hbox (badness 4967) in paragraph at lines 40524--40529 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [624] [625] Underfull \hbox (badness 1616) in paragraph at lines 40644--40649 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 1472) in paragraph at lines 41191--41194 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [634] [635] [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] Underfull \hbox (badness 10000) in paragraph at lines 42117--42121 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4/ m/n/10 length(bin) > [649] [650] [651] [652] Underfull \hbox (badness 10000) in paragraph at lines 42368--42371 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [653] [654] [655] Underfull \hbox (badness 10000) in paragraph at lines 42552--42556 [][][]\T1/zi4/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [656] [657] [658] [659] [660] [661] [662] [663] [664] Underfull \hbox (badness 10000) in paragraph at lines 43191--43194 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [665] [666] [667] [668] [669] [670] Underfull \vbox (badness 10000) has occurred while \output is active [671] [672] [673] [674] [675] [676] [677] [678] Underfull \hbox (badness 1990) in paragraph at lines 44113--44121 []\T1/zi4/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 44113--44121 \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 [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] Underfull \hbox (badness 2452) in paragraph at lines 45082--45088 [][][]\T1/zi4/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 3668) in paragraph at lines 45480--45482 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [700] [701] Underfull \hbox (badness 2401) in paragraph at lines 45610--45614 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/n/10 options[][][]("w arn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [702] [703] [704] Underfull \hbox (badness 2111) in paragraph at lines 45818--45823 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/n/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [705] [706] [707] [708] Underfull \hbox (badness 4001) in paragraph at lines 46064--46066 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/n/10 https : / / developer . [709] [710] [711] [712] [713] [714] Underfull \hbox (badness 5417) in paragraph at lines 46429--46433 []\T1/zi4/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [715] Underfull \hbox (badness 10000) in paragraph at lines 46490--46494 []\T1/zi4/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [716]) (./compiler-pkg.tex Chapter 2. [717] [718] [719] [720]) (./datasets-pkg.tex Chapter 3. [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\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. [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803]) (./grDevices-pkg.tex [804] Chapter 4. [805] [806] [807] [808] [809] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/n/10 c(mi, ma, n.)[]\ T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] Underfull \hbox (badness 1424) in paragraph at lines 898--900 [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) an d []\T1/zi4/m/n/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i-fied as [820] [821] [822] [823] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\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 [824] [825] Underfull \hbox (badness 2512) in paragraph at lines 1311--1313 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/n/10 https : / / web . arc hive . org / web / 20190613001950 / http : / / efg2 . com / [826] [827] [828] [829] [830] Underfull \hbox (badness 1490) in paragraph at lines 1611--1616 \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 []\T 1/zi4/m/n/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [831] [832] [833] [834] [835] [836] [837] Underfull \hbox (badness 1325) in paragraph at lines 2038--2048 []\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 "pngalph a"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/1 0 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp32b"[]\T1/ptm/m/n/10 , [838] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [839] [840] [841] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [842] [843] [844] [845] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] Underfull \vbox (badness 3803) has occurred while \output is active [864] [865] [866] [867] Underfull \vbox (badness 3803) has occurred while \output is active [868] Underfull \hbox (badness 10000) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/zi4/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] Underfull \hbox (badness 1584) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 For type []\T1/zi4/m/n/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1/ zi4/m/n/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 4914--4921 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [883] [884] [885] [886] Underfull \hbox (badness 1377) in paragraph at lines 5220--5225 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [887] Underfull \hbox (badness 1418) in paragraph at lines 5296--5303 \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 "Helvet ica-Narrow"[]\T1/ptm/m/n/10 , [888] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [889] Underfull \hbox (badness 1377) in paragraph at lines 5425--5430 []\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 [890] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\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 [891] Underfull \vbox (badness 3803) has occurred while \output is active [892] Underfull \hbox (badness 2035) in paragraph at lines 5632--5641 []\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 5632--5641 \T1/ptm/m/n/10 vided: []\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-Na rrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/zi4/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/zi 4/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "URWBookman"[]\T1/ptm/m /n/10 , [893] [894] Underfull \hbox (badness 10000) in paragraph at lines 5700--5702 []\T1/zi4/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/z i4/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [895] [896] Underfull \hbox (badness 1546) in paragraph at lines 5844--5852 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi4 /m/n/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 title[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 bg[]\T1/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 , [897] [898] [899] [900] [901] [902] [903] [904] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/zi4/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [905] [906] Underfull \vbox (badness 3803) has occurred while \output is active [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [919] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [920] [921] [922] [923] [924] Underfull \hbox (badness 3780) in paragraph at lines 7630--7636 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/n /10 "AvantGarde"[]\T1/ptm/m/n/10 , [925] [926] [927] [928] [929] [930]) (./graphics-pkg.tex Chapter 5. [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] Overfull \hbox (12.71341pt too wide) in paragraph at lines 983--983 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 4634) in paragraph at lines 1357--1360 [][][]\T1/zi4/m/n/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready work s nowa-days with data.frames; [][][]\T1/zi4/m/n/10 boxplot.formula[][][][]\T1/p tm/m/n/10 , [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] Underfull \hbox (badness 1728) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [970] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \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 [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] Underfull \vbox (badness 10000) has occurred while \output is active [994] Underfull \vbox (badness 10000) has occurred while \output is active [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\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 [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 1107) in paragraph at lines 5081--5087 []\T1/ptm/m/n/10 is []\T1/zi4/m/n/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sca led to user co-or-di-nates. Note that []\T1/zi4/m/n/10 c([][]strwidth[][][](ch) , [1012] [1013] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [1014 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 Underfull \vbox (badness 10000) has occurred while \output is active [1015] [1016 ] [1017] [1018] Underfull \vbox (badness 3803) has occurred while \output is active [1019] [1020] [1021] [1022] [1023] [1024] [1025] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [1040 ] [1041] Underfull \vbox (badness 3803) has occurred while \output is active [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] Underfull \hbox (badness 4954) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /n/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 8938--8940 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/n/10 par (c("font.lab", "cex.lab", [1075] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1076] [1077] [1078] [1079]) (./grid-pkg.tex [1080] Chapter 6. [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 2680) in paragraph at lines 550--553 []\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-c u-la-tion of [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] Underfull \hbox (badness 4279) in paragraph at lines 1187--1196 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/n/10 pushViewport[][][][]\T1/p tm/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 seekViewpo rt[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 upViewport[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/n/10 unit[][][][]\T1/ptm/m/n/10 , [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \vbox (badness 10000) has occurred while \output is active [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\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 [1162] [1163] [1164] [1165] [1166] [1167] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 2142) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/n/10 gridGTreeCoords []\T1/ptm/m/n/1 0 a list of ei-ther []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1175] [1176] Underfull \hbox (badness 4699) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/zi4/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208]) (./methods-pkg.tex Chapter 7. [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] 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-ten ds []\T1/zi4/m/n/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/n/1 0 "package"[]\T1/ptm/m/n/10 , also of class [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] 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 can 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/10 it calls []\T1/zi4/m/n/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1237] [1238] [1239] Underfull \hbox (badness 2213) in paragraph at lines 2213--2218 []\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 = [1240] [1241] [1242] [1243] [1244] Underfull \hbox (badness 10000) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/zi4/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class [1245] [1246] Underfull \hbox (badness 1132) in paragraph at lines 2713--2717 []\T1/ptm/m/n/10 In []\T1/zi4/m/n/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi4 /m/n/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/n/10 package []\T1/ptm/m/n/10 sl ot of the re-turned re-sult is in [1247] Underfull \hbox (badness 1033) in paragraph at lines 2745--2750 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/n/10 removeGeneric []\T1/ptm/m/n/10 r e-moves the func-tion it-self; []\T1/zi4/m/n/10 removeMethods []\T1/ptm/m/n/10 re-stores the [1248] [1249] [1250] [1251] [1252] [1253] [1254] Underfull \hbox (badness 1102) in paragraph at lines 3302--3304 []\T1/zi4/m/n/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1255] [1256] [1257] [1258] [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 3641--3650 []\T1/ptm/m/n/10 The [1261] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = "numeric", [1262] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] Underfull \hbox (badness 1769) in paragraph at lines 4476--4482 []\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 4476--4482 []\T1/zi4/m/n/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [] [][]\T1/zi4/m/n/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion use d by [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] Underfull \vbox (badness 10000) has occurred while \output is active [1283] [1284] [1285] Underfull \hbox (badness 4036) in paragraph at lines 5445--5448 []\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 [1286] [1287] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1288] [1289] [1290] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\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 [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1675) in paragraph at lines 6459--6465 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/n/10 externalRef Method(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1300] [1301] [1302] [1303] Underfull \vbox (badness 10000) has occurred while \output is active [1304] [1305] [1306] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1307] [1308] [1309] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} [1310] Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\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 [1311] [1312] [1313] Underfull \hbox (badness 1286) in paragraph at lines 7492--7494 []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 .selectSuperClasses() []\T1/ptm/m/n/10 on ly, a [][][]\T1/zi4/m/n/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, t yp-i-cally [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\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., [1356] [1357] [1358] [1359]) (./parallel-pkg.tex [1360] 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/z i4/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1361] [1362] [1363] [1364] [1365] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] Underfull \hbox (badness 3386) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1383] [1384] [1385]) (./splines-pkg.tex [1386] 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 [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]) (./stats-pkg.tex Chapter 10. [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] Underfull \hbox (badness 1412) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 2503) in paragraph at lines 1369--1372 []\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 , [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 2503) in paragraph at lines 3530--3533 []\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 , [1459] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\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 = [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2556) in paragraph at lines 5424--5427 []\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 "fi lter"[]\T1/ptm/m/n/10 . For [1489] [1490] [1491] [1492] [1493] [1494] [1495] Underfull \hbox (badness 2503) in paragraph at lines 5838--5842 []\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 , [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 7081) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n 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 6636--6638 []\T1/zi4/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 10000) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \vbox (badness 10000) has occurred while \output is active [1544] [1545] [1546] [1547] [1548] Underfull \hbox (badness 2626) in paragraph at lines 9185--9188 []\T1/ptm/m/n/10 Either []\T1/zi4/m/n/10 "convolution" []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1549] [1550] Underfull \hbox (badness 2503) in paragraph at lines 9292--9296 []\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 , [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] [1574] [1575] [1576] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\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 11024--11027 []\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, [1577] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1578] [1579] [1580] [1581] [1582] [1583] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} [1592] [1593] Underfull \hbox (badness 1484) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/n/10 SSinit = [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1610] [1611] [1612] [1613] [1614] [1615] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1616] [1617] [1618] [1619] [1620] [1621] [1622] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1633] [1634] Underfull \hbox (badness 6412) in paragraph at lines 14660--14664 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/n/10 (surface = "inte rpolate", statistics = [1635] Underfull \hbox (badness 1199) in paragraph at lines 14667--14669 []\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 [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 2503) in paragraph at lines 15743--15747 []\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 , [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/n/ 10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 model.re sponse(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/n/10 model.offset []\T1/ ptm/m/n/10 sums any terms [1662] [1663] [1664] [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 1158) in paragraph at lines 17906--17909 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/n/10 nls []\T1 /ptm/m/n/10 as the data ar-gu-ment. The ac- [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] Underfull \vbox (badness 10000) has occurred while \output is active [1691] Underfull \vbox (badness 10000) has occurred while \output is active [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1377) in paragraph at lines 18933--18938 []\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 18938--18941 []\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 2343) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18951--18955 \T1/ptm/m/n/10 the 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 18959--18963 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/n/10 "BFGS"[]\T 1/ptm/m/n/10 , []\T1/zi4/m/n/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/1 0 "SANN" []\T1/ptm/m/n/10 meth-ods if [1706] [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19184--19184 []\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 19187--19187 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1710] [1711] [1712] [1713] [1714] [1715] [1716] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\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 [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/zi4/m/n/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 s distance", lty = cook.lty, col = cook.col, text.col [1726] [1727] [1728] [1729] [1730] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1731] [1732] [1733] [1734] [1735] [1736] Underfull \hbox (badness 2503) in paragraph at lines 20826--20829 []\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 , [1737] Underfull \hbox (badness 3919) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 "Comparison of Poisson [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\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/1 0 , [][][]\T1/zi4/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\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 [1779] [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 1436) in paragraph at lines 23714--23717 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/n/10 max(2, [1786] Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] Underfull \hbox (badness 1824) in paragraph at lines 24827--24833 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 are f irst re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1803] Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/n/10 y[j] = [1804] Underfull \vbox (badness 3803) has occurred while \output is active [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 2165) in paragraph at lines 25429--25434 []\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/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1813] [1814] [1815] [1816] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\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 25653--25657 []\T1/ptm/m/n/10 where []\T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 PP <- [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] [1841] Underfull \vbox (badness 10000) has occurred while \output is active [1842] [1843] Underfull \hbox (badness 3514) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1844] [1845] [1846] [1847] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27535--27535 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1848] Overfull \hbox (20.23795pt too wide) in paragraph at lines 27628--27628 []\T1/zi4/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (11.22874pt too wide) in paragraph at lines 27630--27630 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1849] [1850] [1851] Underfull \hbox (badness 3514) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1852] [1853] Underfull \hbox (badness 3514) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1854] Underfull \hbox (badness 3514) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1855] [1856] Underfull \hbox (badness 3514) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1857] [1858] Underfull \hbox (badness 6691) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] Underfull \hbox (badness 4024) in paragraph at lines 28633--28636 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] Underfull \hbox (badness 5431) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1877] [1878] [1879] Underfull \hbox (badness 5431) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1880] [1881] [1882] [1883] [1884] [1885] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\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 [1886] [1887] [1888] [1889] [1890] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 3557) in paragraph at lines 31217--31221 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/n/10 extendInt []\T1/ptm/m/n/10 to a non-[ ]\T1/zi4/m/n/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-rect []\T1/zi4/m/n/10 interval = [1910] [1911] [1912] Underfull \vbox (badness 10000) has occurred while \output is active [1913] [1914] [1915] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\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 [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\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 [1925] [1926] [1927] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32317--32317 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1928] [1929] [1930] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32478--32478 [] \T1/zi4/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1931] [1932] [1933] [1934] [1935]) (./stats4-pkg.tex [1936] Chapter 11. [1937] [1938] [1939] Underfull \vbox (badness 10000) has occurred while \output is active [1940] Underfull \vbox (badness 10000) has occurred while \output is active [1941] [1942] [1943] [1944] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1945] [1946] [1947]) (./tcltk-pkg.tex [1948] Chapter 12. [1949] [1950] [1951] [1952] [1953] [1954] [1955] Underfull \vbox (badness 10000) has occurred while \output is active [1956] Underfull \vbox (badness 10000) has occurred while \output is active [1957] Underfull \hbox (badness 1546) in paragraph at lines 666--673 []\T1/zi4/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1958] [1959] [1960] [1961] [1962] Underfull \vbox (badness 10000) has occurred while \output is active [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970]) (./tools-pkg.tex Chapter 13. [1971] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1972] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1973] [1974] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\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 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/n/10 bi bentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/n/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatIn Proceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatManual[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/n/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\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/zi 4/m/n/10 formatTechreport []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1977] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\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 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1990] Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\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 1217--1220 []\T1/zi4/m/n/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and [ ]\T1/zi4/m/n/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 2293) in paragraph at lines 1569--1571 []\T1/zi4/m/n/10 CRAN_memtest_notes() []\T1/ptm/m/n/10 is now dep-re-cated, wit h its func-tion-al-ity in-te-grated into that of Underfull \hbox (badness 10000) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/zi4/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1996] [1997] Underfull \hbox (badness 4096) in paragraph at lines 1714--1722 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1724--1726 []\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 [1998] [1999] [2000] [2001] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2002] [2003] [2004] [2005] [2006] Overfull \hbox (8.25941pt too wide) in paragraph at lines 2230--2230 [] \T1/zi4/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] [2007] [2008] [2009] Underfull \hbox (badness 4096) in paragraph at lines 2399--2407 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2010] [2011] [2012] [2013] [2014] [2015] [2016] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2893. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. [2017] [2018] [2019] [2020] [2021] Underfull \hbox (badness 1424) in paragraph at lines 3196--3198 []\T1/zi4/m/it/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2034] [2035] Underfull \hbox (badness 10000) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/it/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/it/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 1796) in paragraph at lines 4399--4404 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/it/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/it/10 type = = Underfull \hbox (badness 4699) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/zi4/m/it/10 msgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 1946) in paragraph at lines 4449--4453 []\T1/zi4/m/it/10 "--update"[]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m /n/10 4.2.0, []\T1/zi4/m/it/10 "--no-wrap" []\T1/ptm/m/n/10 is used when called from [2042] Underfull \hbox (badness 1838) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [2043] [2044] [2045] [2046] Underfull \hbox (badness 2197) in paragraph at lines 4750--4760 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/it/10 available.packages[][][][]\T1/ptm/m/n/10 : [2047] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\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 [2048] [2049] [2050] [2051]) (./utils-pkg.tex [2052] Chapter 14. [2053] 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 `[] \T1/zi4/m/it/10 insertions[]\T1/ptm/m/n/10 ', [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/it/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/it/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 726--732 []\T1/zi4/m/it/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2064] [2065] [2066] Underfull \hbox (badness 3861) in paragraph at lines 931--936 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/it/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/it/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2067] [2068] [2069] Underfull \hbox (badness 3323) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/zi4/m/it /10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m $\T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 2875) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 taken as [][][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex. max", 1) []\T1/ptm/m/n/10 which is []\T1/zi4/m/it/10 1 []\T1/ptm/m/n/10 typ-i-c ally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \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 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1371) in paragraph at lines 1638--1640 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2078] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1708. [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] Underfull \hbox (badness 2057) in paragraph at lines 2359--2361 []\T1/ptm/m/n/10 None for []\T1/zi4/m/it/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2089] [2090] [2091] [2092] [2093] [2094] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 6842) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/it/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2115] Underfull \hbox (badness 1430) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/it/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2116] Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/it/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/it/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 able []\T1/zi4/m/it/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2117] [2118] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/it/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2140] [2141] [2142] [2143] [2144] [2145] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 6502. Underfull \hbox (badness 1371) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2154] Underfull \hbox (badness 1502) in paragraph at lines 6595--6600 []\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 6595--6600 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2155] [2156] [2157] Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2158] Underfull \hbox (badness 2150) in paragraph at lines 6832--6835 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2159] [2160] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\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 [2161] [2162] [2163] Underfull \hbox (badness 1325) in paragraph at lines 7150--7154 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/it/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2164] Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2165] Underfull \hbox (badness 3219) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/i t/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \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 7313--7320 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 7313--7320 [][][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")[] \T1/ptm/m/n/10 . []\T1/zi4/m/it/10 type = "both" []\T1/ptm/m/n/10 will be silen tly Underfull \hbox (badness 2932) in paragraph at lines 7321--7324 []\T1/ptm/m/n/10 Using pack-ages with []\T1/zi4/m/it/10 type = "source" []\T1/p tm/m/n/10 al-ways works pro-vided the pack-age con-tains no [2166] Underfull \hbox (badness 1024) in paragraph at lines 7448--7451 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing []\T1/zi4/m/it/10 available. packages(filters = "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 , ] []\T1/ ptm/m/n/10 will [2167] Underfull \hbox (badness 10000) in paragraph at lines 7481--7486 [][][]\T1/zi4/m/it/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/i t/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 download. packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 installed.packages[][][] []\T1/ptm/m/n/10 , [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] Underfull \hbox (badness 10000) in paragraph at lines 8185--8187 []\T1/ptm/m/n/10 typically the re-sult of []\T1/zi4/m/it/10 methods(..)[]\T1/pt m/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] Underfull \hbox (badness 2310) in paragraph at lines 8945--8950 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] Underfull \hbox (badness 1248) in paragraph at lines 9471--9475 []\T1/zi4/m/it/10 R CMD build []\T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/ m/n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2200] Underfull \hbox (badness 1789) in paragraph at lines 9551--9553 []\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 [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] Underfull \hbox (badness 1097) in paragraph at lines 10388--10391 []\T1/ptm/m/n/10 The name []\T1/zi4/m/it/10 "clipboard" []\T1/ptm/m/n/10 may al so be used on Win-dows, in which case [2214] [2215] Underfull \hbox (badness 3000) in paragraph at lines 10524--10529 [][][]\T1/zi4/m/it/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/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/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ it/10 read.table[][][][]\T1/ptm/m/n/10 ; [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] Underfull \hbox (badness 2134) in paragraph at lines 11113--11118 [][][]\T1/zi4/m/it/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/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/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ it/10 write.table[][][][]\T1/ptm/m/n/10 ; [2225] Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/zi4/m/it/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/it/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] Underfull \hbox (badness 2469) in paragraph at lines 11663--11667 []\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 11663--11667 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (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.knitr} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mathjaxr} has been referenced but does not exis t, 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 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replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt0900 mkdir: cannot create directory '././nonexistent': Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tctt0900 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt0900.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] 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Output written on tctt0900.600gf (128 characters, 17564 bytes). Transcript written on tctt0900.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tctt0900.600pk: successfully generated. {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/ usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on refman.pdf (2305 pages, 5798257 bytes). Transcript written on refman.log. This is makeindex, version 2.16 [TeX Live 2022] (kpathsea + Thai support). Scanning input file refman.idx..................done (14740 entries accepted, 36 rejected). Sorting entries.........................................................................................................................................................done (224536 comparisons). Generating output file refman.ind.................done (14703 lines written, 56 warnings). Output written in refman.ind. Transcript written in refman.ilg. 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[1] [2] Underfull \hbox (badness 6252) in paragraph at lines 143--151 []\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 . It Underfull \hbox (badness 10000) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/zi4/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 143--151 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/z i4/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 143--151 []\T1/zi4/m/n/10 double.neg.ulp.digits []\T1/ptm/m/n/10 is bounded be-low by [] \T1/zi4/m/n/10 -(double.digits + 3)[]\T1/ptm/m/n/10 , [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 335--338 []\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] [7] [8] [9] Underfull \hbox (badness 2556) in paragraph at lines 574--580 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/zi4/m/n/10 insertions[]\T1/ptm/m/n/10 ', [10] [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1586--1592 [26] [27] [28] [29] [30] [31] [32] Overfull \hbox (26.27782pt too wide) in paragraph at lines 2064--2064 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] Underfull \hbox (badness 1721) in paragraph at lines 2721--2725 [][][]\T1/zi4/m/n/10 assign[][][] []\T1/ptm/m/n/10 (and its in-verse [][][]\T1/ zi4/m/n/10 get[][][][]\T1/ptm/m/n/10 ), for ``sub-assign-ment'' such as []\T1/z i4/m/n/10 x[i] <- v[]\T1/ptm/m/n/10 , see [][][]\T1/zi4/m/n/10 [<-[][][][]\T1/p tm/m/n/10 ; fur-ther, [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 2521) in paragraph at lines 5197--5199 []\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 [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6388--6388 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] Underfull \hbox (badness 1303) in paragraph at lines 7281--7288 []\T1/zi4/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/zi4/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/zi4/m/n/10 "r" []\T1/ptm/m/n /10 only. This reads the Underfull \hbox (badness 2111) in paragraph at lines 7292--7297 []\T1/ptm/m/n/10 Unix users wish-ing to \T1/ptm/m/it/10 write \T1/ptm/m/n/10 to one of the X11 se-lec-tions may be able to do so via [113] [114] Underfull \vbox (badness 3803) has occurred while \output is active [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] [117] [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 2096) in paragraph at lines 7962--7966 \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 . [124] [125] Underfull \hbox (badness 2351) in paragraph at lines 8076--8079 [][][]\T1/zi4/m/n/10 split[][][] []\T1/ptm/m/n/10 for split-ting a vari-able ac -cord-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 t able[][][][]\T1/ptm/m/n/10 , [126] [127] [128] [129] [130] Underfull \hbox (badness 4479) in paragraph at lines 8393--8404 [][][]\T1/zi4/m/n/10 I[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 plot.data.f rame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 print.data.frame[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 row.names[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 names[][][] []\T1/ptm/m/n/10 (for the col-umn names), [131] [132] [133] [134] [135] [136] [137] Underfull \hbox (badness 1629) in paragraph at lines 8861--8873 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 2875) in paragraph at lines 8861--8873 []\T1/zi4/m/n/10 NA[]\T1/ptm/m/n/10 , and hence []\T1/zi4/m/n/10 as.POSIXct("19 69-12-31 23:59:59", tz = "UTC") []\T1/ptm/m/n/10 will give []\T1/zi4/m/n/10 "19 69-12-31 [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] Underfull \hbox (badness 1178) in paragraph at lines 9629--9633 []\T1/ptm/m/n/10 If true, [][][]\T1/zi4/m/n/10 list[][][][]\T1/ptm/m/n/10 s and atomic vec-tors with non-[][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 names (see [][][]\T1/zi4/m/n/10 names[][][][]\T1/ptm/m/n/10 ) are de- [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 2744) in paragraph at lines 11938--11940 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] Underfull \hbox (badness 2253) in paragraph at lines 14134--14136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. 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Co n-sider [221] Underfull \hbox (badness 1466) in paragraph at lines 14451--14454 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [222] [223] Underfull \hbox (badness 10000) in paragraph at lines 14582--14586 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\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 14593--14596 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [224] [225] [226] [227] [228] Underfull \hbox (badness 3965) in paragraph at lines 14890--14894 []\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, [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 4429) in paragraph at lines 15679--15682 []\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 [241] [242] Underfull \hbox (badness 10000) in paragraph at lines 15785--15787 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [243] Underfull \hbox (badness 2035) in paragraph at lines 15858--15862 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 2452) in paragraph at lines 16471--16475 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment 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 16471--16475 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s 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 [254] [255] Underfull \hbox (badness 1092) in paragraph at lines 16644--16649 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [256] [257] [258] [259] Underfull \hbox (badness 6741) in paragraph at lines 16897--16901 \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/pt m/m/n/10 , [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \vbox (badness 10000) has occurred while \output is active [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1478) in paragraph at lines 18349--18352 []\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 [282] [283] [284] [285] Underfull \hbox (badness 10000) in paragraph at lines 18621--18623 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 18627--18636 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1442) in paragraph at lines 19235--19237 []\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 [296] [297] [298] [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 19566--19572 [301] [302] [303] [304] Underfull \hbox (badness 1248) in paragraph at lines 19811--19814 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\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 , [305] [306] [307] [308] Underfull \hbox (badness 4739) in paragraph at lines 20074--20076 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] Underfull \hbox (badness 2469) in paragraph at lines 21158--21163 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [326] [327] Underfull \hbox (badness 1675) in paragraph at lines 21246--21255 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21256--21271 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the Underfull \hbox (badness 10000) in paragraph at lines 21306--21309 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21306--21309 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [328] [329] Underfull \hbox (badness 1014) in paragraph at lines 21440--21445 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 1264) in paragraph at lines 22289--22297 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [343] Underfull \hbox (badness 4441) in paragraph at lines 22323--22326 []\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/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 5231) in paragraph at lines 23120--23122 []\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 []\T1/zi4/m/n/10 make.unique(c(A, B)) == [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / zlib . net/$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m /n/10 https : / / en . wikipedia . org / wiki / Gzip$[][]\T1/ptm/m/n/10 , [][]$ \T1/zi4/m/n/10 http : / / www . bzip . org/$[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , [][]$\T1/zi4/m/n/10 https : / / tukaani . org / xz/$[][] \T1/ptm/m/n/ 10 and [][]$\T1/zi4/m/n/10 https : [373] [374] [375] [376] [377] [378] [379] [380] Underfull \hbox (badness 2790) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [381] [382] [383] [384] [385] Underfull \hbox (badness 1194) in paragraph at lines 25033--25036 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [386] [387] [388] Underfull \hbox (badness 2368) in paragraph at lines 25240--25246 []\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-r e-spond-ing list, i.e., [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 25630--25633 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [395] [396] [397] [398] [399] [400] [401] [402] [403] [404] Underfull \hbox (badness 10000) in paragraph at lines 26251--26253 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 1881) in paragraph at lines 27146--27149 []\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 27171--27173 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [418] [419] Underfull \hbox (badness 2142) in paragraph at lines 27312--27316 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 27369--27374 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [420] [421] [422] [423] Underfull \hbox (badness 10000) in paragraph at lines 27663--27669 []\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 27663--27669 \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 27663--27669 \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 27676--27679 []\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/pt m/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 27702--27704 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [424] Underfull \hbox (badness 10000) in paragraph at lines 27744--27749 []\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 2529) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 27762--27765 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [425] [426] [427] [428] [429] Underfull \vbox (badness 3803) has occurred while \output is active [430] Underfull \hbox (badness 10000) in paragraph at lines 28162--28166 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [431] [432] Underfull \hbox (badness 10000) in paragraph at lines 28309--28312 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [433] Underfull \hbox (badness 7925) in paragraph at lines 28390--28394 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 28390--28394 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 28395--28404 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] Underfull \hbox (badness 2726) in paragraph at lines 29391--29394 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 1533) in paragraph at lines 31181--31184 []\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 [477] [478] [479] Underfull \hbox (badness 1163) in paragraph at lines 31344--31355 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 10000) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33029--33031 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33032--33036 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [506] [507] Underfull \vbox (badness 10000) has occurred while \output is active [508] [509] [510] [511] [512] [513] [514] [515] Underfull \hbox (badness 1655) in paragraph at lines 33626--33628 []\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 [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] Underfull \hbox (badness 2261) in paragraph at lines 34832--34837 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 10000) in paragraph at lines 35952--35963 \T1/zi4/m/n/10 / / docs . microsoft . com / en-[]us / cpp / c-[]language / pars ing-[]c-[]command-[]line-[]arguments ? [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 10000) in paragraph at lines 37483--37485 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [576] Underfull \vbox (badness 10000) has occurred while \output is active [577] [578] [579] [580] [581] [582] Underfull \hbox (badness 2913) in paragraph at lines 37903--37907 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [583] [584] [585] Underfull \hbox (badness 1072) in paragraph at lines 38149--38153 []\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 38154--38158 []\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/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', [586] Underfull \hbox (badness 10000) in paragraph at lines 38194--38200 []\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 38194--38200 \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 38194--38200 \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 Underfull \hbox (badness 3009) in paragraph at lines 38209--38216 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38209--38216 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38209--38216 \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 38209--38216 \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 [587] [588] [589] Underfull \hbox (badness 2644) in paragraph at lines 38444--38448 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [590] [591] [592] Underfull \hbox (badness 1142) in paragraph at lines 38597--38603 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] Underfull \hbox (badness 1158) in paragraph at lines 39914--39916 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 1137) in paragraph at lines 40505--40511 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails [623] Underfull \hbox (badness 4967) in paragraph at lines 40524--40529 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [624] [625] Underfull \hbox (badness 1616) in paragraph at lines 40644--40649 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 1472) in paragraph at lines 41191--41194 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [634] [635] [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] Underfull \hbox (badness 10000) in paragraph at lines 42117--42121 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4/ m/n/10 length(bin) > [649] [650] [651] [652] Underfull \hbox (badness 10000) in paragraph at lines 42368--42371 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [653] [654] [655] Underfull \hbox (badness 10000) in paragraph at lines 42552--42556 [][][]\T1/zi4/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [656] [657] [658] [659] [660] [661] [662] [663] [664] Underfull \hbox (badness 10000) in paragraph at lines 43191--43194 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [665] [666] [667] [668] [669] [670] Underfull \vbox (badness 10000) has occurred while \output is active [671] [672] [673] [674] [675] [676] [677] [678] Underfull \hbox (badness 1990) in paragraph at lines 44113--44121 []\T1/zi4/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 44113--44121 \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 [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] Underfull \hbox (badness 2452) in paragraph at lines 45082--45088 [][][]\T1/zi4/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 3668) in paragraph at lines 45480--45482 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [700] [701] Underfull \hbox (badness 2401) in paragraph at lines 45610--45614 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/n/10 options[][][]("w arn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [702] [703] [704] Underfull \hbox (badness 2111) in paragraph at lines 45818--45823 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/n/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [705] [706] [707] [708] Underfull \hbox (badness 4001) in paragraph at lines 46064--46066 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/n/10 https : / / developer . [709] [710] [711] [712] [713] [714] Underfull \hbox (badness 5417) in paragraph at lines 46429--46433 []\T1/zi4/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [715] Underfull \hbox (badness 10000) in paragraph at lines 46490--46494 []\T1/zi4/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [716]) (./compiler-pkg.tex Chapter 2. [717] [718] [719] [720]) (./datasets-pkg.tex Chapter 3. [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\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. [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803]) (./grDevices-pkg.tex [804] Chapter 4. [805] [806] [807] [808] [809] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/n/10 c(mi, ma, n.)[]\ T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] Underfull \hbox (badness 1424) in paragraph at lines 898--900 [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) an d []\T1/zi4/m/n/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i-fied as [820] [821] [822] [823] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\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 [824] [825] Underfull \hbox (badness 2512) in paragraph at lines 1311--1313 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/n/10 https : / / web . arc hive . org / web / 20190613001950 / http : / / efg2 . com / [826] [827] [828] [829] [830] Underfull \hbox (badness 1490) in paragraph at lines 1611--1616 \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 []\T 1/zi4/m/n/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [831] [832] [833] [834] [835] [836] [837] Underfull \hbox (badness 1325) in paragraph at lines 2038--2048 []\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 "pngalph a"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/1 0 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp32b"[]\T1/ptm/m/n/10 , [838] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [839] [840] [841] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [842] [843] [844] [845] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] Underfull \vbox (badness 3803) has occurred while \output is active [864] [865] [866] [867] Underfull \vbox (badness 3803) has occurred while \output is active [868] Underfull \hbox (badness 10000) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/zi4/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] Underfull \hbox (badness 1584) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 For type []\T1/zi4/m/n/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1/ zi4/m/n/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 4914--4921 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [883] [884] [885] [886] Underfull \hbox (badness 1377) in paragraph at lines 5220--5225 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [887] Underfull \hbox (badness 1418) in paragraph at lines 5296--5303 \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 "Helvet ica-Narrow"[]\T1/ptm/m/n/10 , [888] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [889] Underfull \hbox (badness 1377) in paragraph at lines 5425--5430 []\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 [890] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\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 [891] Underfull \vbox (badness 3803) has occurred while \output is active [892] Underfull \hbox (badness 2035) in paragraph at lines 5632--5641 []\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 5632--5641 \T1/ptm/m/n/10 vided: []\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-Na rrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/zi4/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/zi 4/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "URWBookman"[]\T1/ptm/m /n/10 , [893] [894] Underfull \hbox (badness 10000) in paragraph at lines 5700--5702 []\T1/zi4/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/z i4/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [895] [896] Underfull \hbox (badness 1546) in paragraph at lines 5844--5852 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi4 /m/n/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 title[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 bg[]\T1/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 , [897] [898] [899] [900] [901] [902] [903] [904] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/zi4/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [905] [906] Underfull \vbox (badness 3803) has occurred while \output is active [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [919] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [920] [921] [922] [923] [924] Underfull \hbox (badness 3780) in paragraph at lines 7630--7636 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/n /10 "AvantGarde"[]\T1/ptm/m/n/10 , [925] [926] [927] [928] [929] [930]) (./graphics-pkg.tex Chapter 5. [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] Overfull \hbox (12.71341pt too wide) in paragraph at lines 983--983 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 4634) in paragraph at lines 1357--1360 [][][]\T1/zi4/m/n/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready work s nowa-days with data.frames; [][][]\T1/zi4/m/n/10 boxplot.formula[][][][]\T1/p tm/m/n/10 , [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] Underfull \hbox (badness 1728) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [970] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \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 [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] Underfull \vbox (badness 10000) has occurred while \output is active [994] Underfull \vbox (badness 10000) has occurred while \output is active [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\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 [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 1107) in paragraph at lines 5081--5087 []\T1/ptm/m/n/10 is []\T1/zi4/m/n/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sca led to user co-or-di-nates. Note that []\T1/zi4/m/n/10 c([][]strwidth[][][](ch) , [1012] [1013] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [1014 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 Underfull \vbox (badness 10000) has occurred while \output is active [1015] [1016 ] [1017] [1018] Underfull \vbox (badness 3803) has occurred while \output is active [1019] [1020] [1021] [1022] [1023] [1024] [1025] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [1040 ] [1041] Underfull \vbox (badness 3803) has occurred while \output is active [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] Underfull \hbox (badness 4954) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /n/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 8938--8940 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/n/10 par (c("font.lab", "cex.lab", [1075] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1076] [1077] [1078] [1079]) (./grid-pkg.tex [1080] Chapter 6. [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 2680) in paragraph at lines 550--553 []\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-c u-la-tion of [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] Underfull \hbox (badness 4279) in paragraph at lines 1187--1196 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/n/10 pushViewport[][][][]\T1/p tm/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 seekViewpo rt[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 upViewport[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/n/10 unit[][][][]\T1/ptm/m/n/10 , [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \vbox (badness 10000) has occurred while \output is active [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\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 [1162] [1163] [1164] [1165] [1166] [1167] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 2142) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/n/10 gridGTreeCoords []\T1/ptm/m/n/1 0 a list of ei-ther []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1175] [1176] Underfull \hbox (badness 4699) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/zi4/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208]) (./methods-pkg.tex Chapter 7. [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] 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-ten ds []\T1/zi4/m/n/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/n/1 0 "package"[]\T1/ptm/m/n/10 , also of class [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] 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 can 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/10 it calls []\T1/zi4/m/n/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1237] [1238] [1239] Underfull \hbox (badness 2213) in paragraph at lines 2213--2218 []\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 = [1240] [1241] [1242] [1243] [1244] Underfull \hbox (badness 10000) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/zi4/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class [1245] [1246] Underfull \hbox (badness 1132) in paragraph at lines 2713--2717 []\T1/ptm/m/n/10 In []\T1/zi4/m/n/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi4 /m/n/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/n/10 package []\T1/ptm/m/n/10 sl ot of the re-turned re-sult is in [1247] Underfull \hbox (badness 1033) in paragraph at lines 2745--2750 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/n/10 removeGeneric []\T1/ptm/m/n/10 r e-moves the func-tion it-self; []\T1/zi4/m/n/10 removeMethods []\T1/ptm/m/n/10 re-stores the [1248] [1249] [1250] [1251] [1252] [1253] [1254] Underfull \hbox (badness 1102) in paragraph at lines 3302--3304 []\T1/zi4/m/n/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1255] [1256] [1257] [1258] [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 3641--3650 []\T1/ptm/m/n/10 The [1261] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = "numeric", [1262] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] Underfull \hbox (badness 1769) in paragraph at lines 4476--4482 []\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 4476--4482 []\T1/zi4/m/n/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [] [][]\T1/zi4/m/n/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion use d by [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] Underfull \vbox (badness 10000) has occurred while \output is active [1283] [1284] [1285] Underfull \hbox (badness 4036) in paragraph at lines 5445--5448 []\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 [1286] [1287] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1288] [1289] [1290] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\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 [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1675) in paragraph at lines 6459--6465 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/n/10 externalRef Method(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1300] [1301] [1302] [1303] Underfull \vbox (badness 10000) has occurred while \output is active [1304] [1305] [1306] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1307] [1308] [1309] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} [1310] Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\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 [1311] [1312] [1313] Underfull \hbox (badness 1286) in paragraph at lines 7492--7494 []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 .selectSuperClasses() []\T1/ptm/m/n/10 on ly, a [][][]\T1/zi4/m/n/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, t yp-i-cally [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\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., [1356] [1357] [1358] [1359]) (./parallel-pkg.tex [1360] 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/z i4/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1361] [1362] [1363] [1364] [1365] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] Underfull \hbox (badness 3386) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1383] [1384] [1385]) (./splines-pkg.tex [1386] 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 [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]) (./stats-pkg.tex Chapter 10. [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] Underfull \hbox (badness 1412) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 2503) in paragraph at lines 1369--1372 []\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 , [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 2503) in paragraph at lines 3530--3533 []\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 , [1459] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\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 = [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2556) in paragraph at lines 5424--5427 []\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 "fi lter"[]\T1/ptm/m/n/10 . For [1489] [1490] [1491] [1492] [1493] [1494] [1495] Underfull \hbox (badness 2503) in paragraph at lines 5838--5842 []\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 , [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 7081) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n 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 6636--6638 []\T1/zi4/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 10000) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \vbox (badness 10000) has occurred while \output is active [1544] [1545] [1546] [1547] [1548] Underfull \hbox (badness 2626) in paragraph at lines 9185--9188 []\T1/ptm/m/n/10 Either []\T1/zi4/m/n/10 "convolution" []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1549] [1550] Underfull \hbox (badness 2503) in paragraph at lines 9292--9296 []\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 , [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] [1574] [1575] [1576] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\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 11024--11027 []\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, [1577] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1578] [1579] [1580] [1581] [1582] [1583] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} [1592] [1593] Underfull \hbox (badness 1484) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/n/10 SSinit = [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1610] [1611] [1612] [1613] [1614] [1615] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1616] [1617] [1618] [1619] [1620] [1621] [1622] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1633] [1634] Underfull \hbox (badness 6412) in paragraph at lines 14660--14664 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/n/10 (surface = "inte rpolate", statistics = [1635] Underfull \hbox (badness 1199) in paragraph at lines 14667--14669 []\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 [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 2503) in paragraph at lines 15743--15747 []\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 , [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/n/ 10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 model.re sponse(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/n/10 model.offset []\T1/ ptm/m/n/10 sums any terms [1662] [1663] [1664] [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 1158) in paragraph at lines 17906--17909 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/n/10 nls []\T1 /ptm/m/n/10 as the data ar-gu-ment. The ac- [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] Underfull \vbox (badness 10000) has occurred while \output is active [1691] Underfull \vbox (badness 10000) has occurred while \output is active [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1377) in paragraph at lines 18933--18938 []\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 18938--18941 []\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 2343) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18951--18955 \T1/ptm/m/n/10 the 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 18959--18963 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/n/10 "BFGS"[]\T 1/ptm/m/n/10 , []\T1/zi4/m/n/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/1 0 "SANN" []\T1/ptm/m/n/10 meth-ods if [1706] [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19184--19184 []\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 19187--19187 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1710] [1711] [1712] [1713] [1714] [1715] [1716] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\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 [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/zi4/m/n/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 s distance", lty = cook.lty, col = cook.col, text.col [1726] [1727] [1728] [1729] [1730] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1731] [1732] [1733] [1734] [1735] [1736] Underfull \hbox (badness 2503) in paragraph at lines 20826--20829 []\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 , [1737] Underfull \hbox (badness 3919) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 "Comparison of Poisson [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\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/1 0 , [][][]\T1/zi4/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\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 [1779] [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 1436) in paragraph at lines 23714--23717 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/n/10 max(2, [1786] Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] Underfull \hbox (badness 1824) in paragraph at lines 24827--24833 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 are f irst re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1803] Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/n/10 y[j] = [1804] Underfull \vbox (badness 3803) has occurred while \output is active [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 2165) in paragraph at lines 25429--25434 []\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/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1813] [1814] [1815] [1816] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\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 25653--25657 []\T1/ptm/m/n/10 where []\T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 PP <- [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] [1841] Underfull \vbox (badness 10000) has occurred while \output is active [1842] [1843] Underfull \hbox (badness 3514) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1844] [1845] [1846] [1847] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27535--27535 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1848] Overfull \hbox (20.23795pt too wide) in paragraph at lines 27628--27628 []\T1/zi4/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (11.22874pt too wide) in paragraph at lines 27630--27630 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1849] [1850] [1851] Underfull \hbox (badness 3514) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1852] [1853] Underfull \hbox (badness 3514) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1854] Underfull \hbox (badness 3514) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1855] [1856] Underfull \hbox (badness 3514) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1857] [1858] Underfull \hbox (badness 6691) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] Underfull \hbox (badness 4024) in paragraph at lines 28633--28636 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] Underfull \hbox (badness 5431) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1877] [1878] [1879] Underfull \hbox (badness 5431) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1880] [1881] [1882] [1883] [1884] [1885] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\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 [1886] [1887] [1888] [1889] [1890] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 3557) in paragraph at lines 31217--31221 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/n/10 extendInt []\T1/ptm/m/n/10 to a non-[ ]\T1/zi4/m/n/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-rect []\T1/zi4/m/n/10 interval = [1910] [1911] [1912] Underfull \vbox (badness 10000) has occurred while \output is active [1913] [1914] [1915] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\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 [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\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 [1925] [1926] [1927] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32317--32317 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1928] [1929] [1930] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32478--32478 [] \T1/zi4/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1931] [1932] [1933] [1934] [1935]) (./stats4-pkg.tex [1936] Chapter 11. [1937] [1938] [1939] Underfull \vbox (badness 10000) has occurred while \output is active [1940] Underfull \vbox (badness 10000) has occurred while \output is active [1941] [1942] [1943] [1944] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1945] [1946] [1947]) (./tcltk-pkg.tex [1948] Chapter 12. [1949] [1950] [1951] [1952] [1953] [1954] [1955] Underfull \vbox (badness 10000) has occurred while \output is active [1956] Underfull \vbox (badness 10000) has occurred while \output is active [1957] Underfull \hbox (badness 1546) in paragraph at lines 666--673 []\T1/zi4/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1958] [1959] [1960] [1961] [1962] Underfull \vbox (badness 10000) has occurred while \output is active [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970]) (./tools-pkg.tex Chapter 13. [1971] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1972] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1973] [1974] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\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 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/n/10 bi bentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/n/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatIn Proceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatManual[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/n/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\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/zi 4/m/n/10 formatTechreport []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1977] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\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 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1990] Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\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 1217--1220 []\T1/zi4/m/n/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and [ ]\T1/zi4/m/n/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 2293) in paragraph at lines 1569--1571 []\T1/zi4/m/n/10 CRAN_memtest_notes() []\T1/ptm/m/n/10 is now dep-re-cated, wit h its func-tion-al-ity in-te-grated into that of Underfull \hbox (badness 10000) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/zi4/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1996] [1997] Underfull \hbox (badness 4096) in paragraph at lines 1714--1722 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1724--1726 []\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 [1998] [1999] [2000] [2001] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2002] [2003] [2004] [2005] [2006] Overfull \hbox (8.25941pt too wide) in paragraph at lines 2230--2230 [] \T1/zi4/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] [2007] [2008] [2009] Underfull \hbox (badness 4096) in paragraph at lines 2399--2407 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2010] [2011] [2012] [2013] [2014] [2015] [2016] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2893. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. [2017] [2018] [2019] [2020] [2021] Underfull \hbox (badness 1424) in paragraph at lines 3196--3198 []\T1/zi4/m/it/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2034] [2035] Underfull \hbox (badness 10000) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/it/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/it/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 1796) in paragraph at lines 4399--4404 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/it/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/it/10 type = = Underfull \hbox (badness 4699) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/zi4/m/it/10 msgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 1946) in paragraph at lines 4449--4453 []\T1/zi4/m/it/10 "--update"[]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m /n/10 4.2.0, []\T1/zi4/m/it/10 "--no-wrap" []\T1/ptm/m/n/10 is used when called from [2042] Underfull \hbox (badness 1838) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [2043] [2044] [2045] [2046] Underfull \hbox (badness 2197) in paragraph at lines 4750--4760 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/it/10 available.packages[][][][]\T1/ptm/m/n/10 : [2047] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\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 [2048] [2049] [2050] [2051]) (./utils-pkg.tex [2052] Chapter 14. [2053] 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 `[] \T1/zi4/m/it/10 insertions[]\T1/ptm/m/n/10 ', [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/it/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/it/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 726--732 []\T1/zi4/m/it/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2064] [2065] [2066] Underfull \hbox (badness 3861) in paragraph at lines 931--936 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/it/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/it/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2067] [2068] [2069] Underfull \hbox (badness 3323) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/zi4/m/it /10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m $\T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 2875) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 taken as [][][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex. max", 1) []\T1/ptm/m/n/10 which is []\T1/zi4/m/it/10 1 []\T1/ptm/m/n/10 typ-i-c ally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \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 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1371) in paragraph at lines 1638--1640 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2078] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1708. [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] Underfull \hbox (badness 2057) in paragraph at lines 2359--2361 []\T1/ptm/m/n/10 None for []\T1/zi4/m/it/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2089] [2090] [2091] [2092] [2093] [2094] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 6842) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/it/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2115] Underfull \hbox (badness 1430) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/it/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2116] Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/it/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/it/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 able []\T1/zi4/m/it/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2117] [2118] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/it/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2140] [2141] [2142] [2143] [2144] [2145] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 6502. 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See [2159] [2160] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\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 [2161] [2162] [2163] Underfull \hbox (badness 1325) in paragraph at lines 7150--7154 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/it/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2164] Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2165] Underfull \hbox (badness 3219) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/i t/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. 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The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/zi4/m/it/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/it/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] Underfull \hbox (badness 2469) in paragraph at lines 11663--11667 []\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 11663--11667 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (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.knitr} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mathjaxr} has been referenced but does not exis t, 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 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This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2022/07/02 v1.4n 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/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[1] [2] Underfull \hbox (badness 6252) in paragraph at lines 143--151 []\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 . It Underfull \hbox (badness 10000) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/zi4/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 143--151 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/z i4/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . 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This reads the Underfull \hbox (badness 2111) in paragraph at lines 7292--7297 []\T1/ptm/m/n/10 Unix users wish-ing to \T1/ptm/m/it/10 write \T1/ptm/m/n/10 to one of the X11 se-lec-tions may be able to do so via [113] [114] Underfull \vbox (badness 3803) has occurred while \output is active [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] [117] [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 2096) in paragraph at lines 7962--7966 \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 . [124] [125] Underfull \hbox (badness 2351) in paragraph at lines 8076--8079 [][][]\T1/zi4/m/n/10 split[][][] []\T1/ptm/m/n/10 for split-ting a vari-able ac -cord-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 t able[][][][]\T1/ptm/m/n/10 , [126] [127] [128] [129] [130] Underfull \hbox (badness 4479) in paragraph at lines 8393--8404 [][][]\T1/zi4/m/n/10 I[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 plot.data.f rame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 print.data.frame[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 row.names[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 names[][][] []\T1/ptm/m/n/10 (for the col-umn names), [131] [132] [133] [134] [135] [136] [137] Underfull \hbox (badness 1629) in paragraph at lines 8861--8873 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 2875) in paragraph at lines 8861--8873 []\T1/zi4/m/n/10 NA[]\T1/ptm/m/n/10 , and hence []\T1/zi4/m/n/10 as.POSIXct("19 69-12-31 23:59:59", tz = "UTC") []\T1/ptm/m/n/10 will give []\T1/zi4/m/n/10 "19 69-12-31 [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] Underfull \hbox (badness 1178) in paragraph at lines 9629--9633 []\T1/ptm/m/n/10 If true, [][][]\T1/zi4/m/n/10 list[][][][]\T1/ptm/m/n/10 s and atomic vec-tors with non-[][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 names (see [][][]\T1/zi4/m/n/10 names[][][][]\T1/ptm/m/n/10 ) are de- [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 2744) in paragraph at lines 11938--11940 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] Underfull \hbox (badness 2253) in paragraph at lines 14134--14136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. 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Co n-sider [221] Underfull \hbox (badness 1466) in paragraph at lines 14451--14454 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [222] [223] Underfull \hbox (badness 10000) in paragraph at lines 14582--14586 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\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 14593--14596 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [224] [225] [226] [227] [228] Underfull \hbox (badness 3965) in paragraph at lines 14890--14894 []\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, [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 4429) in paragraph at lines 15679--15682 []\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 [241] [242] Underfull \hbox (badness 10000) in paragraph at lines 15785--15787 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [243] Underfull \hbox (badness 2035) in paragraph at lines 15858--15862 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 2452) in paragraph at lines 16471--16475 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment 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 16471--16475 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s 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 [254] [255] Underfull \hbox (badness 1092) in paragraph at lines 16644--16649 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [256] [257] [258] [259] Underfull \hbox (badness 6741) in paragraph at lines 16897--16901 \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/pt m/m/n/10 , [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \vbox (badness 10000) has occurred while \output is active [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1478) in paragraph at lines 18349--18352 []\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 [282] [283] [284] [285] Underfull \hbox (badness 10000) in paragraph at lines 18621--18623 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 18627--18636 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1442) in paragraph at lines 19235--19237 []\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 [296] [297] [298] [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 19566--19572 [301] [302] [303] [304] Underfull \hbox (badness 1248) in paragraph at lines 19811--19814 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\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 , [305] [306] [307] [308] Underfull \hbox (badness 4739) in paragraph at lines 20074--20076 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] Underfull \hbox (badness 2469) in paragraph at lines 21158--21163 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [326] [327] Underfull \hbox (badness 1675) in paragraph at lines 21246--21255 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21256--21271 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the Underfull \hbox (badness 10000) in paragraph at lines 21306--21309 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21306--21309 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [328] [329] Underfull \hbox (badness 1014) in paragraph at lines 21440--21445 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 1264) in paragraph at lines 22289--22297 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [343] Underfull \hbox (badness 4441) in paragraph at lines 22323--22326 []\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/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 5231) in paragraph at lines 23120--23122 []\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 []\T1/zi4/m/n/10 make.unique(c(A, B)) == [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / zlib . net/$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m /n/10 https : / / en . wikipedia . org / wiki / Gzip$[][]\T1/ptm/m/n/10 , [][]$ \T1/zi4/m/n/10 http : / / www . bzip . org/$[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , [][]$\T1/zi4/m/n/10 https : / / tukaani . org / xz/$[][] \T1/ptm/m/n/ 10 and [][]$\T1/zi4/m/n/10 https : [373] [374] [375] [376] [377] [378] [379] [380] Underfull \hbox (badness 2790) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [381] [382] [383] [384] [385] Underfull \hbox (badness 1194) in paragraph at lines 25033--25036 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [386] [387] [388] Underfull \hbox (badness 2368) in paragraph at lines 25240--25246 []\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-r e-spond-ing list, i.e., [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 25630--25633 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [395] [396] [397] [398] [399] [400] [401] [402] [403] [404] Underfull \hbox (badness 10000) in paragraph at lines 26251--26253 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 1881) in paragraph at lines 27146--27149 []\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 27171--27173 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [418] [419] Underfull \hbox (badness 2142) in paragraph at lines 27312--27316 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 27369--27374 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [420] [421] [422] [423] Underfull \hbox (badness 10000) in paragraph at lines 27663--27669 []\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 27663--27669 \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 27663--27669 \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 27676--27679 []\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/pt m/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 27702--27704 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [424] Underfull \hbox (badness 10000) in paragraph at lines 27744--27749 []\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 2529) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 27762--27765 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [425] [426] [427] [428] [429] Underfull \vbox (badness 3803) has occurred while \output is active [430] Underfull \hbox (badness 10000) in paragraph at lines 28162--28166 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [431] [432] Underfull \hbox (badness 10000) in paragraph at lines 28309--28312 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [433] Underfull \hbox (badness 7925) in paragraph at lines 28390--28394 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 28390--28394 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 28395--28404 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] Underfull \hbox (badness 2726) in paragraph at lines 29391--29394 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 1533) in paragraph at lines 31181--31184 []\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 [477] [478] [479] Underfull \hbox (badness 1163) in paragraph at lines 31344--31355 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 10000) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33029--33031 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33032--33036 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [506] [507] Underfull \vbox (badness 10000) has occurred while \output is active [508] [509] [510] [511] [512] [513] [514] [515] Underfull \hbox (badness 1655) in paragraph at lines 33626--33628 []\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 [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] Underfull \hbox (badness 2261) in paragraph at lines 34832--34837 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 10000) in paragraph at lines 35952--35963 \T1/zi4/m/n/10 / / docs . microsoft . com / en-[]us / cpp / c-[]language / pars ing-[]c-[]command-[]line-[]arguments ? [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 10000) in paragraph at lines 37483--37485 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [576] Underfull \vbox (badness 10000) has occurred while \output is active [577] [578] [579] [580] [581] [582] Underfull \hbox (badness 2913) in paragraph at lines 37903--37907 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [583] [584] [585] Underfull \hbox (badness 1072) in paragraph at lines 38149--38153 []\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 38154--38158 []\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/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', [586] Underfull \hbox (badness 10000) in paragraph at lines 38194--38200 []\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 38194--38200 \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 38194--38200 \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 Underfull \hbox (badness 3009) in paragraph at lines 38209--38216 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38209--38216 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38209--38216 \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 38209--38216 \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 [587] [588] [589] Underfull \hbox (badness 2644) in paragraph at lines 38444--38448 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [590] [591] [592] Underfull \hbox (badness 1142) in paragraph at lines 38597--38603 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] Underfull \hbox (badness 1158) in paragraph at lines 39914--39916 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 1137) in paragraph at lines 40505--40511 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails [623] Underfull \hbox (badness 4967) in paragraph at lines 40524--40529 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [624] [625] Underfull \hbox (badness 1616) in paragraph at lines 40644--40649 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 1472) in paragraph at lines 41191--41194 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [634] [635] [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] Underfull \hbox (badness 10000) in paragraph at lines 42117--42121 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4/ m/n/10 length(bin) > [649] [650] [651] [652] Underfull \hbox (badness 10000) in paragraph at lines 42368--42371 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [653] [654] [655] Underfull \hbox (badness 10000) in paragraph at lines 42552--42556 [][][]\T1/zi4/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [656] [657] [658] [659] [660] [661] [662] [663] [664] Underfull \hbox (badness 10000) in paragraph at lines 43191--43194 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [665] [666] [667] [668] [669] [670] Underfull \vbox (badness 10000) has occurred while \output is active [671] [672] [673] [674] [675] [676] [677] [678] Underfull \hbox (badness 1990) in paragraph at lines 44113--44121 []\T1/zi4/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 44113--44121 \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 [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] Underfull \hbox (badness 2452) in paragraph at lines 45082--45088 [][][]\T1/zi4/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 3668) in paragraph at lines 45480--45482 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [700] [701] Underfull \hbox (badness 2401) in paragraph at lines 45610--45614 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/n/10 options[][][]("w arn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [702] [703] [704] Underfull \hbox (badness 2111) in paragraph at lines 45818--45823 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/n/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [705] [706] [707] [708] Underfull \hbox (badness 4001) in paragraph at lines 46064--46066 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/n/10 https : / / developer . [709] [710] [711] [712] [713] [714] Underfull \hbox (badness 5417) in paragraph at lines 46429--46433 []\T1/zi4/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [715] Underfull \hbox (badness 10000) in paragraph at lines 46490--46494 []\T1/zi4/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [716]) (./compiler-pkg.tex Chapter 2. [717] [718] [719] [720]) (./datasets-pkg.tex Chapter 3. [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\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. [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803]) (./grDevices-pkg.tex [804] Chapter 4. [805] [806] [807] [808] [809] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/n/10 c(mi, ma, n.)[]\ T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] Underfull \hbox (badness 1424) in paragraph at lines 898--900 [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) an d []\T1/zi4/m/n/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i-fied as [820] [821] [822] [823] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\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 [824] [825] Underfull \hbox (badness 2512) in paragraph at lines 1311--1313 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/n/10 https : / / web . arc hive . org / web / 20190613001950 / http : / / efg2 . com / [826] [827] [828] [829] [830] Underfull \hbox (badness 1490) in paragraph at lines 1611--1616 \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 []\T 1/zi4/m/n/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [831] [832] [833] [834] [835] [836] [837] Underfull \hbox (badness 1325) in paragraph at lines 2038--2048 []\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 "pngalph a"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/1 0 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp32b"[]\T1/ptm/m/n/10 , [838] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [839] [840] [841] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [842] [843] [844] [845] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] Underfull \vbox (badness 3803) has occurred while \output is active [864] [865] [866] [867] Underfull \vbox (badness 3803) has occurred while \output is active [868] Underfull \hbox (badness 10000) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/zi4/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] Underfull \hbox (badness 1584) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 For type []\T1/zi4/m/n/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1/ zi4/m/n/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 4914--4921 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [883] [884] [885] [886] Underfull \hbox (badness 1377) in paragraph at lines 5220--5225 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [887] Underfull \hbox (badness 1418) in paragraph at lines 5296--5303 \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 "Helvet ica-Narrow"[]\T1/ptm/m/n/10 , [888] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [889] Underfull \hbox (badness 1377) in paragraph at lines 5425--5430 []\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 [890] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\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 [891] Underfull \vbox (badness 3803) has occurred while \output is active [892] Underfull \hbox (badness 2035) in paragraph at lines 5632--5641 []\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 5632--5641 \T1/ptm/m/n/10 vided: []\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-Na rrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/zi4/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/zi 4/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "URWBookman"[]\T1/ptm/m /n/10 , [893] [894] Underfull \hbox (badness 10000) in paragraph at lines 5700--5702 []\T1/zi4/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/z i4/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [895] [896] Underfull \hbox (badness 1546) in paragraph at lines 5844--5852 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi4 /m/n/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 title[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 bg[]\T1/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 , [897] [898] [899] [900] [901] [902] [903] [904] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/zi4/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [905] [906] Underfull \vbox (badness 3803) has occurred while \output is active [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [919] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [920] [921] [922] [923] [924] Underfull \hbox (badness 3780) in paragraph at lines 7630--7636 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/n /10 "AvantGarde"[]\T1/ptm/m/n/10 , [925] [926] [927] [928] [929] [930]) (./graphics-pkg.tex Chapter 5. [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] Overfull \hbox (12.71341pt too wide) in paragraph at lines 983--983 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 4634) in paragraph at lines 1357--1360 [][][]\T1/zi4/m/n/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready work s nowa-days with data.frames; [][][]\T1/zi4/m/n/10 boxplot.formula[][][][]\T1/p tm/m/n/10 , [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] Underfull \hbox (badness 1728) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [970] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \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 [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] Underfull \vbox (badness 10000) has occurred while \output is active [994] Underfull \vbox (badness 10000) has occurred while \output is active [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\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 [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 1107) in paragraph at lines 5081--5087 []\T1/ptm/m/n/10 is []\T1/zi4/m/n/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sca led to user co-or-di-nates. Note that []\T1/zi4/m/n/10 c([][]strwidth[][][](ch) , [1012] [1013] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [1014 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 Underfull \vbox (badness 10000) has occurred while \output is active [1015] [1016 ] [1017] [1018] Underfull \vbox (badness 3803) has occurred while \output is active [1019] [1020] [1021] [1022] [1023] [1024] [1025] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [1040 ] [1041] Underfull \vbox (badness 3803) has occurred while \output is active [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] Underfull \hbox (badness 4954) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /n/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 8938--8940 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/n/10 par (c("font.lab", "cex.lab", [1075] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1076] [1077] [1078] [1079]) (./grid-pkg.tex [1080] Chapter 6. [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 2680) in paragraph at lines 550--553 []\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-c u-la-tion of [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] Underfull \hbox (badness 4279) in paragraph at lines 1187--1196 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/n/10 pushViewport[][][][]\T1/p tm/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 seekViewpo rt[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 upViewport[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/n/10 unit[][][][]\T1/ptm/m/n/10 , [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \vbox (badness 10000) has occurred while \output is active [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\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 [1162] [1163] [1164] [1165] [1166] [1167] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 2142) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/n/10 gridGTreeCoords []\T1/ptm/m/n/1 0 a list of ei-ther []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1175] [1176] Underfull \hbox (badness 4699) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/zi4/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208]) (./methods-pkg.tex Chapter 7. [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] 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-ten ds []\T1/zi4/m/n/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/n/1 0 "package"[]\T1/ptm/m/n/10 , also of class [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] 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 can 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/10 it calls []\T1/zi4/m/n/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1237] [1238] [1239] Underfull \hbox (badness 2213) in paragraph at lines 2213--2218 []\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 = [1240] [1241] [1242] [1243] [1244] Underfull \hbox (badness 10000) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/zi4/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class [1245] [1246] Underfull \hbox (badness 1132) in paragraph at lines 2713--2717 []\T1/ptm/m/n/10 In []\T1/zi4/m/n/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi4 /m/n/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/n/10 package []\T1/ptm/m/n/10 sl ot of the re-turned re-sult is in [1247] Underfull \hbox (badness 1033) in paragraph at lines 2745--2750 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/n/10 removeGeneric []\T1/ptm/m/n/10 r e-moves the func-tion it-self; []\T1/zi4/m/n/10 removeMethods []\T1/ptm/m/n/10 re-stores the [1248] [1249] [1250] [1251] [1252] [1253] [1254] Underfull \hbox (badness 1102) in paragraph at lines 3302--3304 []\T1/zi4/m/n/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1255] [1256] [1257] [1258] [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 3641--3650 []\T1/ptm/m/n/10 The [1261] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = "numeric", [1262] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] Underfull \hbox (badness 1769) in paragraph at lines 4476--4482 []\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 4476--4482 []\T1/zi4/m/n/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [] [][]\T1/zi4/m/n/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion use d by [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] Underfull \vbox (badness 10000) has occurred while \output is active [1283] [1284] [1285] Underfull \hbox (badness 4036) in paragraph at lines 5445--5448 []\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 [1286] [1287] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1288] [1289] [1290] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\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 [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1675) in paragraph at lines 6459--6465 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/n/10 externalRef Method(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1300] [1301] [1302] [1303] Underfull \vbox (badness 10000) has occurred while \output is active [1304] [1305] [1306] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1307] [1308] [1309] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} [1310] Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\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 [1311] [1312] [1313] Underfull \hbox (badness 1286) in paragraph at lines 7492--7494 []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 .selectSuperClasses() []\T1/ptm/m/n/10 on ly, a [][][]\T1/zi4/m/n/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, t yp-i-cally [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\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., [1356] [1357] [1358] [1359]) (./parallel-pkg.tex [1360] 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/z i4/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1361] [1362] [1363] [1364] [1365] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] Underfull \hbox (badness 3386) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1383] [1384] [1385]) (./splines-pkg.tex [1386] 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 [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]) (./stats-pkg.tex Chapter 10. [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] Underfull \hbox (badness 1412) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 2503) in paragraph at lines 1369--1372 []\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 , [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 2503) in paragraph at lines 3530--3533 []\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 , [1459] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\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 = [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2556) in paragraph at lines 5424--5427 []\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 "fi lter"[]\T1/ptm/m/n/10 . For [1489] [1490] [1491] [1492] [1493] [1494] [1495] Underfull \hbox (badness 2503) in paragraph at lines 5838--5842 []\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 , [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 7081) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n 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 6636--6638 []\T1/zi4/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 10000) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \vbox (badness 10000) has occurred while \output is active [1544] [1545] [1546] [1547] [1548] Underfull \hbox (badness 2626) in paragraph at lines 9185--9188 []\T1/ptm/m/n/10 Either []\T1/zi4/m/n/10 "convolution" []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1549] [1550] Underfull \hbox (badness 2503) in paragraph at lines 9292--9296 []\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 , [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] [1574] [1575] [1576] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\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 11024--11027 []\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, [1577] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1578] [1579] [1580] [1581] [1582] [1583] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} [1592] [1593] Underfull \hbox (badness 1484) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/n/10 SSinit = [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1610] [1611] [1612] [1613] [1614] [1615] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1616] [1617] [1618] [1619] [1620] [1621] [1622] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1633] [1634] Underfull \hbox (badness 6412) in paragraph at lines 14660--14664 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/n/10 (surface = "inte rpolate", statistics = [1635] Underfull \hbox (badness 1199) in paragraph at lines 14667--14669 []\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 [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 2503) in paragraph at lines 15743--15747 []\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 , [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/n/ 10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 model.re sponse(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/n/10 model.offset []\T1/ ptm/m/n/10 sums any terms [1662] [1663] [1664] [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 1158) in paragraph at lines 17906--17909 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/n/10 nls []\T1 /ptm/m/n/10 as the data ar-gu-ment. The ac- [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] Underfull \vbox (badness 10000) has occurred while \output is active [1691] Underfull \vbox (badness 10000) has occurred while \output is active [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1377) in paragraph at lines 18933--18938 []\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 18938--18941 []\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 2343) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18951--18955 \T1/ptm/m/n/10 the 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 18959--18963 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/n/10 "BFGS"[]\T 1/ptm/m/n/10 , []\T1/zi4/m/n/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/1 0 "SANN" []\T1/ptm/m/n/10 meth-ods if [1706] [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19184--19184 []\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 19187--19187 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1710] [1711] [1712] [1713] [1714] [1715] [1716] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\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 [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/zi4/m/n/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 s distance", lty = cook.lty, col = cook.col, text.col [1726] [1727] [1728] [1729] [1730] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1731] [1732] [1733] [1734] [1735] [1736] Underfull \hbox (badness 2503) in paragraph at lines 20826--20829 []\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 , [1737] Underfull \hbox (badness 3919) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 "Comparison of Poisson [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\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/1 0 , [][][]\T1/zi4/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\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 [1779] [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 1436) in paragraph at lines 23714--23717 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/n/10 max(2, [1786] Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] Underfull \hbox (badness 1824) in paragraph at lines 24827--24833 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 are f irst re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1803] Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/n/10 y[j] = [1804] Underfull \vbox (badness 3803) has occurred while \output is active [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 2165) in paragraph at lines 25429--25434 []\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/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1813] [1814] [1815] [1816] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\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 25653--25657 []\T1/ptm/m/n/10 where []\T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 PP <- [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] [1841] Underfull \vbox (badness 10000) has occurred while \output is active [1842] [1843] Underfull \hbox (badness 3514) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1844] [1845] [1846] [1847] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27535--27535 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1848] Overfull \hbox (20.23795pt too wide) in paragraph at lines 27628--27628 []\T1/zi4/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (11.22874pt too wide) in paragraph at lines 27630--27630 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1849] [1850] [1851] Underfull \hbox (badness 3514) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1852] [1853] Underfull \hbox (badness 3514) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1854] Underfull \hbox (badness 3514) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1855] [1856] Underfull \hbox (badness 3514) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1857] [1858] Underfull \hbox (badness 6691) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] Underfull \hbox (badness 4024) in paragraph at lines 28633--28636 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] Underfull \hbox (badness 5431) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1877] [1878] [1879] Underfull \hbox (badness 5431) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1880] [1881] [1882] [1883] [1884] [1885] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\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 [1886] [1887] [1888] [1889] [1890] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 3557) in paragraph at lines 31217--31221 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/n/10 extendInt []\T1/ptm/m/n/10 to a non-[ ]\T1/zi4/m/n/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-rect []\T1/zi4/m/n/10 interval = [1910] [1911] [1912] Underfull \vbox (badness 10000) has occurred while \output is active [1913] [1914] [1915] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\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 [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\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 [1925] [1926] [1927] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32317--32317 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1928] [1929] [1930] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32478--32478 [] \T1/zi4/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1931] [1932] [1933] [1934] [1935]) (./stats4-pkg.tex [1936] Chapter 11. [1937] [1938] [1939] Underfull \vbox (badness 10000) has occurred while \output is active [1940] Underfull \vbox (badness 10000) has occurred while \output is active [1941] [1942] [1943] [1944] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1945] [1946] [1947]) (./tcltk-pkg.tex [1948] Chapter 12. [1949] [1950] [1951] [1952] [1953] [1954] [1955] Underfull \vbox (badness 10000) has occurred while \output is active [1956] Underfull \vbox (badness 10000) has occurred while \output is active [1957] Underfull \hbox (badness 1546) in paragraph at lines 666--673 []\T1/zi4/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1958] [1959] [1960] [1961] [1962] Underfull \vbox (badness 10000) has occurred while \output is active [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970]) (./tools-pkg.tex Chapter 13. [1971] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1972] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1973] [1974] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\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 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/n/10 bi bentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/n/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatIn Proceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatManual[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/n/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\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/zi 4/m/n/10 formatTechreport []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1977] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\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 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1990] Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\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 1217--1220 []\T1/zi4/m/n/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and [ ]\T1/zi4/m/n/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 2293) in paragraph at lines 1569--1571 []\T1/zi4/m/n/10 CRAN_memtest_notes() []\T1/ptm/m/n/10 is now dep-re-cated, wit h its func-tion-al-ity in-te-grated into that of Underfull \hbox (badness 10000) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/zi4/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1996] [1997] Underfull \hbox (badness 4096) in paragraph at lines 1714--1722 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1724--1726 []\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 [1998] [1999] [2000] [2001] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2002] [2003] [2004] [2005] [2006] Overfull \hbox (8.25941pt too wide) in paragraph at lines 2230--2230 [] \T1/zi4/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] [2007] [2008] [2009] Underfull \hbox (badness 4096) in paragraph at lines 2399--2407 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2010] [2011] [2012] [2013] [2014] [2015] [2016] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2893. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. [2017] [2018] [2019] [2020] [2021] Underfull \hbox (badness 1424) in paragraph at lines 3196--3198 []\T1/zi4/m/it/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2034] [2035] Underfull \hbox (badness 10000) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/it/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/it/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 1796) in paragraph at lines 4399--4404 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/it/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/it/10 type = = Underfull \hbox (badness 4699) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/zi4/m/it/10 msgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 1946) in paragraph at lines 4449--4453 []\T1/zi4/m/it/10 "--update"[]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m /n/10 4.2.0, []\T1/zi4/m/it/10 "--no-wrap" []\T1/ptm/m/n/10 is used when called from [2042] Underfull \hbox (badness 1838) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [2043] [2044] [2045] [2046] Underfull \hbox (badness 2197) in paragraph at lines 4750--4760 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/it/10 available.packages[][][][]\T1/ptm/m/n/10 : [2047] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\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 [2048] [2049] [2050] [2051]) (./utils-pkg.tex [2052] Chapter 14. [2053] 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 `[] \T1/zi4/m/it/10 insertions[]\T1/ptm/m/n/10 ', [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/it/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/it/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 726--732 []\T1/zi4/m/it/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2064] [2065] [2066] Underfull \hbox (badness 3861) in paragraph at lines 931--936 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/it/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/it/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2067] [2068] [2069] Underfull \hbox (badness 3323) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/zi4/m/it /10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m $\T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 2875) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 taken as [][][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex. max", 1) []\T1/ptm/m/n/10 which is []\T1/zi4/m/it/10 1 []\T1/ptm/m/n/10 typ-i-c ally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \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 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1371) in paragraph at lines 1638--1640 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2078] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1708. [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] Underfull \hbox (badness 2057) in paragraph at lines 2359--2361 []\T1/ptm/m/n/10 None for []\T1/zi4/m/it/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2089] [2090] [2091] [2092] [2093] [2094] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 6842) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/it/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2115] Underfull \hbox (badness 1430) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/it/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2116] Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/it/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/it/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 able []\T1/zi4/m/it/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2117] [2118] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/it/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2140] [2141] [2142] [2143] [2144] [2145] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 6502. 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See [2159] [2160] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\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 [2161] [2162] [2163] Underfull \hbox (badness 1325) in paragraph at lines 7150--7154 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/it/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2164] Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2165] Underfull \hbox (badness 3219) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/i t/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. 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The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/zi4/m/it/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/it/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] Underfull \hbox (badness 2469) in paragraph at lines 11663--11667 []\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 11663--11667 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . 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referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.roundX} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.default.stringsAsFactors} has been referenced b ut does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/ usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on refman.pdf (2415 pages, 6535325 bytes). Transcript written on refman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi @setfilename R-admin.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-admin.t2d/pdf/xtr/ R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/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] [14] [15] Chapter 3 [16] Underfull \hbox (badness 10000) in paragraph at lines 1433--1439 @textrm (@texttt https:// cran. r-project. org/ bin/ windows/ Rtools/ rt ools42/ rtools. html[]@textrm )[][]. [17] [18] Chapter 4 [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 1749--1759 @texttt org.R-project.R.fw.pkg[]@textrm , @texttt org.R-project.R.GUI.pkg[]@tex trm , @texttt org.r-project.x86_ Chapter 5 [22] Chapter 6 [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1895--1895 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2124--2132 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- Underfull \hbox (badness 10000) in paragraph at lines 2124--2132 @textrm pack-ages (@texttt https:// cran. r-project. org/ bin/ windows/ b ase/ howto-R-4. 2. html[]@textrm )[][] for [26] [27] [28] Overfull \hbox (78.17732pt too wide) in paragraph at lines 2344--2344 []@texttt ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm 64" CXXFLAGS=-O2[] [29] [30] [31] [32] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2661--2661 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [33] [34] [35] Chapter 8 [36] Chapter 9 [37] [38] [39] Appendix A [40] [41] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3303--3303 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [42] [43] [44] [45] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3607--3607 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-6.fc34.x86_6 4/jre[] [46] [47] [48] [49] [50] [51] [52] [53] Appendix B [54] [55] [56] [57] [58] [59] Appendix C [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4953--4953 []@texttt -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSER TIONS[] [64] [65] [66] Overfull \hbox (134.35066pt too wide) in paragraph at lines 5184--5184 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/pcre2-10.39-d arwin.17-x86_64.tar.xz[] Overfull \hbox (117.1046pt too wide) in paragraph at lines 5186--5186 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/xz-5.2.5-darw in.17-x86_64.tar.xz[] [67] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5300--5300 []@texttt curl -OL https://mac.r-project.org/tools/subversion-1.14.0-darwin15. 6.tar.gz[] Overfull \hbox (38.79282pt too wide) in paragraph at lines 5340--5341 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [68] Underfull \hbox (badness 10000) in paragraph at lines 5368--5372 []@textrm For In-tel Big Sur and later there is [][]@texttt https:// github. com/ fxcoudert/ Underfull \hbox (badness 10000) in paragraph at lines 5368--5372 @texttt gfortran-for-macOS/ releases/ download/ 11. 2-bigsur-intel/ gfortr an-Intel-11. Underfull \hbox (badness 10000) in paragraph at lines 5368--5372 @texttt gfortran-for-macOS/ releases/ download/ 12. 1-monterey/ gfortran-I ntel-12. [69] Overfull \hbox (83.92601pt too wide) in paragraph at lines 5433--5433 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$LOCAL/lib/pkgconfig:/ usr/lib/pkgconfig[] [70] Overfull \hbox (72.77429pt too wide) in paragraph at lines 5539--5539 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [71] [72] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5707--5707 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/termurin-17.jdk/Contents /Home[] Underfull \hbox (badness 10000) in paragraph at lines 5716--5725 @texttt downloads/ zulu-community/ ? os=macos& architecture=arm-64-bit& pa ckage=jdk[][][] @textrm and [73] [74] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5836--5836 []@texttt install_name_tool -change /usr/local/gfortran/lib/libgfortran.5.dyli b \[] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5854--5854 []@texttt PKG_LIBS = /usr/local/llvm/lib/libc++.a /usr/local/llvm/lib/libc++ab i.a[] Underfull \hbox (badness 6842) in paragraph at lines 5856--5862 @textrm in @texttt src/Makevars[]@textrm . It would also be pos-si-ble to stat ic link the For- Underfull \hbox (badness 10000) in paragraph at lines 5856--5862 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and [75] Overfull \hbox (43.6852pt too wide) in paragraph at lines 6042--6042 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [76] (Function and variable index) [77] No file R-admin.vrs. (Concept index) [78] No file R-admin.cps. (Environment variable index) [79] No file R-admin.ens. [80] ) (see the transcript file for additional information) pdfTeX warning (dest): name{\040Tcl/Tk\040headers\040and\040libraries} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (83 pages, 476951 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-admin.t2d/pdf/xtr/ R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-admin.toc [-1] [-2]) [-3] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-admin.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-admin.toc) Chapter 1 (/build/reproducible-path/r-base-4.2.2.20221110/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] [14] [15] Chapter 3 [16] Underfull \hbox (badness 10000) in paragraph at lines 1433--1439 @textrm (@texttt https:// cran. r-project. org/ bin/ windows/ Rtools/ rt ools42/ rtools. html[]@textrm )[][]. [17] [18] Chapter 4 [19] [20] [21] Underfull \hbox (badness 10000) in paragraph at lines 1749--1759 @texttt org.R-project.R.fw.pkg[]@textrm , @texttt org.R-project.R.GUI.pkg[]@tex trm , @texttt org.r-project.x86_ Chapter 5 [22] Chapter 6 [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1895--1895 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2124--2132 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- Underfull \hbox (badness 10000) in paragraph at lines 2124--2132 @textrm pack-ages (@texttt https:// cran. r-project. org/ bin/ windows/ b ase/ howto-R-4. 2. html[]@textrm )[][] for [26] [27] [28] Overfull \hbox (78.17732pt too wide) in paragraph at lines 2344--2344 []@texttt ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm 64" CXXFLAGS=-O2[] [29] [30] [31] [32] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2661--2661 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [33] [34] [35] Chapter 8 [36] Chapter 9 [37] [38] [39] Appendix A [40] [41] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3303--3303 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [42] [43] [44] [45] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3607--3607 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-6.fc34.x86_6 4/jre[] [46] [47] [48] [49] [50] [51] [52] [53] Appendix B [54] [55] [56] [57] [58] [59] Appendix C [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4953--4953 []@texttt -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSER TIONS[] [64] [65] [66] Overfull \hbox (134.35066pt too wide) in paragraph at lines 5184--5184 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/pcre2-10.39-d arwin.17-x86_64.tar.xz[] Overfull \hbox (117.1046pt too wide) in paragraph at lines 5186--5186 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/xz-5.2.5-darw in.17-x86_64.tar.xz[] l.5233: Undefined cross reference ` Tcl/Tk headers and libraries-snt'. l.5233: Undefined cross reference ` Tcl/Tk headers and libraries-snt'. l.5233: Undefined cross reference ` Tcl/Tk headers and libraries-pg'. [67] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5300--5300 []@texttt curl -OL https://mac.r-project.org/tools/subversion-1.14.0-darwin15. 6.tar.gz[] Overfull \hbox (38.79282pt too wide) in paragraph at lines 5340--5341 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [68] Underfull \hbox (badness 10000) in paragraph at lines 5368--5372 []@textrm For In-tel Big Sur and later there is [][]@texttt https:// github. com/ fxcoudert/ Underfull \hbox (badness 10000) in paragraph at lines 5368--5372 @texttt gfortran-for-macOS/ releases/ download/ 11. 2-bigsur-intel/ gfortr an-Intel-11. Underfull \hbox (badness 10000) in paragraph at lines 5368--5372 @texttt gfortran-for-macOS/ releases/ download/ 12. 1-monterey/ gfortran-I ntel-12. [69] Overfull \hbox (83.92601pt too wide) in paragraph at lines 5433--5433 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$LOCAL/lib/pkgconfig:/ usr/lib/pkgconfig[] [70] Overfull \hbox (72.77429pt too wide) in paragraph at lines 5539--5539 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [71] [72] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5707--5707 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/termurin-17.jdk/Contents /Home[] Underfull \hbox (badness 10000) in paragraph at lines 5716--5725 @texttt downloads/ zulu-community/ ? os=macos& architecture=arm-64-bit& pa ckage=jdk[][][] @textrm and [73] [74] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5836--5836 []@texttt install_name_tool -change /usr/local/gfortran/lib/libgfortran.5.dyli b \[] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5854--5854 []@texttt PKG_LIBS = /usr/local/llvm/lib/libc++.a /usr/local/llvm/lib/libc++ab i.a[] Underfull \hbox (badness 6842) in paragraph at lines 5856--5862 @textrm in @texttt src/Makevars[]@textrm . It would also be pos-si-ble to stat ic link the For- Underfull \hbox (badness 10000) in paragraph at lines 5856--5862 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and [75] Overfull \hbox (43.6852pt too wide) in paragraph at lines 6042--6042 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [76] (Function and variable index) [77] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-admin.vrs) (Concept index) [78] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-admin.cps) (Environment variable index) [79] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-admin.ens) [80] ) (see the transcript file for additional information) pdfTeX warning (dest): name{\040Tcl/Tk\040headers\040and\040libraries} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (85 pages, 521065 bytes). Transcript written on R-admin.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi @setfilename R-data.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.t2d/pdf/xtr/R -data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) [1] Chapter 1 [2] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 434--437 []@textrm Function @texttt write.matrix[] @textrm in pack-age [][]@textbf MASS @textrm (@texttt https:// CRAN. R-project. org/ Underfull \hbox (badness 10000) in paragraph at lines 445--449 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ [6] Chapter 2 [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1219--1231 @textrm (@texttt https:// www. ibm. com/ software/ data/ informix/ []@te xtrm )[][]; [][]Oracle (@texttt https:// www. oracle. [17] [18] [19] [20] [21] [22] Chapter 5 [23] Underfull \hbox (badness 10000) in paragraph at lines 1793--1799 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[][], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [24] Chapter 7 [25] [26] [27] [28] [29] Chapter 8 [30] Chapter 9 [31] Appendix A [32] (Function and variable index) [33] No file R-data.vrs. (Concept index) [34] No file R-data.cps. [35] ) (see the transcript file for additional information) Output written on R-data.pdf (38 pages, 269305 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.t2d/pdf/xtr/R -data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.toc [-1]) [-2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.toc) (Acknowledgements) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.aux) [1] Chapter 1 [2] Writing index file R-data.cp [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 434--437 []@textrm Function @texttt write.matrix[] @textrm in pack-age [][]@textbf MASS @textrm (@texttt https:// CRAN. R-project. org/ Underfull \hbox (badness 10000) in paragraph at lines 445--449 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ [6] Chapter 2 [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1219--1231 @textrm (@texttt https:// www. ibm. com/ software/ data/ informix/ []@te xtrm )[][]; [][]Oracle (@texttt https:// www. oracle. [17] [18] [19] [20] [21] [22] Chapter 5 [23] Underfull \hbox (badness 10000) in paragraph at lines 1793--1799 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[][], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [24] Chapter 7 [25] [26] [27] [28] [29] Chapter 8 [30] Chapter 9 [31] Appendix A [32] (Function and variable index) [33] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.vrs [34]) (Concept index) [35] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.cps) [36] [37] ) (see the transcript file for additional information) Output written on R-data.pdf (41 pages, 309060 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.t2d/pdf/xtr/R -data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.toc [-1]) [-2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.toc) (Acknowledgements) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.aux) [1] Chapter 1 [2] Writing index file R-data.cp [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 434--437 []@textrm Function @texttt write.matrix[] @textrm in pack-age [][]@textbf MASS @textrm (@texttt https:// CRAN. R-project. org/ Underfull \hbox (badness 10000) in paragraph at lines 445--449 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ [6] Chapter 2 [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1219--1231 @textrm (@texttt https:// www. ibm. com/ software/ data/ informix/ []@te xtrm )[][]; [][]Oracle (@texttt https:// www. oracle. [17] [18] [19] [20] [21] [22] Chapter 5 [23] Underfull \hbox (badness 10000) in paragraph at lines 1793--1799 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[][], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [24] Chapter 7 [25] [26] [27] [28] [29] Chapter 8 [30] Chapter 9 [31] Appendix A [32] (Function and variable index) [33] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.vrs [34]) (Concept index) [35] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-data.cps) [36] [37] ) (see the transcript file for additional information) Output written on R-data.pdf (41 pages, 309064 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi @setfilename R-exts.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.t2d/pdf/xtr/R -exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/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 500--503 []@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] Overfull \hbox (95.42339pt too wide) in paragraph at lines 1539--1539 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 1540--1540 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 1541--1541 [] @texttt res[z] <- file.size(file.path(lib, pkg_name, "data", "Rdata. rdb"))[] [20] Underfull \hbox (badness 10000) in paragraph at lines 1572--1579 @texttt org/ package=amap[]@textrm )[][]), Python or Tcl ([][]@textbf Simile @ textrm (@texttt https:// CRAN. R-project. org/ [21] [22] [23] [24] [25] Overfull \hbox (32.18782pt too wide) in paragraph at lines 1964--1964 []@texttt $ pkg-config --exists 'libtiff-4 >= 4.1.0' --print-errors # check th e status[] [26] [27] [28] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2201--2201 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [29] [30] [31] [32] [33] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2603--2603 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2605--2605 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [34] [35] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2743--2743 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [36] [37] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2924--2924 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [38] Underfull \hbox (badness 7221) in paragraph at lines 2947--2953 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [39] [40] Overfull \hbox (43.6852pt too wide) in paragraph at lines 3138--3138 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] Overfull \hbox (20.69044pt too wide) in paragraph at lines 4537--4537 []@texttt importFrom("stats", approx, optim, pchisq, predict, qchisq, qnorm, s pline)[] [58] [59] [60] Overfull \hbox (81.29893pt too wide) in paragraph at lines 4762--4762 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] [61] Overfull \hbox (59.61772pt too wide) in paragraph at lines 4781--4781 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [62] [63] [64] [65] [66] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5213--5213 []@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19 20 21)[] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5223--5223 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5225--5225 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 5226--5226 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [67] Overfull \hbox (76.86378pt too wide) in paragraph at lines 5241--5241 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [68] [69] [70] [71] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5592--5592 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 5755--5758 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [74] [75] Overfull \hbox (19.3769pt too wide) in paragraph at lines 5848--5848 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [76] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5979--5979 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [77] Overfull \hbox (13.62822pt too wide) in paragraph at lines 6033--6033 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [78] Underfull \hbox (badness 10000) in paragraph at lines 6104--6105 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [79] [80] [81] Overfull \hbox (19.3769pt too wide) in paragraph at lines 6345--6345 []@texttt #define dngettext(pkg, String, StringP, N) (N == 1 ? String : String P)[] [82] [83] [84] Chapter 2 [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 7607--7614 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [99] [100] [101] [102] [103] [104] Chapter 3 [105] [106] [107] [108] [109] [110] Overfull \hbox (20.69044pt too wide) in paragraph at lines 8531--8531 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [111] [112] Chapter 4 [113] [114] [115] [116] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [117] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8937--8937 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [118] Overfull \hbox (20.53261pt too wide) in paragraph at lines 9041--9041 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 9071--9080 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 9340--9352 @texttt controlling-code-generation[][][]@textrm , [][]@texttt https:// clang. llvm. org/ docs/ AddressSanitizer. Overfull \hbox (48.90796pt too wide) in paragraph at lines 9356--9357 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [123] [124] Overfull \hbox (78.17732pt too wide) in paragraph at lines 9495--9495 []@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 9528--9530 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [125] Underfull \hbox (badness 10000) in paragraph at lines 9616--9620 [][]@texttt https:// blog. llvm. org/ 2011/ 05/ what-every-c-programmer-s hould-know. html[][][] [126] Overfull \hbox (2.03816pt too wide) in paragraph at lines 9651--9655 []@textrm See [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc-10. 1. 0/ gcc/ Static-Analyzer-Options. 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"better safe than s orry"[] [172] [173] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13306--13306 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [174] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13311--13311 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13366--13366 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13379--13379 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [175] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13478--13478 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [176] [177] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13627--13627 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [178] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13717--13717 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [179] [180] Overfull \hbox (72.42863pt too wide) in paragraph at lines 13812--13812 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [181] [182] [183] [184] [185] [186] [187] [188] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14547--14547 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 [][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d ocumentation/ Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] Underfull \hbox (badness 10000) in paragraph at lines 15293--15297 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [199] Warning: unbalanced parentheses in @def... [200] [201] Overfull \hbox (26.43913pt too wide) in paragraph at lines 15516--15516 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [202] [203] [204] [205] [206] Chapter 7 [207] [208] Chapter 8 [209] [210] [211] Overfull \hbox (43.6852pt too wide) in paragraph at lines 16276--16276 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [212] Overfull \hbox (20.69044pt too wide) in paragraph at lines 16319--16319 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 16334--16334 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 10000) in paragraph at lines 16984--16988 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [222] No file R-exts.vrs. (Concept index) [223] No file R-exts.cps. [224] ) (see the transcript file for additional information) Output written on R-exts.pdf (227 pages, 974302 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.t2d/pdf/xtr/R -exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.toc) (Acknowledgements) (/build/reproducible-path/r-base-4.2.2.20221110/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 500--503 []@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] Overfull \hbox (95.42339pt too wide) in paragraph at lines 1539--1539 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 1540--1540 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 1541--1541 [] @texttt res[z] <- file.size(file.path(lib, pkg_name, "data", "Rdata. rdb"))[] [20] Underfull \hbox (badness 10000) in paragraph at lines 1572--1579 @texttt org/ package=amap[]@textrm )[][]), Python or Tcl ([][]@textbf Simile @ textrm (@texttt https:// CRAN. R-project. org/ [21] [22] [23] [24] [25] Overfull \hbox (32.18782pt too wide) in paragraph at lines 1964--1964 []@texttt $ pkg-config --exists 'libtiff-4 >= 4.1.0' --print-errors # check th e status[] [26] [27] [28] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2201--2201 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [29] [30] [31] [32] [33] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2603--2603 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2605--2605 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [34] [35] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2743--2743 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [36] [37] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2924--2924 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [38] Underfull \hbox (badness 7221) in paragraph at lines 2947--2953 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [39] [40] Overfull \hbox (43.6852pt too wide) in paragraph at lines 3138--3138 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] Overfull \hbox (20.69044pt too wide) in paragraph at lines 4537--4537 []@texttt importFrom("stats", approx, optim, pchisq, predict, qchisq, qnorm, s pline)[] [58] [59] [60] Overfull \hbox (81.29893pt too wide) in paragraph at lines 4762--4762 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (59.61772pt too wide) in paragraph at lines 4781--4781 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [61] [62] [63] [64] [65] [66] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5213--5213 []@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19 20 21)[] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5223--5223 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5225--5225 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 5226--5226 [] @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 5241--5241 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [67] [68] [69] [70] [71] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5592--5592 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 5755--5758 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [74] [75] Overfull \hbox (19.3769pt too wide) in paragraph at lines 5848--5848 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [76] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5979--5979 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [77] Overfull \hbox (13.62822pt too wide) in paragraph at lines 6033--6033 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [78] Underfull \hbox (badness 10000) in paragraph at lines 6104--6105 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [79] [80] [81] Overfull \hbox (19.3769pt too wide) in paragraph at lines 6345--6345 []@texttt #define dngettext(pkg, String, StringP, N) (N == 1 ? String : String P)[] [82] [83] Chapter 2 [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 7607--7614 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [99] [100] [101] [102] [103] [104] Chapter 3 [105] [106] [107] [108] [109] [110] Overfull \hbox (20.69044pt too wide) in paragraph at lines 8531--8531 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [111] [112] Chapter 4 [113] [114] [115] [116] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [117] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8937--8937 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [118] Overfull \hbox (20.53261pt too wide) in paragraph at lines 9041--9041 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 9071--9080 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 9340--9352 @texttt controlling-code-generation[][][]@textrm , [][]@texttt https:// clang. llvm. org/ docs/ AddressSanitizer. Overfull \hbox (48.90796pt too wide) in paragraph at lines 9356--9357 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [123] [124] Overfull \hbox (78.17732pt too wide) in paragraph at lines 9495--9495 []@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 9528--9530 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [125] Underfull \hbox (badness 10000) in paragraph at lines 9616--9620 [][]@texttt https:// blog. llvm. org/ 2011/ 05/ what-every-c-programmer-s hould-know. html[][][] [126] Overfull \hbox (2.03816pt too wide) in paragraph at lines 9651--9655 []@textrm See [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc-10. 1. 0/ gcc/ Static-Analyzer-Options. Overfull \hbox (72.42863pt too wide) in paragraph at lines 9674--9674 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [127] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9719--9719 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9722--9722 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [128] Overfull \hbox (26.43913pt too wide) in paragraph at lines 9801--9801 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [129] [130] [131] Underfull \hbox (badness 10000) in paragraph at lines 10044--10046 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [132] Overfull \hbox (124.16682pt too wide) in paragraph at lines 10101--10101 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (147.16158pt too wide) in paragraph at lines 10120--10120 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (141.41289pt too wide) in paragraph at lines 10131--10131 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] [133] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10151--10151 [] @tex ttt 1[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10160--10160 [] @tex ttt 1[] Overfull \hbox (43.6852pt too wide) in paragraph at lines 10161--10161 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] Overfull \hbox (30.87428pt too wide) in paragraph at lines 10951--10951 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 11015--11015 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [145] [146] Overfull \hbox (60.93126pt too wide) in paragraph at lines 11179--11179 [] @texttt na_omit_xts_func fun = (na_omit_xts_func) R_GetCCallable("xts", "n a_omit_xts");[] [147] [148] [149] [150] [151] [152] Overfull \hbox (37.93651pt too wide) in paragraph at lines 11611--11611 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12471--12471 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [164] Underfull \hbox (badness 10000) in paragraph at lines 12621--12625 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [165] [166] [167] [168] [169] [170] [171] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13182--13182 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [172] [173] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13306--13306 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [174] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13311--13311 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13366--13366 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13379--13379 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [175] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13478--13478 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [176] [177] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13627--13627 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [178] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13717--13717 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [179] [180] Overfull \hbox (72.42863pt too wide) in paragraph at lines 13812--13812 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [181] [182] [183] [184] [185] [186] [187] [188] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14547--14547 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 [][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d ocumentation/ Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] Underfull \hbox (badness 10000) in paragraph at lines 15293--15297 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [199] Warning: unbalanced parentheses in @def... [200] [201] Overfull \hbox (26.43913pt too wide) in paragraph at lines 15516--15516 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [202] [203] [204] [205] [206] Chapter 7 [207] [208] Chapter 8 [209] [210] [211] Overfull \hbox (43.6852pt too wide) in paragraph at lines 16276--16276 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [212] Overfull \hbox (20.69044pt too wide) in paragraph at lines 16319--16319 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 16334--16334 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 10000) in paragraph at lines 16984--16988 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [222] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.vrs [223] [224] [225] [226]) (Concept index) [227] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.cps [228]) [229] ) (see the transcript file for additional information) Output written on R-exts.pdf (236 pages, 1051063 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.t2d/pdf/xtr/R -exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.toc) (Acknowledgements) (/build/reproducible-path/r-base-4.2.2.20221110/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 500--503 []@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] Overfull \hbox (95.42339pt too wide) in paragraph at lines 1539--1539 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 1540--1540 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 1541--1541 [] @texttt res[z] <- file.size(file.path(lib, pkg_name, "data", "Rdata. rdb"))[] [20] Underfull \hbox (badness 10000) in paragraph at lines 1572--1579 @texttt org/ package=amap[]@textrm )[][]), Python or Tcl ([][]@textbf Simile @ textrm (@texttt https:// CRAN. R-project. org/ [21] [22] [23] [24] [25] Overfull \hbox (32.18782pt too wide) in paragraph at lines 1964--1964 []@texttt $ pkg-config --exists 'libtiff-4 >= 4.1.0' --print-errors # check th e status[] [26] [27] [28] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2201--2201 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [29] [30] [31] [32] [33] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2603--2603 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2605--2605 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [34] [35] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2743--2743 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [36] [37] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2924--2924 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [38] Underfull \hbox (badness 7221) in paragraph at lines 2947--2953 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [39] [40] Overfull \hbox (43.6852pt too wide) in paragraph at lines 3138--3138 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] Overfull \hbox (20.69044pt too wide) in paragraph at lines 4537--4537 []@texttt importFrom("stats", approx, optim, pchisq, predict, qchisq, qnorm, s pline)[] [58] [59] [60] Overfull \hbox (81.29893pt too wide) in paragraph at lines 4762--4762 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (59.61772pt too wide) in paragraph at lines 4781--4781 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [61] [62] [63] [64] [65] [66] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5213--5213 []@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19 20 21)[] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5223--5223 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5225--5225 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 5226--5226 [] @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 5241--5241 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [67] [68] [69] [70] [71] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5592--5592 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 5755--5758 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [74] [75] Overfull \hbox (19.3769pt too wide) in paragraph at lines 5848--5848 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [76] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5979--5979 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [77] Overfull \hbox (13.62822pt too wide) in paragraph at lines 6033--6033 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [78] Underfull \hbox (badness 10000) in paragraph at lines 6104--6105 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [79] [80] [81] Overfull \hbox (19.3769pt too wide) in paragraph at lines 6345--6345 []@texttt #define dngettext(pkg, String, StringP, N) (N == 1 ? String : String P)[] [82] [83] Chapter 2 [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 7607--7614 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [99] [100] [101] [102] [103] [104] Chapter 3 [105] [106] [107] [108] [109] [110] Overfull \hbox (20.69044pt too wide) in paragraph at lines 8531--8531 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [111] [112] Chapter 4 [113] [114] [115] [116] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [117] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8937--8937 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [118] Overfull \hbox (20.53261pt too wide) in paragraph at lines 9041--9041 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 9071--9080 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 9340--9352 @texttt controlling-code-generation[][][]@textrm , [][]@texttt https:// clang. llvm. org/ docs/ AddressSanitizer. Overfull \hbox (48.90796pt too wide) in paragraph at lines 9356--9357 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [123] [124] Overfull \hbox (78.17732pt too wide) in paragraph at lines 9495--9495 []@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 9528--9530 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [125] Underfull \hbox (badness 10000) in paragraph at lines 9616--9620 [][]@texttt https:// blog. llvm. org/ 2011/ 05/ what-every-c-programmer-s hould-know. html[][][] [126] Overfull \hbox (2.03816pt too wide) in paragraph at lines 9651--9655 []@textrm See [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc-10. 1. 0/ gcc/ Static-Analyzer-Options. 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"better safe than s orry"[] [172] [173] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13306--13306 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [174] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13311--13311 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13366--13366 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13379--13379 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [175] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13478--13478 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [176] [177] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13627--13627 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [178] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13717--13717 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [179] [180] Overfull \hbox (72.42863pt too wide) in paragraph at lines 13812--13812 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [181] [182] [183] [184] [185] [186] [187] [188] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14547--14547 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 [][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d ocumentation/ Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14565--14570 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] Underfull \hbox (badness 10000) in paragraph at lines 15293--15297 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [199] Warning: unbalanced parentheses in @def... [200] [201] Overfull \hbox (26.43913pt too wide) in paragraph at lines 15516--15516 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [202] [203] [204] [205] [206] Chapter 7 [207] [208] Chapter 8 [209] [210] [211] Overfull \hbox (43.6852pt too wide) in paragraph at lines 16276--16276 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [212] Overfull \hbox (20.69044pt too wide) in paragraph at lines 16319--16319 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 16334--16334 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 10000) in paragraph at lines 16984--16988 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [222] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.vrs [223] [224] [225] [226]) (Concept index) [227] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-exts.cps [228]) [229] ) (see the transcript file for additional information) Output written on R-exts.pdf (236 pages, 1051008 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi @setfilename R-FAQ.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-FAQ.t2d/pdf/xtr/R- FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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] Underfull \hbox (badness 10000) in paragraph at lines 292--314 @textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd . debian. org/ build. php? & pkg=r-base[][][]@textrm ), [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 641--644 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 641--644 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 10000) in paragraph at lines 641--644 [][]@texttt https:// master. bioconductor. org/ help/ publications/ book s/ [7] Underfull \hbox (badness 10000) in paragraph at lines 668--673 @textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/ 10. 1080/ 10618600. 1996. [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 10000) in paragraph at lines 1538--1541 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1538--1541 @texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia l-ized ver-sions of Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] Underfull \hbox (badness 10000) in paragraph at lines 3135--3149 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [40] [41] [42] Chapter 8 [43] Chapter 9 [44] [45] [46] Chapter 10 [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (50 pages, 353798 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-FAQ.t2d/pdf/xtr/R- FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-FAQ.toc ) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-FAQ.toc) Chapter 1 (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] Underfull \hbox (badness 10000) in paragraph at lines 292--314 @textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd . debian. org/ build. php? & pkg=r-base[][][]@textrm ), [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 641--644 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 641--644 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 10000) in paragraph at lines 641--644 [][]@texttt https:// master. bioconductor. org/ help/ publications/ book s/ [7] Underfull \hbox (badness 10000) in paragraph at lines 668--673 @textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/ 10. 1080/ 10618600. 1996. [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 10000) in paragraph at lines 1538--1541 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1538--1541 @texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia l-ized ver-sions of Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] Underfull \hbox (badness 10000) in paragraph at lines 3135--3149 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [40] [41] [42] Chapter 8 [43] Chapter 9 [44] [45] [46] Chapter 10 [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 370129 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi @setfilename R-intro.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.t2d/pdf/xtr/ R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] 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] Underfull \hbox (badness 10000) in paragraph at lines 4842--4844 @texttt logit[]@textrm , @texttt probit[]@textrm , @texttt cloglog[]@textrm , @texttt identity[]@textrm , [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5257--5267 [][]@textbf Mixed mod-els. @textrm The rec-om-mended [][]@textbf nlme @textrm (@texttt https:// CRAN. R-project. org/ [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5737--5737 []@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 6443--6448 []@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 6644--6649 []@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, 574905 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.t2d/pdf/xtr/ R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.toc) (Preface) (/build/reproducible-path/r-base-4.2.2.20221110/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] Underfull \hbox (badness 10000) in paragraph at lines 4842--4844 @texttt logit[]@textrm , @texttt probit[]@textrm , @texttt cloglog[]@textrm , @texttt identity[]@textrm , [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5257--5267 [][]@textbf Mixed mod-els. @textrm The rec-om-mended [][]@textbf nlme @textrm (@texttt https:// CRAN. R-project. org/ [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5737--5737 []@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 6443--6448 []@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 6644--6649 []@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] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.vrs [102] [103]) Appendix E [104] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.cps [105]) Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 631967 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.t2d/pdf/xtr/ R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.toc) (Preface) (/build/reproducible-path/r-base-4.2.2.20221110/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] Underfull \hbox (badness 10000) in paragraph at lines 4842--4844 @texttt logit[]@textrm , @texttt probit[]@textrm , @texttt cloglog[]@textrm , @texttt identity[]@textrm , [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5257--5267 [][]@textbf Mixed mod-els. @textrm The rec-om-mended [][]@textbf nlme @textrm (@texttt https:// CRAN. R-project. org/ [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5737--5737 []@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 6443--6448 []@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 6644--6649 []@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] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.vrs [102] [103]) Appendix E [104] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-intro.cps [105]) Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 632031 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi @setfilename R-ints.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.t2d/pdf/xtr/R -ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/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 1501--1501 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1502--1502 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1503--1503 [] @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 1504--1504 [] @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 2022--2022 [] @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] [48] Chapter 7 [49] Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [50] Overfull \hbox (16.81319pt too wide) in paragraph at lines 3819--3823 []@textrm The de-fault path for a per-sonal li-brary di-rec-tory is set as @te xttt ~/Library/R/arch/x.y/library[]@textrm . Chapter 8 [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[][] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4629--4629 []@texttt _R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,abort,ve rbose[] [64] Chapter 9 [65] [66] Chapter 10 [67] Chapter 11 [68] Chapter 12 [69] [70] (Function and variable index) [71] [72] No file R-ints.vrs. (Concept index) [73] No file R-ints.cps. [74] ) (see the transcript file for additional information) Output written on R-ints.pdf (77 pages, 416685 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.t2d/pdf/xtr/R -ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.toc [-1] [-2]) [-3] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.toc) Chapter 1 (/build/reproducible-path/r-base-4.2.2.20221110/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 1501--1501 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1502--1502 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1503--1503 [] @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 1504--1504 [] @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 2022--2022 [] @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] [48] Chapter 7 [49] Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [50] Overfull \hbox (16.81319pt too wide) in paragraph at lines 3819--3823 []@textrm The de-fault path for a per-sonal li-brary di-rec-tory is set as @te xttt ~/Library/R/arch/x.y/library[]@textrm . Chapter 8 [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[][] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4629--4629 []@texttt _R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,abort,ve rbose[] [64] Chapter 9 [65] [66] Chapter 10 [67] Chapter 11 [68] Chapter 12 [69] [70] (Function and variable index) [71] [72] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.vrs [73] [74]) (Concept index) [75] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.cps) [76] ) (see the transcript file for additional information) Output written on R-ints.pdf (81 pages, 469124 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.t2d/pdf/xtr/R -ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.toc [-1] [-2]) [-3] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.toc) Chapter 1 (/build/reproducible-path/r-base-4.2.2.20221110/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 1501--1501 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1502--1502 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1503--1503 [] @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 1504--1504 [] @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 2022--2022 [] @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] [48] Chapter 7 [49] Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [50] Overfull \hbox (16.81319pt too wide) in paragraph at lines 3819--3823 []@textrm The de-fault path for a per-sonal li-brary di-rec-tory is set as @te xttt ~/Library/R/arch/x.y/library[]@textrm . Chapter 8 [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[][] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4139--4147 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4629--4629 []@texttt _R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,abort,ve rbose[] [64] Chapter 9 [65] [66] Chapter 10 [67] Chapter 11 [68] Chapter 12 [69] [70] (Function and variable index) [71] [72] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.vrs [73] [74]) (Concept index) [75] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-ints.cps) [76] ) (see the transcript file for additional information) Output written on R-ints.pdf (81 pages, 469127 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi @setfilename R-lang.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.t2d/pdf/xtr/R -lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/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] Chapter 5 [28] [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, 330831 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.t2d/pdf/xtr/R -lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.toc [-1] [-2]) [-3] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.toc) Chapter 1 (/build/reproducible-path/r-base-4.2.2.20221110/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] Chapter 5 [28] [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] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.vrs [60]) (Concept Index) [61] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.cps) [62] Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 380218 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.t2d/pdf/xtr/R -lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2021-04-25.21]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.toc [-1] [-2]) [-3] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.toc) (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.toc) Chapter 1 (/build/reproducible-path/r-base-4.2.2.20221110/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] Chapter 5 [28] [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] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.vrs [60]) (Concept Index) [61] (/build/reproducible-path/r-base-4.2.2.20221110/doc/manual/R-lang.cps) [62] Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 380214 bytes). Transcript written on R-lang.log. make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' /usr/bin/make -k pdf make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' PDF/LaTeX documentation: full reference index ... 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Tilde-expansion is done: see [217] Underfull \hbox (badness 1490) in paragraph at lines 14169--14172 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [218] Underfull \hbox (badness 1565) in paragraph at lines 14251--14255 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] []\T1/ptm/m/n/10 to find out about sym- bolic links, [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 file.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.files[][][] []\T1/ptm/m/n/10 , and [219] Underfull \hbox (badness 4927) in paragraph at lines 14302--14304 []\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 []\T1/zi4/m/n/10 fsep = [220] Underfull \hbox (badness 3148) in paragraph at lines 14404--14409 [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.fi les[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 help[][][][]\T1/ptm/m/n/10 ; [ ][][]\T1/zi4/m/n/10 RShowDoc[][][] []\T1/ptm/m/n/10 call []\T1/zi4/m/n/10 file. show() []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 type = "text"[]\T1/ptm/m/n/10 . Co n-sider [221] Underfull \hbox (badness 1466) in paragraph at lines 14451--14454 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [222] [223] Underfull \hbox (badness 10000) in paragraph at lines 14582--14586 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\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 14593--14596 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [224] [225] [226] [227] [228] Underfull \hbox (badness 3965) in paragraph at lines 14890--14894 []\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, [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 4429) in paragraph at lines 15679--15682 []\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 [241] [242] Underfull \hbox (badness 10000) in paragraph at lines 15785--15787 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [243] Underfull \hbox (badness 2035) in paragraph at lines 15858--15862 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 2452) in paragraph at lines 16471--16475 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment 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 16471--16475 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s 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 [254] [255] Underfull \hbox (badness 1092) in paragraph at lines 16644--16649 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [256] [257] [258] [259] Underfull \hbox (badness 6741) in paragraph at lines 16897--16901 \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/pt m/m/n/10 , [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \vbox (badness 10000) has occurred while \output is active [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1478) in paragraph at lines 18349--18352 []\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 [282] [283] [284] [285] Underfull \hbox (badness 10000) in paragraph at lines 18621--18623 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 18627--18636 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1442) in paragraph at lines 19235--19237 []\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 [296] [297] [298] [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 19566--19572 [301] [302] [303] [304] Underfull \hbox (badness 1248) in paragraph at lines 19811--19814 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\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 , [305] [306] [307] [308] Underfull \hbox (badness 4739) in paragraph at lines 20074--20076 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] Underfull \hbox (badness 2469) in paragraph at lines 21158--21163 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [326] [327] Underfull \hbox (badness 1675) in paragraph at lines 21246--21255 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21256--21271 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the Underfull \hbox (badness 10000) in paragraph at lines 21306--21309 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21306--21309 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [328] [329] Underfull \hbox (badness 1014) in paragraph at lines 21440--21445 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 1264) in paragraph at lines 22289--22297 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [343] Underfull \hbox (badness 4441) in paragraph at lines 22323--22326 []\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/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 5231) in paragraph at lines 23120--23122 []\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 []\T1/zi4/m/n/10 make.unique(c(A, B)) == [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / zlib . net/$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m /n/10 https : / / en . wikipedia . org / wiki / Gzip$[][]\T1/ptm/m/n/10 , [][]$ \T1/zi4/m/n/10 http : / / www . bzip . org/$[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , [][]$\T1/zi4/m/n/10 https : / / tukaani . org / xz/$[][] \T1/ptm/m/n/ 10 and [][]$\T1/zi4/m/n/10 https : [373] [374] [375] [376] [377] [378] [379] [380] Underfull \hbox (badness 2790) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [381] [382] [383] [384] [385] Underfull \hbox (badness 1194) in paragraph at lines 25033--25036 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [386] [387] [388] Underfull \hbox (badness 2368) in paragraph at lines 25240--25246 []\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-r e-spond-ing list, i.e., [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 25630--25633 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [395] [396] [397] [398] [399] [400] [401] [402] [403] [404] Underfull \hbox (badness 10000) in paragraph at lines 26251--26253 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 1881) in paragraph at lines 27146--27149 []\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 27171--27173 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [418] [419] Underfull \hbox (badness 2142) in paragraph at lines 27312--27316 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 27369--27374 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [420] [421] [422] [423] Underfull \hbox (badness 10000) in paragraph at lines 27663--27669 []\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 27663--27669 \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 27663--27669 \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 27676--27679 []\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/pt m/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 27702--27704 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [424] Underfull \hbox (badness 10000) in paragraph at lines 27744--27749 []\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 2529) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 27762--27765 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [425] [426] [427] [428] [429] Underfull \vbox (badness 3803) has occurred while \output is active [430] Underfull \hbox (badness 10000) in paragraph at lines 28162--28166 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [431] [432] Underfull \hbox (badness 10000) in paragraph at lines 28309--28312 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [433] Underfull \hbox (badness 7925) in paragraph at lines 28390--28394 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 28390--28394 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 28395--28404 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] Underfull \hbox (badness 2726) in paragraph at lines 29391--29394 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 1533) in paragraph at lines 31181--31184 []\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 [477] [478] [479] Underfull \hbox (badness 1163) in paragraph at lines 31344--31355 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 10000) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33029--33031 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33032--33036 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [506] [507] Underfull \vbox (badness 10000) has occurred while \output is active [508] [509] [510] [511] [512] [513] [514] [515] Underfull \hbox (badness 1655) in paragraph at lines 33626--33628 []\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 [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] Underfull \hbox (badness 2261) in paragraph at lines 34832--34837 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 10000) in paragraph at lines 35952--35963 \T1/zi4/m/n/10 / / docs . microsoft . com / en-[]us / cpp / c-[]language / pars ing-[]c-[]command-[]line-[]arguments ? [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 10000) in paragraph at lines 37483--37485 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [576] Underfull \vbox (badness 10000) has occurred while \output is active [577] [578] [579] [580] [581] [582] Underfull \hbox (badness 2913) in paragraph at lines 37903--37907 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [583] [584] [585] Underfull \hbox (badness 1072) in paragraph at lines 38149--38153 []\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 38154--38158 []\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/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', [586] Underfull \hbox (badness 10000) in paragraph at lines 38194--38200 []\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 38194--38200 \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 38194--38200 \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 Underfull \hbox (badness 3009) in paragraph at lines 38209--38216 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38209--38216 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38209--38216 \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 38209--38216 \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 [587] [588] [589] Underfull \hbox (badness 2644) in paragraph at lines 38444--38448 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [590] [591] [592] Underfull \hbox (badness 1142) in paragraph at lines 38597--38603 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] Underfull \hbox (badness 1158) in paragraph at lines 39914--39916 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 1137) in paragraph at lines 40505--40511 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails [623] Underfull \hbox (badness 4967) in paragraph at lines 40524--40529 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [624] [625] Underfull \hbox (badness 1616) in paragraph at lines 40644--40649 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 1472) in paragraph at lines 41191--41194 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [634] [635] [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] Underfull \hbox (badness 10000) in paragraph at lines 42117--42121 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4/ m/n/10 length(bin) > [649] [650] [651] [652] Underfull \hbox (badness 10000) in paragraph at lines 42368--42371 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [653] [654] [655] Underfull \hbox (badness 10000) in paragraph at lines 42552--42556 [][][]\T1/zi4/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [656] [657] [658] [659] [660] [661] [662] [663] [664] Underfull \hbox (badness 10000) in paragraph at lines 43191--43194 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [665] [666] [667] [668] [669] [670] Underfull \vbox (badness 10000) has occurred while \output is active [671] [672] [673] [674] [675] [676] [677] [678] Underfull \hbox (badness 1990) in paragraph at lines 44113--44121 []\T1/zi4/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 44113--44121 \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 [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] Underfull \hbox (badness 2452) in paragraph at lines 45082--45088 [][][]\T1/zi4/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 3668) in paragraph at lines 45480--45482 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [700] [701] Underfull \hbox (badness 2401) in paragraph at lines 45610--45614 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/n/10 options[][][]("w arn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [702] [703] [704] Underfull \hbox (badness 2111) in paragraph at lines 45818--45823 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/n/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [705] [706] [707] [708] Underfull \hbox (badness 4001) in paragraph at lines 46064--46066 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/n/10 https : / / developer . [709] [710] [711] [712] [713] [714] Underfull \hbox (badness 5417) in paragraph at lines 46429--46433 []\T1/zi4/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [715] Underfull \hbox (badness 10000) in paragraph at lines 46490--46494 []\T1/zi4/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [716]) (./compiler-pkg.tex Chapter 2. [717] [718] [719] [720]) (./datasets-pkg.tex Chapter 3. [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\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. [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803]) (./grDevices-pkg.tex [804] Chapter 4. [805] [806] [807] [808] [809] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/n/10 c(mi, ma, n.)[]\ T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] Underfull \hbox (badness 1424) in paragraph at lines 898--900 [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) an d []\T1/zi4/m/n/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i-fied as [820] [821] [822] [823] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\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 [824] [825] Underfull \hbox (badness 2512) in paragraph at lines 1311--1313 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/n/10 https : / / web . arc hive . org / web / 20190613001950 / http : / / efg2 . com / [826] [827] [828] [829] [830] Underfull \hbox (badness 1490) in paragraph at lines 1611--1616 \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 []\T 1/zi4/m/n/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [831] [832] [833] [834] [835] [836] [837] Underfull \hbox (badness 1325) in paragraph at lines 2038--2048 []\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 "pngalph a"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/1 0 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp32b"[]\T1/ptm/m/n/10 , [838] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [839] [840] [841] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [842] [843] [844] [845] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] Underfull \vbox (badness 3803) has occurred while \output is active [864] [865] [866] [867] Underfull \vbox (badness 3803) has occurred while \output is active [868] Underfull \hbox (badness 10000) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/zi4/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] Underfull \hbox (badness 1584) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 For type []\T1/zi4/m/n/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1/ zi4/m/n/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 4914--4921 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [883] [884] [885] [886] Underfull \hbox (badness 1377) in paragraph at lines 5220--5225 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [887] Underfull \hbox (badness 1418) in paragraph at lines 5296--5303 \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 "Helvet ica-Narrow"[]\T1/ptm/m/n/10 , [888] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [889] Underfull \hbox (badness 1377) in paragraph at lines 5425--5430 []\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 [890] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\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 [891] Underfull \vbox (badness 3803) has occurred while \output is active [892] Underfull \hbox (badness 2035) in paragraph at lines 5632--5641 []\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 5632--5641 \T1/ptm/m/n/10 vided: []\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-Na rrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/zi4/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/zi 4/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "URWBookman"[]\T1/ptm/m /n/10 , [893] [894] Underfull \hbox (badness 10000) in paragraph at lines 5700--5702 []\T1/zi4/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/z i4/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [895] [896] Underfull \hbox (badness 1546) in paragraph at lines 5844--5852 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi4 /m/n/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 title[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 bg[]\T1/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 , [897] [898] [899] [900] [901] [902] [903] [904] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/zi4/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [905] [906] Underfull \vbox (badness 3803) has occurred while \output is active [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [919] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [920] [921] [922] [923] [924] Underfull \hbox (badness 3780) in paragraph at lines 7630--7636 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/n /10 "AvantGarde"[]\T1/ptm/m/n/10 , [925] [926] [927] [928] [929] [930]) (./graphics-pkg.tex Chapter 5. [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] Overfull \hbox (12.71341pt too wide) in paragraph at lines 983--983 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 4634) in paragraph at lines 1357--1360 [][][]\T1/zi4/m/n/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready work s nowa-days with data.frames; [][][]\T1/zi4/m/n/10 boxplot.formula[][][][]\T1/p tm/m/n/10 , [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] Underfull \hbox (badness 1728) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [970] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \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 [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] Underfull \vbox (badness 10000) has occurred while \output is active [994] Underfull \vbox (badness 10000) has occurred while \output is active [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\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 [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 1107) in paragraph at lines 5081--5087 []\T1/ptm/m/n/10 is []\T1/zi4/m/n/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sca led to user co-or-di-nates. Note that []\T1/zi4/m/n/10 c([][]strwidth[][][](ch) , [1012] [1013] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [1014 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 Underfull \vbox (badness 10000) has occurred while \output is active [1015] [1016 ] [1017] [1018] Underfull \vbox (badness 3803) has occurred while \output is active [1019] [1020] [1021] [1022] [1023] [1024] [1025] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [1040 ] [1041] Underfull \vbox (badness 3803) has occurred while \output is active [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] Underfull \hbox (badness 4954) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /n/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 8938--8940 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/n/10 par (c("font.lab", "cex.lab", [1075] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1076] [1077] [1078] [1079]) (./grid-pkg.tex [1080] Chapter 6. [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 2680) in paragraph at lines 550--553 []\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-c u-la-tion of [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] Underfull \hbox (badness 4279) in paragraph at lines 1187--1196 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/n/10 pushViewport[][][][]\T1/p tm/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 seekViewpo rt[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 upViewport[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/n/10 unit[][][][]\T1/ptm/m/n/10 , [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \vbox (badness 10000) has occurred while \output is active [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\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 [1162] [1163] [1164] [1165] [1166] [1167] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 2142) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/n/10 gridGTreeCoords []\T1/ptm/m/n/1 0 a list of ei-ther []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1175] [1176] Underfull \hbox (badness 4699) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/zi4/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208]) (./methods-pkg.tex Chapter 7. [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] 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-ten ds []\T1/zi4/m/n/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/n/1 0 "package"[]\T1/ptm/m/n/10 , also of class [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] 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 can 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/10 it calls []\T1/zi4/m/n/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1237] [1238] [1239] Underfull \hbox (badness 2213) in paragraph at lines 2213--2218 []\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 = [1240] [1241] [1242] [1243] [1244] Underfull \hbox (badness 10000) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/zi4/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class [1245] [1246] Underfull \hbox (badness 1132) in paragraph at lines 2713--2717 []\T1/ptm/m/n/10 In []\T1/zi4/m/n/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi4 /m/n/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/n/10 package []\T1/ptm/m/n/10 sl ot of the re-turned re-sult is in [1247] Underfull \hbox (badness 1033) in paragraph at lines 2745--2750 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/n/10 removeGeneric []\T1/ptm/m/n/10 r e-moves the func-tion it-self; []\T1/zi4/m/n/10 removeMethods []\T1/ptm/m/n/10 re-stores the [1248] [1249] [1250] [1251] [1252] [1253] [1254] Underfull \hbox (badness 1102) in paragraph at lines 3302--3304 []\T1/zi4/m/n/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1255] [1256] [1257] [1258] [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 3641--3650 []\T1/ptm/m/n/10 The [1261] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = "numeric", [1262] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] Underfull \hbox (badness 1769) in paragraph at lines 4476--4482 []\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 4476--4482 []\T1/zi4/m/n/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [] [][]\T1/zi4/m/n/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion use d by [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] Underfull \vbox (badness 10000) has occurred while \output is active [1283] [1284] [1285] Underfull \hbox (badness 4036) in paragraph at lines 5445--5448 []\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 [1286] [1287] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1288] [1289] [1290] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\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 [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1675) in paragraph at lines 6459--6465 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/n/10 externalRef Method(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1300] [1301] [1302] [1303] Underfull \vbox (badness 10000) has occurred while \output is active [1304] [1305] [1306] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1307] [1308] [1309] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} [1310] Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\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 [1311] [1312] [1313] Underfull \hbox (badness 1286) in paragraph at lines 7492--7494 []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 .selectSuperClasses() []\T1/ptm/m/n/10 on ly, a [][][]\T1/zi4/m/n/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, t yp-i-cally [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\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., [1356] [1357] [1358] [1359]) (./parallel-pkg.tex [1360] 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/z i4/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1361] [1362] [1363] [1364] [1365] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] Underfull \hbox (badness 3386) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1383] [1384] [1385]) (./splines-pkg.tex [1386] 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 [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]) (./stats-pkg.tex Chapter 10. [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] Underfull \hbox (badness 1412) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 2503) in paragraph at lines 1369--1372 []\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 , [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 2503) in paragraph at lines 3530--3533 []\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 , [1459] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\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 = [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2556) in paragraph at lines 5424--5427 []\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 "fi lter"[]\T1/ptm/m/n/10 . For [1489] [1490] [1491] [1492] [1493] [1494] [1495] Underfull \hbox (badness 2503) in paragraph at lines 5838--5842 []\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 , [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 7081) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n 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 6636--6638 []\T1/zi4/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 10000) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \vbox (badness 10000) has occurred while \output is active [1544] [1545] [1546] [1547] [1548] Underfull \hbox (badness 2626) in paragraph at lines 9185--9188 []\T1/ptm/m/n/10 Either []\T1/zi4/m/n/10 "convolution" []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1549] [1550] Underfull \hbox (badness 2503) in paragraph at lines 9292--9296 []\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 , [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] [1574] [1575] [1576] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\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 11024--11027 []\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, [1577] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1578] [1579] [1580] [1581] [1582] [1583] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} [1592] [1593] Underfull \hbox (badness 1484) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/n/10 SSinit = [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1610] [1611] [1612] [1613] [1614] [1615] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1616] [1617] [1618] [1619] [1620] [1621] [1622] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1633] [1634] Underfull \hbox (badness 6412) in paragraph at lines 14660--14664 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/n/10 (surface = "inte rpolate", statistics = [1635] Underfull \hbox (badness 1199) in paragraph at lines 14667--14669 []\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 [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 2503) in paragraph at lines 15743--15747 []\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 , [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/n/ 10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 model.re sponse(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/n/10 model.offset []\T1/ ptm/m/n/10 sums any terms [1662] [1663] [1664] [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 1158) in paragraph at lines 17906--17909 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/n/10 nls []\T1 /ptm/m/n/10 as the data ar-gu-ment. The ac- [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] Underfull \vbox (badness 10000) has occurred while \output is active [1691] Underfull \vbox (badness 10000) has occurred while \output is active [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1377) in paragraph at lines 18933--18938 []\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 18938--18941 []\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 2343) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18951--18955 \T1/ptm/m/n/10 the 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 18959--18963 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/n/10 "BFGS"[]\T 1/ptm/m/n/10 , []\T1/zi4/m/n/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/1 0 "SANN" []\T1/ptm/m/n/10 meth-ods if [1706] [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19184--19184 []\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 19187--19187 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1710] [1711] [1712] [1713] [1714] [1715] [1716] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\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 [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/zi4/m/n/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 s distance", lty = cook.lty, col = cook.col, text.col [1726] [1727] [1728] [1729] [1730] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1731] [1732] [1733] [1734] [1735] [1736] Underfull \hbox (badness 2503) in paragraph at lines 20826--20829 []\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 , [1737] Underfull \hbox (badness 3919) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 "Comparison of Poisson [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\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/1 0 , [][][]\T1/zi4/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\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 [1779] [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 1436) in paragraph at lines 23714--23717 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/n/10 max(2, [1786] Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] Underfull \hbox (badness 1824) in paragraph at lines 24827--24833 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 are f irst re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1803] Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/n/10 y[j] = [1804] Underfull \vbox (badness 3803) has occurred while \output is active [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 2165) in paragraph at lines 25429--25434 []\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/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1813] [1814] [1815] [1816] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\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 25653--25657 []\T1/ptm/m/n/10 where []\T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 PP <- [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] [1841] Underfull \vbox (badness 10000) has occurred while \output is active [1842] [1843] Underfull \hbox (badness 3514) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1844] [1845] [1846] [1847] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27535--27535 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1848] Overfull \hbox (20.23795pt too wide) in paragraph at lines 27628--27628 []\T1/zi4/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (11.22874pt too wide) in paragraph at lines 27630--27630 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1849] [1850] [1851] Underfull \hbox (badness 3514) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1852] [1853] Underfull \hbox (badness 3514) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1854] Underfull \hbox (badness 3514) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1855] [1856] Underfull \hbox (badness 3514) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1857] [1858] Underfull \hbox (badness 6691) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] Underfull \hbox (badness 4024) in paragraph at lines 28633--28636 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] Underfull \hbox (badness 5431) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1877] [1878] [1879] Underfull \hbox (badness 5431) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1880] [1881] [1882] [1883] [1884] [1885] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\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 [1886] [1887] [1888] [1889] [1890] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 3557) in paragraph at lines 31217--31221 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/n/10 extendInt []\T1/ptm/m/n/10 to a non-[ ]\T1/zi4/m/n/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-rect []\T1/zi4/m/n/10 interval = [1910] [1911] [1912] Underfull \vbox (badness 10000) has occurred while \output is active [1913] [1914] [1915] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\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 [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\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 [1925] [1926] [1927] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32317--32317 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1928] [1929] [1930] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32478--32478 [] \T1/zi4/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1931] [1932] [1933] [1934] [1935]) (./stats4-pkg.tex [1936] Chapter 11. [1937] [1938] [1939] Underfull \vbox (badness 10000) has occurred while \output is active [1940] Underfull \vbox (badness 10000) has occurred while \output is active [1941] [1942] [1943] [1944] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1945] [1946] [1947]) (./tcltk-pkg.tex [1948] Chapter 12. [1949] [1950] [1951] [1952] [1953] [1954] [1955] Underfull \vbox (badness 10000) has occurred while \output is active [1956] Underfull \vbox (badness 10000) has occurred while \output is active [1957] Underfull \hbox (badness 1546) in paragraph at lines 666--673 []\T1/zi4/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1958] [1959] [1960] [1961] [1962] Underfull \vbox (badness 10000) has occurred while \output is active [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970]) (./tools-pkg.tex Chapter 13. [1971] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1972] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1973] [1974] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\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 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/n/10 bi bentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/n/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatIn Proceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatManual[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/n/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\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/zi 4/m/n/10 formatTechreport []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1977] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\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 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1990] Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\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 1217--1220 []\T1/zi4/m/n/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and [ ]\T1/zi4/m/n/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 2293) in paragraph at lines 1569--1571 []\T1/zi4/m/n/10 CRAN_memtest_notes() []\T1/ptm/m/n/10 is now dep-re-cated, wit h its func-tion-al-ity in-te-grated into that of Underfull \hbox (badness 10000) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/zi4/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1996] [1997] Underfull \hbox (badness 4096) in paragraph at lines 1714--1722 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1724--1726 []\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 [1998] [1999] [2000] [2001] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2002] [2003] [2004] [2005] [2006] Overfull \hbox (8.25941pt too wide) in paragraph at lines 2230--2230 [] \T1/zi4/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] [2007] [2008] [2009] Underfull \hbox (badness 4096) in paragraph at lines 2399--2407 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2010] [2011] [2012] [2013] [2014] [2015] [2016] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2893. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. [2017] [2018] [2019] [2020] [2021] Underfull \hbox (badness 1424) in paragraph at lines 3196--3198 []\T1/zi4/m/it/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2034] [2035] Underfull \hbox (badness 10000) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/it/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/it/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 1796) in paragraph at lines 4399--4404 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/it/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/it/10 type = = Underfull \hbox (badness 4699) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/zi4/m/it/10 msgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 1946) in paragraph at lines 4449--4453 []\T1/zi4/m/it/10 "--update"[]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m /n/10 4.2.0, []\T1/zi4/m/it/10 "--no-wrap" []\T1/ptm/m/n/10 is used when called from [2042] Underfull \hbox (badness 1838) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [2043] [2044] [2045] [2046] Underfull \hbox (badness 2197) in paragraph at lines 4750--4760 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/it/10 available.packages[][][][]\T1/ptm/m/n/10 : [2047] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\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 [2048] [2049] [2050] [2051]) (./utils-pkg.tex [2052] Chapter 14. [2053] 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 `[] \T1/zi4/m/it/10 insertions[]\T1/ptm/m/n/10 ', [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/it/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/it/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 726--732 []\T1/zi4/m/it/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2064] [2065] [2066] Underfull \hbox (badness 3861) in paragraph at lines 931--936 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/it/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/it/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2067] [2068] [2069] Underfull \hbox (badness 3323) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/zi4/m/it /10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m $\T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 2875) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 taken as [][][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex. max", 1) []\T1/ptm/m/n/10 which is []\T1/zi4/m/it/10 1 []\T1/ptm/m/n/10 typ-i-c ally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \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 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1371) in paragraph at lines 1638--1640 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2078] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1708. [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] Underfull \hbox (badness 2057) in paragraph at lines 2359--2361 []\T1/ptm/m/n/10 None for []\T1/zi4/m/it/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2089] [2090] [2091] [2092] [2093] [2094] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 6842) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/it/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2115] Underfull \hbox (badness 1430) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/it/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2116] Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/it/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/it/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 able []\T1/zi4/m/it/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2117] [2118] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/it/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2140] [2141] [2142] [2143] [2144] [2145] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 6502. Underfull \hbox (badness 1371) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2154] Underfull \hbox (badness 1502) in paragraph at lines 6595--6600 []\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 6595--6600 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2155] [2156] [2157] Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2158] Underfull \hbox (badness 2150) in paragraph at lines 6832--6835 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2159] [2160] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\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 [2161] [2162] [2163] Underfull \hbox (badness 1325) in paragraph at lines 7150--7154 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/it/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2164] Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2165] Underfull \hbox (badness 3219) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/i t/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \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 7313--7320 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 7313--7320 [][][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")[] \T1/ptm/m/n/10 . []\T1/zi4/m/it/10 type = "both" []\T1/ptm/m/n/10 will be silen tly Underfull \hbox (badness 2932) in paragraph at lines 7321--7324 []\T1/ptm/m/n/10 Using pack-ages with []\T1/zi4/m/it/10 type = "source" []\T1/p tm/m/n/10 al-ways works pro-vided the pack-age con-tains no [2166] Underfull \hbox (badness 1024) in paragraph at lines 7448--7451 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing []\T1/zi4/m/it/10 available. packages(filters = "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 , ] []\T1/ ptm/m/n/10 will [2167] Underfull \hbox (badness 10000) in paragraph at lines 7481--7486 [][][]\T1/zi4/m/it/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/i t/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 download. packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 installed.packages[][][] []\T1/ptm/m/n/10 , [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] Underfull \hbox (badness 10000) in paragraph at lines 8185--8187 []\T1/ptm/m/n/10 typically the re-sult of []\T1/zi4/m/it/10 methods(..)[]\T1/pt m/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] Underfull \hbox (badness 2310) in paragraph at lines 8945--8950 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] Underfull \hbox (badness 1248) in paragraph at lines 9471--9475 []\T1/zi4/m/it/10 R CMD build []\T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/ m/n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2200] Underfull \hbox (badness 1789) in paragraph at lines 9551--9553 []\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 [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] Underfull \hbox (badness 1097) in paragraph at lines 10388--10391 []\T1/ptm/m/n/10 The name []\T1/zi4/m/it/10 "clipboard" []\T1/ptm/m/n/10 may al so be used on Win-dows, in which case [2214] [2215] Underfull \hbox (badness 3000) in paragraph at lines 10524--10529 [][][]\T1/zi4/m/it/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/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/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ it/10 read.table[][][][]\T1/ptm/m/n/10 ; [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] Underfull \hbox (badness 2134) in paragraph at lines 11113--11118 [][][]\T1/zi4/m/it/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/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/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ it/10 write.table[][][][]\T1/ptm/m/n/10 ; [2225] Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/zi4/m/it/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/it/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] Underfull \hbox (badness 2469) in paragraph at lines 11663--11667 []\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 11663--11667 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2234] [2235] [2236] [2237] [2238] [2239] Underfull \hbox (badness 4060) in paragraph at lines 12087--12090 []\T1/ptm/m/n/10 If `[]\T1/zi4/m/it/10 --default-packages[]\T1/ptm/m/n/10 ' is not used, then []\T1/zi4/m/it/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron- ment vari-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 12110--12110 []\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 '[] [2240] [2241] [2242] [2243] Underfull \hbox (badness 2150) in paragraph at lines 12365--12367 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / www . gnu . org / software / emac s / manual / [2244] [2245] [2246] [2247] Underfull \hbox (badness 10000) in paragraph at lines 12585--12589 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/it/10 stylepath []\T1/ptm/m/n/10 is now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12618--12624 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2248] Underfull \hbox (badness 2762) in paragraph at lines 12633--12641 \T1/ptm/m/n/10 UTF-8 lo-cales (note that pdf-TeX as-sumes UTF-8 by de-fault sin ce 2018). 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If Underfull \hbox (badness 4779) in paragraph at lines 12852--12854 []\T1/ptm/m/n/10 The file `\T1/zi4/m/it/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI ([]\T1/zi4/m/it/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-do ws and [2251] Underfull \hbox (badness 1077) in paragraph at lines 12882--12889 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2252] [2253] [2254] [2255] [2256] [2257] [2258] Underfull \hbox (badness 3780) in paragraph at lines 13290--13294 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][][]\ T1/zi4/m/it/10 options[][][]("BioC_mirror")[]\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 13306--13309 []\T1/ptm/m/n/10 Repository `[]\T1/zi4/m/it/10 CRAN[]\T1/ptm/m/n/10 ' is treate d spe-cially: the value is taken from the cur-rent set-ting of [2259] [2260] [2261] Underfull \hbox (badness 2302) in paragraph at lines 13511--13513 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2262] [2263] [2264] [2265] [2266] Underfull \hbox (badness 10000) in paragraph at lines 13810--13815 []\T1/ptm/m/n/10 logical; if []\T1/zi4/m/it/10 TRUE []\T1/ptm/m/n/10 (de-fault) , [][][]\T1/zi4/m/it/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13819--13822 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2267] [2268] [2269] [2270] [2271] [2272] [2273] Underfull \hbox (badness 2932) in paragraph at lines 14252--14259 []\T1/ptm/m/n/10 If []\T1/zi4/m/it/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fa ult) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 and se-lected if their []\T1/zi4/m/it/10 extension []\T1/ptm/m/n /10 com-po-nent matches (as a reg-exp) the file name. 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This reads the Underfull \hbox (badness 2111) in paragraph at lines 7292--7297 []\T1/ptm/m/n/10 Unix users wish-ing to \T1/ptm/m/it/10 write \T1/ptm/m/n/10 to one of the X11 se-lec-tions may be able to do so via [113] [114] Underfull \vbox (badness 3803) has occurred while \output is active [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] [117] [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 2096) in paragraph at lines 7962--7966 \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 . [124] [125] Underfull \hbox (badness 2351) in paragraph at lines 8076--8079 [][][]\T1/zi4/m/n/10 split[][][] []\T1/ptm/m/n/10 for split-ting a vari-able ac -cord-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 t able[][][][]\T1/ptm/m/n/10 , [126] [127] [128] [129] [130] Underfull \hbox (badness 4479) in paragraph at lines 8393--8404 [][][]\T1/zi4/m/n/10 I[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 plot.data.f rame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 print.data.frame[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 row.names[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 names[][][] []\T1/ptm/m/n/10 (for the col-umn names), [131] [132] [133] [134] [135] [136] [137] Underfull \hbox (badness 1629) in paragraph at lines 8861--8873 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 2875) in paragraph at lines 8861--8873 []\T1/zi4/m/n/10 NA[]\T1/ptm/m/n/10 , and hence []\T1/zi4/m/n/10 as.POSIXct("19 69-12-31 23:59:59", tz = "UTC") []\T1/ptm/m/n/10 will give []\T1/zi4/m/n/10 "19 69-12-31 [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] Underfull \hbox (badness 1178) in paragraph at lines 9629--9633 []\T1/ptm/m/n/10 If true, [][][]\T1/zi4/m/n/10 list[][][][]\T1/ptm/m/n/10 s and atomic vec-tors with non-[][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 names (see [][][]\T1/zi4/m/n/10 names[][][][]\T1/ptm/m/n/10 ) are de- [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 2744) in paragraph at lines 11938--11940 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] Underfull \hbox (badness 2253) in paragraph at lines 14134--14136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [217] Underfull \hbox (badness 1490) in paragraph at lines 14169--14172 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [218] Underfull \hbox (badness 1565) in paragraph at lines 14251--14255 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] []\T1/ptm/m/n/10 to find out about sym- bolic links, [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 file.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.files[][][] []\T1/ptm/m/n/10 , and [219] Underfull \hbox (badness 4927) in paragraph at lines 14302--14304 []\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 []\T1/zi4/m/n/10 fsep = [220] Underfull \hbox (badness 3148) in paragraph at lines 14404--14409 [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.fi les[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 help[][][][]\T1/ptm/m/n/10 ; [ ][][]\T1/zi4/m/n/10 RShowDoc[][][] []\T1/ptm/m/n/10 call []\T1/zi4/m/n/10 file. show() []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 type = "text"[]\T1/ptm/m/n/10 . Co n-sider [221] Underfull \hbox (badness 1466) in paragraph at lines 14451--14454 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [222] [223] Underfull \hbox (badness 10000) in paragraph at lines 14582--14586 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\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 14593--14596 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [224] [225] [226] [227] [228] Underfull \hbox (badness 3965) in paragraph at lines 14890--14894 []\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, [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 4429) in paragraph at lines 15679--15682 []\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 [241] [242] Underfull \hbox (badness 10000) in paragraph at lines 15785--15787 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [243] Underfull \hbox (badness 2035) in paragraph at lines 15858--15862 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 2452) in paragraph at lines 16471--16475 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment 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 16471--16475 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s 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 [254] [255] Underfull \hbox (badness 1092) in paragraph at lines 16644--16649 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [256] [257] [258] [259] Underfull \hbox (badness 6741) in paragraph at lines 16897--16901 \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/pt m/m/n/10 , [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \vbox (badness 10000) has occurred while \output is active [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1478) in paragraph at lines 18349--18352 []\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 [282] [283] [284] [285] Underfull \hbox (badness 10000) in paragraph at lines 18621--18623 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 18627--18636 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1442) in paragraph at lines 19235--19237 []\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 [296] [297] [298] [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 19566--19572 [301] [302] [303] [304] Underfull \hbox (badness 1248) in paragraph at lines 19811--19814 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\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 , [305] [306] [307] [308] Underfull \hbox (badness 4739) in paragraph at lines 20074--20076 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] Underfull \hbox (badness 2469) in paragraph at lines 21158--21163 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [326] [327] Underfull \hbox (badness 1675) in paragraph at lines 21246--21255 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21256--21271 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the Underfull \hbox (badness 10000) in paragraph at lines 21306--21309 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21306--21309 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [328] [329] Underfull \hbox (badness 1014) in paragraph at lines 21440--21445 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 1264) in paragraph at lines 22289--22297 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [343] Underfull \hbox (badness 4441) in paragraph at lines 22323--22326 []\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/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 5231) in paragraph at lines 23120--23122 []\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 []\T1/zi4/m/n/10 make.unique(c(A, B)) == [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / zlib . net/$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m /n/10 https : / / en . wikipedia . org / wiki / Gzip$[][]\T1/ptm/m/n/10 , [][]$ \T1/zi4/m/n/10 http : / / www . bzip . org/$[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , [][]$\T1/zi4/m/n/10 https : / / tukaani . org / xz/$[][] \T1/ptm/m/n/ 10 and [][]$\T1/zi4/m/n/10 https : [373] [374] [375] [376] [377] [378] [379] [380] Underfull \hbox (badness 2790) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [381] [382] [383] [384] [385] Underfull \hbox (badness 1194) in paragraph at lines 25033--25036 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [386] [387] [388] Underfull \hbox (badness 2368) in paragraph at lines 25240--25246 []\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-r e-spond-ing list, i.e., [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 25630--25633 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [395] [396] [397] [398] [399] [400] [401] [402] [403] [404] Underfull \hbox (badness 10000) in paragraph at lines 26251--26253 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 1881) in paragraph at lines 27146--27149 []\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 27171--27173 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [418] [419] Underfull \hbox (badness 2142) in paragraph at lines 27312--27316 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 27369--27374 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [420] [421] [422] [423] Underfull \hbox (badness 10000) in paragraph at lines 27663--27669 []\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 27663--27669 \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 27663--27669 \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 27676--27679 []\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/pt m/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 27702--27704 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [424] Underfull \hbox (badness 10000) in paragraph at lines 27744--27749 []\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 2529) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 27762--27765 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [425] [426] [427] [428] [429] Underfull \vbox (badness 3803) has occurred while \output is active [430] Underfull \hbox (badness 10000) in paragraph at lines 28162--28166 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [431] [432] Underfull \hbox (badness 10000) in paragraph at lines 28309--28312 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [433] Underfull \hbox (badness 7925) in paragraph at lines 28390--28394 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 28390--28394 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 28395--28404 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] Underfull \hbox (badness 2726) in paragraph at lines 29391--29394 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 1533) in paragraph at lines 31181--31184 []\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 [477] [478] [479] Underfull \hbox (badness 1163) in paragraph at lines 31344--31355 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 10000) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33029--33031 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33032--33036 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [506] [507] Underfull \vbox (badness 10000) has occurred while \output is active [508] [509] [510] [511] [512] [513] [514] [515] Underfull \hbox (badness 1655) in paragraph at lines 33626--33628 []\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 [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] Underfull \hbox (badness 2261) in paragraph at lines 34832--34837 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 10000) in paragraph at lines 35952--35963 \T1/zi4/m/n/10 / / docs . microsoft . com / en-[]us / cpp / c-[]language / pars ing-[]c-[]command-[]line-[]arguments ? [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 10000) in paragraph at lines 37483--37485 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [576] Underfull \vbox (badness 10000) has occurred while \output is active [577] [578] [579] [580] [581] [582] Underfull \hbox (badness 2913) in paragraph at lines 37903--37907 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [583] [584] [585] Underfull \hbox (badness 1072) in paragraph at lines 38149--38153 []\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 38154--38158 []\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/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', [586] Underfull \hbox (badness 10000) in paragraph at lines 38194--38200 []\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 38194--38200 \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 38194--38200 \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 Underfull \hbox (badness 3009) in paragraph at lines 38209--38216 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38209--38216 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38209--38216 \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 38209--38216 \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 [587] [588] [589] Underfull \hbox (badness 2644) in paragraph at lines 38444--38448 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [590] [591] [592] Underfull \hbox (badness 1142) in paragraph at lines 38597--38603 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] Underfull \hbox (badness 1158) in paragraph at lines 39914--39916 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 1137) in paragraph at lines 40505--40511 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails [623] Underfull \hbox (badness 4967) in paragraph at lines 40524--40529 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [624] [625] Underfull \hbox (badness 1616) in paragraph at lines 40644--40649 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 1472) in paragraph at lines 41191--41194 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [634] [635] [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] Underfull \hbox (badness 10000) in paragraph at lines 42117--42121 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4/ m/n/10 length(bin) > [649] [650] [651] [652] Underfull \hbox (badness 10000) in paragraph at lines 42368--42371 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [653] [654] [655] Underfull \hbox (badness 10000) in paragraph at lines 42552--42556 [][][]\T1/zi4/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [656] [657] [658] [659] [660] [661] [662] [663] [664] Underfull \hbox (badness 10000) in paragraph at lines 43191--43194 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [665] [666] [667] [668] [669] [670] Underfull \vbox (badness 10000) has occurred while \output is active [671] [672] [673] [674] [675] [676] [677] [678] Underfull \hbox (badness 1990) in paragraph at lines 44113--44121 []\T1/zi4/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 44113--44121 \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 [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] Underfull \hbox (badness 2452) in paragraph at lines 45082--45088 [][][]\T1/zi4/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 3668) in paragraph at lines 45480--45482 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [700] [701] Underfull \hbox (badness 2401) in paragraph at lines 45610--45614 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/n/10 options[][][]("w arn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [702] [703] [704] Underfull \hbox (badness 2111) in paragraph at lines 45818--45823 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/n/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [705] [706] [707] [708] Underfull \hbox (badness 4001) in paragraph at lines 46064--46066 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/n/10 https : / / developer . [709] [710] [711] [712] [713] [714] Underfull \hbox (badness 5417) in paragraph at lines 46429--46433 []\T1/zi4/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [715] Underfull \hbox (badness 10000) in paragraph at lines 46490--46494 []\T1/zi4/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [716]) (./compiler-pkg.tex Chapter 2. [717] [718] [719] [720]) (./datasets-pkg.tex Chapter 3. [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\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. [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803]) (./grDevices-pkg.tex [804] Chapter 4. [805] [806] [807] [808] [809] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/n/10 c(mi, ma, n.)[]\ T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] Underfull \hbox (badness 1424) in paragraph at lines 898--900 [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) an d []\T1/zi4/m/n/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i-fied as [820] [821] [822] [823] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\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 [824] [825] Underfull \hbox (badness 2512) in paragraph at lines 1311--1313 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/n/10 https : / / web . arc hive . org / web / 20190613001950 / http : / / efg2 . com / [826] [827] [828] [829] [830] Underfull \hbox (badness 1490) in paragraph at lines 1611--1616 \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 []\T 1/zi4/m/n/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [831] [832] [833] [834] [835] [836] [837] Underfull \hbox (badness 1325) in paragraph at lines 2038--2048 []\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 "pngalph a"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/1 0 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp32b"[]\T1/ptm/m/n/10 , [838] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [839] [840] [841] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [842] [843] [844] [845] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] Underfull \vbox (badness 3803) has occurred while \output is active [864] [865] [866] [867] Underfull \vbox (badness 3803) has occurred while \output is active [868] Underfull \hbox (badness 10000) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/zi4/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] Underfull \hbox (badness 1584) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 For type []\T1/zi4/m/n/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1/ zi4/m/n/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 4914--4921 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [883] [884] [885] [886] Underfull \hbox (badness 1377) in paragraph at lines 5220--5225 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [887] Underfull \hbox (badness 1418) in paragraph at lines 5296--5303 \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 "Helvet ica-Narrow"[]\T1/ptm/m/n/10 , [888] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [889] Underfull \hbox (badness 1377) in paragraph at lines 5425--5430 []\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 [890] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\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 [891] Underfull \vbox (badness 3803) has occurred while \output is active [892] Underfull \hbox (badness 2035) in paragraph at lines 5632--5641 []\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 5632--5641 \T1/ptm/m/n/10 vided: []\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-Na rrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/zi4/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/zi 4/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "URWBookman"[]\T1/ptm/m /n/10 , [893] [894] Underfull \hbox (badness 10000) in paragraph at lines 5700--5702 []\T1/zi4/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/z i4/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [895] [896] Underfull \hbox (badness 1546) in paragraph at lines 5844--5852 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi4 /m/n/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 title[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 bg[]\T1/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 , [897] [898] [899] [900] [901] [902] [903] [904] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/zi4/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [905] [906] Underfull \vbox (badness 3803) has occurred while \output is active [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [919] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [920] [921] [922] [923] [924] Underfull \hbox (badness 3780) in paragraph at lines 7630--7636 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/n /10 "AvantGarde"[]\T1/ptm/m/n/10 , [925] [926] [927] [928] [929] [930]) (./graphics-pkg.tex Chapter 5. [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] Overfull \hbox (12.71341pt too wide) in paragraph at lines 983--983 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 4634) in paragraph at lines 1357--1360 [][][]\T1/zi4/m/n/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready work s nowa-days with data.frames; [][][]\T1/zi4/m/n/10 boxplot.formula[][][][]\T1/p tm/m/n/10 , [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] Underfull \hbox (badness 1728) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [970] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \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 [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] Underfull \vbox (badness 10000) has occurred while \output is active [994] Underfull \vbox (badness 10000) has occurred while \output is active [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\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 [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 1107) in paragraph at lines 5081--5087 []\T1/ptm/m/n/10 is []\T1/zi4/m/n/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sca led to user co-or-di-nates. Note that []\T1/zi4/m/n/10 c([][]strwidth[][][](ch) , [1012] [1013] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [1014 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 Underfull \vbox (badness 10000) has occurred while \output is active [1015] [1016 ] [1017] [1018] Underfull \vbox (badness 3803) has occurred while \output is active [1019] [1020] [1021] [1022] [1023] [1024] [1025] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [1040 ] [1041] Underfull \vbox (badness 3803) has occurred while \output is active [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] Underfull \hbox (badness 4954) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /n/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 8938--8940 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/n/10 par (c("font.lab", "cex.lab", [1075] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1076] [1077] [1078] [1079]) (./grid-pkg.tex [1080] Chapter 6. [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 2680) in paragraph at lines 550--553 []\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-c u-la-tion of [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] Underfull \hbox (badness 4279) in paragraph at lines 1187--1196 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/n/10 pushViewport[][][][]\T1/p tm/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 seekViewpo rt[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 upViewport[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/n/10 unit[][][][]\T1/ptm/m/n/10 , [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \vbox (badness 10000) has occurred while \output is active [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\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 [1162] [1163] [1164] [1165] [1166] [1167] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 2142) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/n/10 gridGTreeCoords []\T1/ptm/m/n/1 0 a list of ei-ther []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1175] [1176] Underfull \hbox (badness 4699) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/zi4/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208]) (./methods-pkg.tex Chapter 7. [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] 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-ten ds []\T1/zi4/m/n/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/n/1 0 "package"[]\T1/ptm/m/n/10 , also of class [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] 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 can 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/10 it calls []\T1/zi4/m/n/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1237] [1238] [1239] Underfull \hbox (badness 2213) in paragraph at lines 2213--2218 []\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 = [1240] [1241] [1242] [1243] [1244] Underfull \hbox (badness 10000) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/zi4/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class [1245] [1246] Underfull \hbox (badness 1132) in paragraph at lines 2713--2717 []\T1/ptm/m/n/10 In []\T1/zi4/m/n/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi4 /m/n/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/n/10 package []\T1/ptm/m/n/10 sl ot of the re-turned re-sult is in [1247] Underfull \hbox (badness 1033) in paragraph at lines 2745--2750 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/n/10 removeGeneric []\T1/ptm/m/n/10 r e-moves the func-tion it-self; []\T1/zi4/m/n/10 removeMethods []\T1/ptm/m/n/10 re-stores the [1248] [1249] [1250] [1251] [1252] [1253] [1254] Underfull \hbox (badness 1102) in paragraph at lines 3302--3304 []\T1/zi4/m/n/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1255] [1256] [1257] [1258] [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 3641--3650 []\T1/ptm/m/n/10 The [1261] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = "numeric", [1262] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] Underfull \hbox (badness 1769) in paragraph at lines 4476--4482 []\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 4476--4482 []\T1/zi4/m/n/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [] [][]\T1/zi4/m/n/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion use d by [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] Underfull \vbox (badness 10000) has occurred while \output is active [1283] [1284] [1285] Underfull \hbox (badness 4036) in paragraph at lines 5445--5448 []\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 [1286] [1287] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1288] [1289] [1290] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\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 [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1675) in paragraph at lines 6459--6465 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/n/10 externalRef Method(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1300] [1301] [1302] [1303] Underfull \vbox (badness 10000) has occurred while \output is active [1304] [1305] [1306] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1307] [1308] [1309] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} [1310] Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\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 [1311] [1312] [1313] Underfull \hbox (badness 1286) in paragraph at lines 7492--7494 []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 .selectSuperClasses() []\T1/ptm/m/n/10 on ly, a [][][]\T1/zi4/m/n/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, t yp-i-cally [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\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., [1356] [1357] [1358] [1359]) (./parallel-pkg.tex [1360] 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/z i4/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1361] [1362] [1363] [1364] [1365] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] Underfull \hbox (badness 3386) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1383] [1384] [1385]) (./splines-pkg.tex [1386] 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 [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]) (./stats-pkg.tex Chapter 10. [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] Underfull \hbox (badness 1412) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 2503) in paragraph at lines 1369--1372 []\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 , [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 2503) in paragraph at lines 3530--3533 []\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 , [1459] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\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 = [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2556) in paragraph at lines 5424--5427 []\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 "fi lter"[]\T1/ptm/m/n/10 . For [1489] [1490] [1491] [1492] [1493] [1494] [1495] Underfull \hbox (badness 2503) in paragraph at lines 5838--5842 []\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 , [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 7081) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n 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 6636--6638 []\T1/zi4/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 10000) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \vbox (badness 10000) has occurred while \output is active [1544] [1545] [1546] [1547] [1548] Underfull \hbox (badness 2626) in paragraph at lines 9185--9188 []\T1/ptm/m/n/10 Either []\T1/zi4/m/n/10 "convolution" []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1549] [1550] Underfull \hbox (badness 2503) in paragraph at lines 9292--9296 []\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 , [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] [1574] [1575] [1576] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\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 11024--11027 []\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, [1577] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1578] [1579] [1580] [1581] [1582] [1583] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} [1592] [1593] Underfull \hbox (badness 1484) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/n/10 SSinit = [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1610] [1611] [1612] [1613] [1614] [1615] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1616] [1617] [1618] [1619] [1620] [1621] [1622] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1633] [1634] Underfull \hbox (badness 6412) in paragraph at lines 14660--14664 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/n/10 (surface = "inte rpolate", statistics = [1635] Underfull \hbox (badness 1199) in paragraph at lines 14667--14669 []\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 [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 2503) in paragraph at lines 15743--15747 []\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 , [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/n/ 10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 model.re sponse(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/n/10 model.offset []\T1/ ptm/m/n/10 sums any terms [1662] [1663] [1664] [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 1158) in paragraph at lines 17906--17909 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/n/10 nls []\T1 /ptm/m/n/10 as the data ar-gu-ment. The ac- [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] Underfull \vbox (badness 10000) has occurred while \output is active [1691] Underfull \vbox (badness 10000) has occurred while \output is active [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1377) in paragraph at lines 18933--18938 []\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 18938--18941 []\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 2343) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18951--18955 \T1/ptm/m/n/10 the 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 18959--18963 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/n/10 "BFGS"[]\T 1/ptm/m/n/10 , []\T1/zi4/m/n/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/1 0 "SANN" []\T1/ptm/m/n/10 meth-ods if [1706] [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19184--19184 []\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 19187--19187 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1710] [1711] [1712] [1713] [1714] [1715] [1716] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\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 [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/zi4/m/n/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 s distance", lty = cook.lty, col = cook.col, text.col [1726] [1727] [1728] [1729] [1730] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1731] [1732] [1733] [1734] [1735] [1736] Underfull \hbox (badness 2503) in paragraph at lines 20826--20829 []\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 , [1737] Underfull \hbox (badness 3919) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 "Comparison of Poisson [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\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/1 0 , [][][]\T1/zi4/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\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 [1779] [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 1436) in paragraph at lines 23714--23717 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/n/10 max(2, [1786] Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] Underfull \hbox (badness 1824) in paragraph at lines 24827--24833 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 are f irst re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1803] Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/n/10 y[j] = [1804] Underfull \vbox (badness 3803) has occurred while \output is active [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 2165) in paragraph at lines 25429--25434 []\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/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1813] [1814] [1815] [1816] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\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 25653--25657 []\T1/ptm/m/n/10 where []\T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 PP <- [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] [1841] Underfull \vbox (badness 10000) has occurred while \output is active [1842] [1843] Underfull \hbox (badness 3514) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1844] [1845] [1846] [1847] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27535--27535 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1848] Overfull \hbox (20.23795pt too wide) in paragraph at lines 27628--27628 []\T1/zi4/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (11.22874pt too wide) in paragraph at lines 27630--27630 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1849] [1850] [1851] Underfull \hbox (badness 3514) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1852] [1853] Underfull \hbox (badness 3514) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1854] Underfull \hbox (badness 3514) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1855] [1856] Underfull \hbox (badness 3514) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1857] [1858] Underfull \hbox (badness 6691) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] Underfull \hbox (badness 4024) in paragraph at lines 28633--28636 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] Underfull \hbox (badness 5431) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1877] [1878] [1879] Underfull \hbox (badness 5431) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1880] [1881] [1882] [1883] [1884] [1885] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\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 [1886] [1887] [1888] [1889] [1890] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 3557) in paragraph at lines 31217--31221 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/n/10 extendInt []\T1/ptm/m/n/10 to a non-[ ]\T1/zi4/m/n/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-rect []\T1/zi4/m/n/10 interval = [1910] [1911] [1912] Underfull \vbox (badness 10000) has occurred while \output is active [1913] [1914] [1915] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\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 [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\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 [1925] [1926] [1927] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32317--32317 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1928] [1929] [1930] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32478--32478 [] \T1/zi4/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1931] [1932] [1933] [1934] [1935]) (./stats4-pkg.tex [1936] Chapter 11. [1937] [1938] [1939] Underfull \vbox (badness 10000) has occurred while \output is active [1940] Underfull \vbox (badness 10000) has occurred while \output is active [1941] [1942] [1943] [1944] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1945] [1946] [1947]) (./tcltk-pkg.tex [1948] Chapter 12. [1949] [1950] [1951] [1952] [1953] [1954] [1955] Underfull \vbox (badness 10000) has occurred while \output is active [1956] Underfull \vbox (badness 10000) has occurred while \output is active [1957] Underfull \hbox (badness 1546) in paragraph at lines 666--673 []\T1/zi4/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1958] [1959] [1960] [1961] [1962] Underfull \vbox (badness 10000) has occurred while \output is active [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970]) (./tools-pkg.tex Chapter 13. [1971] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1972] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1973] [1974] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\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 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/n/10 bi bentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/n/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatIn Proceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatManual[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/n/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\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/zi 4/m/n/10 formatTechreport []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1977] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\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 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1990] Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\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 1217--1220 []\T1/zi4/m/n/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and [ ]\T1/zi4/m/n/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 2293) in paragraph at lines 1569--1571 []\T1/zi4/m/n/10 CRAN_memtest_notes() []\T1/ptm/m/n/10 is now dep-re-cated, wit h its func-tion-al-ity in-te-grated into that of Underfull \hbox (badness 10000) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/zi4/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1996] [1997] Underfull \hbox (badness 4096) in paragraph at lines 1714--1722 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1724--1726 []\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 [1998] [1999] [2000] [2001] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2002] [2003] [2004] [2005] [2006] Overfull \hbox (8.25941pt too wide) in paragraph at lines 2230--2230 [] \T1/zi4/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] [2007] [2008] [2009] Underfull \hbox (badness 4096) in paragraph at lines 2399--2407 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2010] [2011] [2012] [2013] [2014] [2015] [2016] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2893. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. [2017] [2018] [2019] [2020] [2021] Underfull \hbox (badness 1424) in paragraph at lines 3196--3198 []\T1/zi4/m/it/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2034] [2035] Underfull \hbox (badness 10000) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/it/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/it/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 1796) in paragraph at lines 4399--4404 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/it/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/it/10 type = = Underfull \hbox (badness 4699) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/zi4/m/it/10 msgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 1946) in paragraph at lines 4449--4453 []\T1/zi4/m/it/10 "--update"[]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m /n/10 4.2.0, []\T1/zi4/m/it/10 "--no-wrap" []\T1/ptm/m/n/10 is used when called from [2042] Underfull \hbox (badness 1838) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [2043] [2044] [2045] [2046] Underfull \hbox (badness 2197) in paragraph at lines 4750--4760 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/it/10 available.packages[][][][]\T1/ptm/m/n/10 : [2047] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\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 [2048] [2049] [2050] [2051]) (./utils-pkg.tex [2052] Chapter 14. [2053] 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 `[] \T1/zi4/m/it/10 insertions[]\T1/ptm/m/n/10 ', [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/it/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/it/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 726--732 []\T1/zi4/m/it/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2064] [2065] [2066] Underfull \hbox (badness 3861) in paragraph at lines 931--936 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/it/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/it/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2067] [2068] [2069] Underfull \hbox (badness 3323) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/zi4/m/it /10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m $\T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 2875) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 taken as [][][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex. max", 1) []\T1/ptm/m/n/10 which is []\T1/zi4/m/it/10 1 []\T1/ptm/m/n/10 typ-i-c ally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \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 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1371) in paragraph at lines 1638--1640 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2078] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1708. [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] Underfull \hbox (badness 2057) in paragraph at lines 2359--2361 []\T1/ptm/m/n/10 None for []\T1/zi4/m/it/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2089] [2090] [2091] [2092] [2093] [2094] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 6842) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/it/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2115] Underfull \hbox (badness 1430) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/it/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2116] Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/it/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/it/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 able []\T1/zi4/m/it/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2117] [2118] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/it/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2140] [2141] [2142] [2143] [2144] [2145] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 6502. Underfull \hbox (badness 1371) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2154] Underfull \hbox (badness 1502) in paragraph at lines 6595--6600 []\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 6595--6600 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2155] [2156] [2157] Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2158] Underfull \hbox (badness 2150) in paragraph at lines 6832--6835 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2159] [2160] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\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 [2161] [2162] [2163] Underfull \hbox (badness 1325) in paragraph at lines 7150--7154 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/it/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2164] Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2165] Underfull \hbox (badness 3219) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/i t/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \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 7313--7320 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 7313--7320 [][][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")[] \T1/ptm/m/n/10 . []\T1/zi4/m/it/10 type = "both" []\T1/ptm/m/n/10 will be silen tly Underfull \hbox (badness 2932) in paragraph at lines 7321--7324 []\T1/ptm/m/n/10 Using pack-ages with []\T1/zi4/m/it/10 type = "source" []\T1/p tm/m/n/10 al-ways works pro-vided the pack-age con-tains no [2166] Underfull \hbox (badness 1024) in paragraph at lines 7448--7451 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing []\T1/zi4/m/it/10 available. packages(filters = "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 , ] []\T1/ ptm/m/n/10 will [2167] Underfull \hbox (badness 10000) in paragraph at lines 7481--7486 [][][]\T1/zi4/m/it/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/i t/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 download. packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 installed.packages[][][] []\T1/ptm/m/n/10 , [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] Underfull \hbox (badness 10000) in paragraph at lines 8185--8187 []\T1/ptm/m/n/10 typically the re-sult of []\T1/zi4/m/it/10 methods(..)[]\T1/pt m/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] Underfull \hbox (badness 2310) in paragraph at lines 8945--8950 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] Underfull \hbox (badness 1248) in paragraph at lines 9471--9475 []\T1/zi4/m/it/10 R CMD build []\T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/ m/n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2200] Underfull \hbox (badness 1789) in paragraph at lines 9551--9553 []\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 [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] Underfull \hbox (badness 1097) in paragraph at lines 10388--10391 []\T1/ptm/m/n/10 The name []\T1/zi4/m/it/10 "clipboard" []\T1/ptm/m/n/10 may al so be used on Win-dows, in which case [2214] [2215] Underfull \hbox (badness 3000) in paragraph at lines 10524--10529 [][][]\T1/zi4/m/it/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/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/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ it/10 read.table[][][][]\T1/ptm/m/n/10 ; [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] Underfull \hbox (badness 2134) in paragraph at lines 11113--11118 [][][]\T1/zi4/m/it/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/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/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ it/10 write.table[][][][]\T1/ptm/m/n/10 ; [2225] Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/zi4/m/it/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/it/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] Underfull \hbox (badness 2469) in paragraph at lines 11663--11667 []\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 11663--11667 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2234] [2235] [2236] [2237] [2238] [2239] Underfull \hbox (badness 4060) in paragraph at lines 12087--12090 []\T1/ptm/m/n/10 If `[]\T1/zi4/m/it/10 --default-packages[]\T1/ptm/m/n/10 ' is not used, then []\T1/zi4/m/it/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron- ment vari-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 12110--12110 []\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 '[] [2240] [2241] [2242] [2243] Underfull \hbox (badness 2150) in paragraph at lines 12365--12367 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / www . gnu . org / software / emac s / manual / [2244] [2245] [2246] [2247] Underfull \hbox (badness 10000) in paragraph at lines 12585--12589 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/it/10 stylepath []\T1/ptm/m/n/10 is now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12618--12624 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2248] Underfull \hbox (badness 2762) in paragraph at lines 12633--12641 \T1/ptm/m/n/10 UTF-8 lo-cales (note that pdf-TeX as-sumes UTF-8 by de-fault sin ce 2018). 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If Underfull \hbox (badness 4779) in paragraph at lines 12852--12854 []\T1/ptm/m/n/10 The file `\T1/zi4/m/it/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI ([]\T1/zi4/m/it/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-do ws and [2251] Underfull \hbox (badness 1077) in paragraph at lines 12882--12889 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2252] [2253] [2254] [2255] [2256] [2257] [2258] Underfull \hbox (badness 3780) in paragraph at lines 13290--13294 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][][]\ T1/zi4/m/it/10 options[][][]("BioC_mirror")[]\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 13306--13309 []\T1/ptm/m/n/10 Repository `[]\T1/zi4/m/it/10 CRAN[]\T1/ptm/m/n/10 ' is treate d spe-cially: the value is taken from the cur-rent set-ting of [2259] [2260] [2261] Underfull \hbox (badness 2302) in paragraph at lines 13511--13513 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2262] [2263] [2264] [2265] [2266] Underfull \hbox (badness 10000) in paragraph at lines 13810--13815 []\T1/ptm/m/n/10 logical; if []\T1/zi4/m/it/10 TRUE []\T1/ptm/m/n/10 (de-fault) , [][][]\T1/zi4/m/it/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13819--13822 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2267] [2268] [2269] [2270] [2271] [2272] [2273] Underfull \hbox (badness 2932) in paragraph at lines 14252--14259 []\T1/ptm/m/n/10 If []\T1/zi4/m/it/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fa ult) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 and se-lected if their []\T1/zi4/m/it/10 extension []\T1/ptm/m/n /10 com-po-nent matches (as a reg-exp) the file name. 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Val-ues [6] [7] [8] [9] Underfull \hbox (badness 2556) in paragraph at lines 574--580 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/zi4/m/n/10 insertions[]\T1/ptm/m/n/10 ', [10] [11] [12] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1586--1592 [26] [27] [28] [29] [30] [31] [32] Overfull \hbox (26.27782pt too wide) in paragraph at lines 2064--2064 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] Underfull \hbox (badness 1721) in paragraph at lines 2721--2725 [][][]\T1/zi4/m/n/10 assign[][][] []\T1/ptm/m/n/10 (and its in-verse [][][]\T1/ zi4/m/n/10 get[][][][]\T1/ptm/m/n/10 ), for ``sub-assign-ment'' such as []\T1/z i4/m/n/10 x[i] <- v[]\T1/ptm/m/n/10 , see [][][]\T1/zi4/m/n/10 [<-[][][][]\T1/p tm/m/n/10 ; fur-ther, [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 2521) in paragraph at lines 5197--5199 []\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 [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6388--6388 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] Underfull \hbox (badness 1303) in paragraph at lines 7281--7288 []\T1/zi4/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/zi4/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/zi4/m/n/10 "r" []\T1/ptm/m/n /10 only. 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[124] [125] Underfull \hbox (badness 2351) in paragraph at lines 8076--8079 [][][]\T1/zi4/m/n/10 split[][][] []\T1/ptm/m/n/10 for split-ting a vari-able ac -cord-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 t able[][][][]\T1/ptm/m/n/10 , [126] [127] [128] [129] [130] Underfull \hbox (badness 4479) in paragraph at lines 8393--8404 [][][]\T1/zi4/m/n/10 I[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 plot.data.f rame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 print.data.frame[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 row.names[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 names[][][] []\T1/ptm/m/n/10 (for the col-umn names), [131] [132] [133] [134] [135] [136] [137] Underfull \hbox (badness 1629) in paragraph at lines 8861--8873 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 2875) in paragraph at lines 8861--8873 []\T1/zi4/m/n/10 NA[]\T1/ptm/m/n/10 , and hence []\T1/zi4/m/n/10 as.POSIXct("19 69-12-31 23:59:59", tz = "UTC") []\T1/ptm/m/n/10 will give []\T1/zi4/m/n/10 "19 69-12-31 [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] Underfull \hbox (badness 1178) in paragraph at lines 9629--9633 []\T1/ptm/m/n/10 If true, [][][]\T1/zi4/m/n/10 list[][][][]\T1/ptm/m/n/10 s and atomic vec-tors with non-[][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 names (see [][][]\T1/zi4/m/n/10 names[][][][]\T1/ptm/m/n/10 ) are de- [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 2744) in paragraph at lines 11938--11940 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] Underfull \hbox (badness 2253) in paragraph at lines 14134--14136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [217] Underfull \hbox (badness 1490) in paragraph at lines 14169--14172 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [218] Underfull \hbox (badness 1565) in paragraph at lines 14251--14255 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] []\T1/ptm/m/n/10 to find out about sym- bolic links, [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 file.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.files[][][] []\T1/ptm/m/n/10 , and [219] Underfull \hbox (badness 4927) in paragraph at lines 14302--14304 []\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 []\T1/zi4/m/n/10 fsep = [220] Underfull \hbox (badness 3148) in paragraph at lines 14404--14409 [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.fi les[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 help[][][][]\T1/ptm/m/n/10 ; [ ][][]\T1/zi4/m/n/10 RShowDoc[][][] []\T1/ptm/m/n/10 call []\T1/zi4/m/n/10 file. show() []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 type = "text"[]\T1/ptm/m/n/10 . Co n-sider [221] Underfull \hbox (badness 1466) in paragraph at lines 14451--14454 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [222] [223] Underfull \hbox (badness 10000) in paragraph at lines 14582--14586 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\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 14593--14596 [][][]$\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 / [224] [225] [226] [227] [228] Underfull \hbox (badness 3965) in paragraph at lines 14890--14894 []\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, [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 4429) in paragraph at lines 15679--15682 []\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 [241] [242] Underfull \hbox (badness 10000) in paragraph at lines 15785--15787 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [243] Underfull \hbox (badness 2035) in paragraph at lines 15858--15862 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 2452) in paragraph at lines 16471--16475 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment 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 16471--16475 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s 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 [254] [255] Underfull \hbox (badness 1092) in paragraph at lines 16644--16649 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [256] [257] [258] [259] Underfull \hbox (badness 6741) in paragraph at lines 16897--16901 \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/pt m/m/n/10 , [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \vbox (badness 10000) has occurred while \output is active [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1478) in paragraph at lines 18349--18352 []\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 [282] [283] [284] [285] Underfull \hbox (badness 10000) in paragraph at lines 18621--18623 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 18627--18636 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1442) in paragraph at lines 19235--19237 []\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 [296] [297] [298] [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 19566--19572 [301] [302] [303] [304] Underfull \hbox (badness 1248) in paragraph at lines 19811--19814 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\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 , [305] [306] [307] [308] Underfull \hbox (badness 4739) in paragraph at lines 20074--20076 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] Underfull \hbox (badness 2469) in paragraph at lines 21158--21163 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [326] [327] Underfull \hbox (badness 1675) in paragraph at lines 21246--21255 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21256--21271 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the Underfull \hbox (badness 10000) in paragraph at lines 21306--21309 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21306--21309 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [328] [329] Underfull \hbox (badness 1014) in paragraph at lines 21440--21445 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 1264) in paragraph at lines 22289--22297 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [343] Underfull \hbox (badness 4441) in paragraph at lines 22323--22326 []\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/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 5231) in paragraph at lines 23120--23122 []\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 []\T1/zi4/m/n/10 make.unique(c(A, B)) == [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / zlib . net/$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m /n/10 https : / / en . wikipedia . org / wiki / Gzip$[][]\T1/ptm/m/n/10 , [][]$ \T1/zi4/m/n/10 http : / / www . bzip . org/$[][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 24213--24219 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , [][]$\T1/zi4/m/n/10 https : / / tukaani . org / xz/$[][] \T1/ptm/m/n/ 10 and [][]$\T1/zi4/m/n/10 https : [373] [374] [375] [376] [377] [378] [379] [380] Underfull \hbox (badness 2790) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 24710--24713 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [381] [382] [383] [384] [385] Underfull \hbox (badness 1194) in paragraph at lines 25033--25036 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [386] [387] [388] Underfull \hbox (badness 2368) in paragraph at lines 25240--25246 []\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-r e-spond-ing list, i.e., [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 25630--25633 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [395] [396] [397] [398] [399] [400] [401] [402] [403] [404] Underfull \hbox (badness 10000) in paragraph at lines 26251--26253 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] Underfull \hbox (badness 1881) in paragraph at lines 27146--27149 []\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 27171--27173 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [418] [419] Underfull \hbox (badness 2142) in paragraph at lines 27312--27316 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 27369--27374 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [420] [421] [422] [423] Underfull \hbox (badness 10000) in paragraph at lines 27663--27669 []\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 27663--27669 \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 27663--27669 \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 27676--27679 []\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/pt m/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 27702--27704 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [424] Underfull \hbox (badness 10000) in paragraph at lines 27744--27749 []\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 2529) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 27750--27761 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 27762--27765 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [425] [426] [427] [428] [429] Underfull \vbox (badness 3803) has occurred while \output is active [430] Underfull \hbox (badness 10000) in paragraph at lines 28162--28166 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [431] [432] Underfull \hbox (badness 10000) in paragraph at lines 28309--28312 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [433] Underfull \hbox (badness 7925) in paragraph at lines 28390--28394 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 28390--28394 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 28395--28404 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] Underfull \hbox (badness 2726) in paragraph at lines 29391--29394 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 1533) in paragraph at lines 31181--31184 []\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 [477] [478] [479] Underfull \hbox (badness 1163) in paragraph at lines 31344--31355 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [480] [481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 10000) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33008--33012 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33029--33031 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33032--33036 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [506] [507] Underfull \vbox (badness 10000) has occurred while \output is active [508] [509] [510] [511] [512] [513] [514] [515] Underfull \hbox (badness 1655) in paragraph at lines 33626--33628 []\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 [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] Underfull \hbox (badness 2261) in paragraph at lines 34832--34837 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] Underfull \hbox (badness 10000) in paragraph at lines 35952--35963 \T1/zi4/m/n/10 / / docs . microsoft . com / en-[]us / cpp / c-[]language / pars ing-[]c-[]command-[]line-[]arguments ? [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 10000) in paragraph at lines 37483--37485 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [576] Underfull \vbox (badness 10000) has occurred while \output is active [577] [578] [579] [580] [581] [582] Underfull \hbox (badness 2913) in paragraph at lines 37903--37907 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [583] [584] [585] Underfull \hbox (badness 1072) in paragraph at lines 38149--38153 []\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 38154--38158 []\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/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', [586] Underfull \hbox (badness 10000) in paragraph at lines 38194--38200 []\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 38194--38200 \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 38194--38200 \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 Underfull \hbox (badness 3009) in paragraph at lines 38209--38216 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38209--38216 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38209--38216 \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 38209--38216 \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 [587] [588] [589] Underfull \hbox (badness 2644) in paragraph at lines 38444--38448 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [590] [591] [592] Underfull \hbox (badness 1142) in paragraph at lines 38597--38603 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] Underfull \hbox (badness 1158) in paragraph at lines 39914--39916 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 1137) in paragraph at lines 40505--40511 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails [623] Underfull \hbox (badness 4967) in paragraph at lines 40524--40529 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [624] [625] Underfull \hbox (badness 1616) in paragraph at lines 40644--40649 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 1472) in paragraph at lines 41191--41194 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [634] [635] [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] [647] [648] Underfull \hbox (badness 10000) in paragraph at lines 42117--42121 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4/ m/n/10 length(bin) > [649] [650] [651] [652] Underfull \hbox (badness 10000) in paragraph at lines 42368--42371 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [653] [654] [655] Underfull \hbox (badness 10000) in paragraph at lines 42552--42556 [][][]\T1/zi4/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [656] [657] [658] [659] [660] [661] [662] [663] [664] Underfull \hbox (badness 10000) in paragraph at lines 43191--43194 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [665] [666] [667] [668] [669] [670] Underfull \vbox (badness 10000) has occurred while \output is active [671] [672] [673] [674] [675] [676] [677] [678] Underfull \hbox (badness 1990) in paragraph at lines 44113--44121 []\T1/zi4/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 44113--44121 \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 [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] Underfull \hbox (badness 2452) in paragraph at lines 45082--45088 [][][]\T1/zi4/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 3668) in paragraph at lines 45480--45482 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [700] [701] Underfull \hbox (badness 2401) in paragraph at lines 45610--45614 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/n/10 options[][][]("w arn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [702] [703] [704] Underfull \hbox (badness 2111) in paragraph at lines 45818--45823 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/n/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [705] [706] [707] [708] Underfull \hbox (badness 4001) in paragraph at lines 46064--46066 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/n/10 https : / / developer . [709] [710] [711] [712] [713] [714] Underfull \hbox (badness 5417) in paragraph at lines 46429--46433 []\T1/zi4/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [715] Underfull \hbox (badness 10000) in paragraph at lines 46490--46494 []\T1/zi4/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [716]) (./compiler-pkg.tex Chapter 2. [717] [718] [719] [720]) (./datasets-pkg.tex Chapter 3. [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\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. [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803]) (./grDevices-pkg.tex [804] Chapter 4. [805] [806] [807] [808] [809] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/n/10 c(mi, ma, n.)[]\ T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] Underfull \hbox (badness 1424) in paragraph at lines 898--900 [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) an d []\T1/zi4/m/n/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i-fied as [820] [821] [822] [823] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\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 [824] [825] Underfull \hbox (badness 2512) in paragraph at lines 1311--1313 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/n/10 https : / / web . arc hive . org / web / 20190613001950 / http : / / efg2 . com / [826] [827] [828] [829] [830] Underfull \hbox (badness 1490) in paragraph at lines 1611--1616 \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 []\T 1/zi4/m/n/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [831] [832] [833] [834] [835] [836] [837] Underfull \hbox (badness 1325) in paragraph at lines 2038--2048 []\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 "pngalph a"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/1 0 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "bmp32b"[]\T1/ptm/m/n/10 , [838] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [839] [840] [841] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [842] [843] [844] [845] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] Underfull \vbox (badness 3803) has occurred while \output is active [864] [865] [866] [867] Underfull \vbox (badness 3803) has occurred while \output is active [868] Underfull \hbox (badness 10000) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/zi4/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] Underfull \hbox (badness 1584) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 For type []\T1/zi4/m/n/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1/ zi4/m/n/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 4914--4921 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [883] [884] [885] [886] Underfull \hbox (badness 1377) in paragraph at lines 5220--5225 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [887] Underfull \hbox (badness 1418) in paragraph at lines 5296--5303 \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 "Helvet ica-Narrow"[]\T1/ptm/m/n/10 , [888] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [889] Underfull \hbox (badness 1377) in paragraph at lines 5425--5430 []\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 [890] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\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 [891] Underfull \vbox (badness 3803) has occurred while \output is active [892] Underfull \hbox (badness 2035) in paragraph at lines 5632--5641 []\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 5632--5641 \T1/ptm/m/n/10 vided: []\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-Na rrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/zi4/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/zi 4/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "URWBookman"[]\T1/ptm/m /n/10 , [893] [894] Underfull \hbox (badness 10000) in paragraph at lines 5700--5702 []\T1/zi4/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/z i4/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [895] [896] Underfull \hbox (badness 1546) in paragraph at lines 5844--5852 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi4 /m/n/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 title[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 encoding[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 bg[]\T1/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 , [897] [898] [899] [900] [901] [902] [903] [904] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/zi4/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [905] [906] Underfull \vbox (badness 3803) has occurred while \output is active [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [919] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [920] [921] [922] [923] [924] Underfull \hbox (badness 3780) in paragraph at lines 7630--7636 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/n /10 "AvantGarde"[]\T1/ptm/m/n/10 , [925] [926] [927] [928] [929] [930]) (./graphics-pkg.tex Chapter 5. [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] Overfull \hbox (12.71341pt too wide) in paragraph at lines 983--983 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 4634) in paragraph at lines 1357--1360 [][][]\T1/zi4/m/n/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready work s nowa-days with data.frames; [][][]\T1/zi4/m/n/10 boxplot.formula[][][][]\T1/p tm/m/n/10 , [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] Underfull \hbox (badness 1728) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [970] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \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 [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] Underfull \vbox (badness 10000) has occurred while \output is active [994] Underfull \vbox (badness 10000) has occurred while \output is active [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\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 [1007] [1008] [1009] [1010] [1011] Underfull \hbox (badness 1107) in paragraph at lines 5081--5087 []\T1/ptm/m/n/10 is []\T1/zi4/m/n/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sca led to user co-or-di-nates. Note that []\T1/zi4/m/n/10 c([][]strwidth[][][](ch) , [1012] [1013] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [1014 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 Underfull \vbox (badness 10000) has occurred while \output is active [1015] [1016 ] [1017] [1018] Underfull \vbox (badness 3803) has occurred while \output is active [1019] [1020] [1021] [1022] [1023] [1024] [1025] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [1040 ] [1041] Underfull \vbox (badness 3803) has occurred while \output is active [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] Underfull \hbox (badness 4954) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /n/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 8938--8940 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/n/10 par (c("font.lab", "cex.lab", [1075] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1076] [1077] [1078] [1079]) (./grid-pkg.tex [1080] Chapter 6. [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] Underfull \hbox (badness 2680) in paragraph at lines 550--553 []\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-c u-la-tion of [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] Underfull \hbox (badness 4279) in paragraph at lines 1187--1196 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/n/10 pushViewport[][][][]\T1/p tm/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 seekViewpo rt[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 upViewport[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/n/10 unit[][][][]\T1/ptm/m/n/10 , [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \vbox (badness 10000) has occurred while \output is active [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\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 [1162] [1163] [1164] [1165] [1166] [1167] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 2142) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/n/10 gridGTreeCoords []\T1/ptm/m/n/1 0 a list of ei-ther []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1175] [1176] Underfull \hbox (badness 4699) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/zi4/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208]) (./methods-pkg.tex Chapter 7. [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] 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-ten ds []\T1/zi4/m/n/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/n/1 0 "package"[]\T1/ptm/m/n/10 , also of class [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] 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 can 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/10 it calls []\T1/zi4/m/n/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1237] [1238] [1239] Underfull \hbox (badness 2213) in paragraph at lines 2213--2218 []\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 = [1240] [1241] [1242] [1243] [1244] Underfull \hbox (badness 10000) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/zi4/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class [1245] [1246] Underfull \hbox (badness 1132) in paragraph at lines 2713--2717 []\T1/ptm/m/n/10 In []\T1/zi4/m/n/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi4 /m/n/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/n/10 package []\T1/ptm/m/n/10 sl ot of the re-turned re-sult is in [1247] Underfull \hbox (badness 1033) in paragraph at lines 2745--2750 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/n/10 removeGeneric []\T1/ptm/m/n/10 r e-moves the func-tion it-self; []\T1/zi4/m/n/10 removeMethods []\T1/ptm/m/n/10 re-stores the [1248] [1249] [1250] [1251] [1252] [1253] [1254] Underfull \hbox (badness 1102) in paragraph at lines 3302--3304 []\T1/zi4/m/n/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1255] [1256] [1257] [1258] [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 3641--3650 []\T1/ptm/m/n/10 The [1261] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = "numeric", [1262] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] Underfull \hbox (badness 1769) in paragraph at lines 4476--4482 []\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 4476--4482 []\T1/zi4/m/n/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [] [][]\T1/zi4/m/n/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion use d by [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] Underfull \vbox (badness 10000) has occurred while \output is active [1283] [1284] [1285] Underfull \hbox (badness 4036) in paragraph at lines 5445--5448 []\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 [1286] [1287] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1288] [1289] [1290] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\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 [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1675) in paragraph at lines 6459--6465 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/n/10 externalRef Method(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1300] [1301] [1302] [1303] Underfull \vbox (badness 10000) has occurred while \output is active [1304] [1305] [1306] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1307] [1308] [1309] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} [1310] Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\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 [1311] [1312] [1313] Underfull \hbox (badness 1286) in paragraph at lines 7492--7494 []\T1/ptm/m/n/10 for []\T1/zi4/m/n/10 .selectSuperClasses() []\T1/ptm/m/n/10 on ly, a [][][]\T1/zi4/m/n/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, t yp-i-cally [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\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., [1356] [1357] [1358] [1359]) (./parallel-pkg.tex [1360] 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/z i4/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1361] [1362] [1363] [1364] [1365] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] Underfull \hbox (badness 3386) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1383] [1384] [1385]) (./splines-pkg.tex [1386] 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 [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]) (./stats-pkg.tex Chapter 10. [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] Underfull \hbox (badness 1412) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 2503) in paragraph at lines 1369--1372 []\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 , [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 2503) in paragraph at lines 3530--3533 []\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 , [1459] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\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 = [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2556) in paragraph at lines 5424--5427 []\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 "fi lter"[]\T1/ptm/m/n/10 . For [1489] [1490] [1491] [1492] [1493] [1494] [1495] Underfull \hbox (badness 2503) in paragraph at lines 5838--5842 []\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 , [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 7081) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n 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 6636--6638 []\T1/zi4/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 10000) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \vbox (badness 10000) has occurred while \output is active [1544] [1545] [1546] [1547] [1548] Underfull \hbox (badness 2626) in paragraph at lines 9185--9188 []\T1/ptm/m/n/10 Either []\T1/zi4/m/n/10 "convolution" []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1549] [1550] Underfull \hbox (badness 2503) in paragraph at lines 9292--9296 []\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 , [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] [1574] [1575] [1576] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\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 11024--11027 []\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, [1577] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1578] [1579] [1580] [1581] [1582] [1583] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} [1592] [1593] Underfull \hbox (badness 1484) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/n/10 SSinit = [1604] [1605] [1606] [1607] [1608] [1609] Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1610] [1611] [1612] [1613] [1614] [1615] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1616] [1617] [1618] [1619] [1620] [1621] [1622] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1633] [1634] Underfull \hbox (badness 6412) in paragraph at lines 14660--14664 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/n/10 (surface = "inte rpolate", statistics = [1635] Underfull \hbox (badness 1199) in paragraph at lines 14667--14669 []\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 [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 2503) in paragraph at lines 15743--15747 []\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 , [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/n/ 10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16253--16259 []\T1/zi4/m/n/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 model.re sponse(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/n/10 model.offset []\T1/ ptm/m/n/10 sums any terms [1662] [1663] [1664] [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 1158) in paragraph at lines 17906--17909 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/n/10 nls []\T1 /ptm/m/n/10 as the data ar-gu-ment. The ac- [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] Underfull \vbox (badness 10000) has occurred while \output is active [1691] Underfull \vbox (badness 10000) has occurred while \output is active [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 1377) in paragraph at lines 18933--18938 []\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 18938--18941 []\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 2343) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18951--18955 \T1/ptm/m/n/10 the 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 18959--18963 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/n/10 "BFGS"[]\T 1/ptm/m/n/10 , []\T1/zi4/m/n/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/n/1 0 "SANN" []\T1/ptm/m/n/10 meth-ods if [1706] [1707] [1708] Underfull \vbox (badness 10000) has occurred while \output is active [1709] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19184--19184 []\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 19187--19187 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1710] [1711] [1712] [1713] [1714] [1715] [1716] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\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 [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/zi4/m/n/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 s distance", lty = cook.lty, col = cook.col, text.col [1726] [1727] [1728] [1729] [1730] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1731] [1732] [1733] [1734] [1735] [1736] Underfull \hbox (badness 2503) in paragraph at lines 20826--20829 []\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 , [1737] Underfull \hbox (badness 3919) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/zi4/m/n/10 "Comparison of Poisson [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\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/1 0 , [][][]\T1/zi4/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\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 [1779] [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 1436) in paragraph at lines 23714--23717 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/n/10 max(2, [1786] Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] Underfull \hbox (badness 1824) in paragraph at lines 24827--24833 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/n/10 x []\T1/ptm/m/n/10 are f irst re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1803] Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/n/10 y[j] = [1804] Underfull \vbox (badness 3803) has occurred while \output is active [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 2165) in paragraph at lines 25429--25434 []\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/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1813] [1814] [1815] [1816] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\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 25653--25657 []\T1/ptm/m/n/10 where []\T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 PP <- [1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] [1841] Underfull \vbox (badness 10000) has occurred while \output is active [1842] [1843] Underfull \hbox (badness 3514) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1844] [1845] [1846] [1847] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27535--27535 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1848] Overfull \hbox (20.23795pt too wide) in paragraph at lines 27628--27628 []\T1/zi4/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (11.22874pt too wide) in paragraph at lines 27630--27630 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1849] [1850] [1851] Underfull \hbox (badness 3514) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1852] [1853] Underfull \hbox (badness 3514) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1854] Underfull \hbox (badness 3514) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1855] [1856] Underfull \hbox (badness 3514) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1857] [1858] Underfull \hbox (badness 6691) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] Underfull \hbox (badness 4024) in paragraph at lines 28633--28636 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] Underfull \hbox (badness 5431) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1877] [1878] [1879] Underfull \hbox (badness 5431) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1880] [1881] [1882] [1883] [1884] [1885] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\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 [1886] [1887] [1888] [1889] [1890] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] Underfull \hbox (badness 3557) in paragraph at lines 31217--31221 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/n/10 extendInt []\T1/ptm/m/n/10 to a non-[ ]\T1/zi4/m/n/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-rect []\T1/zi4/m/n/10 interval = [1910] [1911] [1912] Underfull \vbox (badness 10000) has occurred while \output is active [1913] [1914] [1915] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\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 [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\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 [1925] [1926] [1927] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32317--32317 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1928] [1929] [1930] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32478--32478 [] \T1/zi4/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1931] [1932] [1933] [1934] [1935]) (./stats4-pkg.tex [1936] Chapter 11. [1937] [1938] [1939] Underfull \vbox (badness 10000) has occurred while \output is active [1940] Underfull \vbox (badness 10000) has occurred while \output is active [1941] [1942] [1943] [1944] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1945] [1946] [1947]) (./tcltk-pkg.tex [1948] Chapter 12. [1949] [1950] [1951] [1952] [1953] [1954] [1955] Underfull \vbox (badness 10000) has occurred while \output is active [1956] Underfull \vbox (badness 10000) has occurred while \output is active [1957] Underfull \hbox (badness 1546) in paragraph at lines 666--673 []\T1/zi4/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1958] [1959] [1960] [1961] [1962] Underfull \vbox (badness 10000) has occurred while \output is active [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970]) (./tools-pkg.tex Chapter 13. [1971] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1972] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1973] [1974] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\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 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/n/10 bi bentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/n/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatIn Proceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 formatManual[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/n/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\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/zi 4/m/n/10 formatTechreport []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1977] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\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 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1990] Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\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 1217--1220 []\T1/zi4/m/n/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and [ ]\T1/zi4/m/n/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 2293) in paragraph at lines 1569--1571 []\T1/zi4/m/n/10 CRAN_memtest_notes() []\T1/ptm/m/n/10 is now dep-re-cated, wit h its func-tion-al-ity in-te-grated into that of Underfull \hbox (badness 10000) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/zi4/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1996] [1997] Underfull \hbox (badness 4096) in paragraph at lines 1714--1722 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1724--1726 []\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 [1998] [1999] [2000] [2001] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2002] [2003] [2004] [2005] [2006] Overfull \hbox (8.25941pt too wide) in paragraph at lines 2230--2230 [] \T1/zi4/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] [2007] [2008] [2009] Underfull \hbox (badness 4096) in paragraph at lines 2399--2407 \T1/zi4/m/n/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2010] [2011] [2012] [2013] [2014] [2015] [2016] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2893. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2894. [2017] [2018] [2019] [2020] [2021] Underfull \hbox (badness 1424) in paragraph at lines 3196--3198 []\T1/zi4/m/it/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2034] [2035] Underfull \hbox (badness 10000) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/it/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/it/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2036] [2037] [2038] [2039] [2040] [2041] Underfull \hbox (badness 1796) in paragraph at lines 4399--4404 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/it/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/it/10 type = = Underfull \hbox (badness 4699) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/zi4/m/it/10 msgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 1946) in paragraph at lines 4449--4453 []\T1/zi4/m/it/10 "--update"[]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m /n/10 4.2.0, []\T1/zi4/m/it/10 "--no-wrap" []\T1/ptm/m/n/10 is used when called from [2042] Underfull \hbox (badness 1838) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [2043] [2044] [2045] [2046] Underfull \hbox (badness 2197) in paragraph at lines 4750--4760 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/it/10 available.packages[][][][]\T1/ptm/m/n/10 : [2047] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\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 [2048] [2049] [2050] [2051]) (./utils-pkg.tex [2052] Chapter 14. [2053] 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 `[] \T1/zi4/m/it/10 insertions[]\T1/ptm/m/n/10 ', [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/it/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/it/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 726--732 []\T1/zi4/m/it/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2064] [2065] [2066] Underfull \hbox (badness 3861) in paragraph at lines 931--936 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/it/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/it/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2067] [2068] [2069] Underfull \hbox (badness 3323) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/zi4/m/it /10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m $\T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 2875) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 taken as [][][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex. max", 1) []\T1/ptm/m/n/10 which is []\T1/zi4/m/it/10 1 []\T1/ptm/m/n/10 typ-i-c ally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \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 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] Underfull \hbox (badness 1371) in paragraph at lines 1638--1640 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2078] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1708. [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] Underfull \hbox (badness 2057) in paragraph at lines 2359--2361 []\T1/ptm/m/n/10 None for []\T1/zi4/m/it/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2089] [2090] [2091] [2092] [2093] [2094] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 6842) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/it/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2115] Underfull \hbox (badness 1430) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/it/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2116] Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/it/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/it/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 able []\T1/zi4/m/it/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2117] [2118] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/it/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2140] [2141] [2142] [2143] [2144] [2145] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 6502. Underfull \hbox (badness 1371) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/it/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/it/10 ccaddress []\T1/ptm/m/n/10 to pass to [2154] Underfull \hbox (badness 1502) in paragraph at lines 6595--6600 []\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 6595--6600 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2155] [2156] [2157] Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2158] Underfull \hbox (badness 2150) in paragraph at lines 6832--6835 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2159] [2160] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\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 [2161] [2162] [2163] Underfull \hbox (badness 1325) in paragraph at lines 7150--7154 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/it/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2164] Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2165] Underfull \hbox (badness 3219) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/i t/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \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 7313--7320 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 7313--7320 [][][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")[] \T1/ptm/m/n/10 . []\T1/zi4/m/it/10 type = "both" []\T1/ptm/m/n/10 will be silen tly Underfull \hbox (badness 2932) in paragraph at lines 7321--7324 []\T1/ptm/m/n/10 Using pack-ages with []\T1/zi4/m/it/10 type = "source" []\T1/p tm/m/n/10 al-ways works pro-vided the pack-age con-tains no [2166] Underfull \hbox (badness 1024) in paragraph at lines 7448--7451 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing []\T1/zi4/m/it/10 available. packages(filters = "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 , ] []\T1/ ptm/m/n/10 will [2167] Underfull \hbox (badness 10000) in paragraph at lines 7481--7486 [][][]\T1/zi4/m/it/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/i t/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 download. packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 installed.packages[][][] []\T1/ptm/m/n/10 , [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] Underfull \hbox (badness 10000) in paragraph at lines 8185--8187 []\T1/ptm/m/n/10 typically the re-sult of []\T1/zi4/m/it/10 methods(..)[]\T1/pt m/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] Underfull \hbox (badness 2310) in paragraph at lines 8945--8950 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] Underfull \hbox (badness 1248) in paragraph at lines 9471--9475 []\T1/zi4/m/it/10 R CMD build []\T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/ m/n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2200] Underfull \hbox (badness 1789) in paragraph at lines 9551--9553 []\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 [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] Underfull \hbox (badness 1097) in paragraph at lines 10388--10391 []\T1/ptm/m/n/10 The name []\T1/zi4/m/it/10 "clipboard" []\T1/ptm/m/n/10 may al so be used on Win-dows, in which case [2214] [2215] Underfull \hbox (badness 3000) in paragraph at lines 10524--10529 [][][]\T1/zi4/m/it/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/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/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ it/10 read.table[][][][]\T1/ptm/m/n/10 ; [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] Underfull \hbox (badness 2134) in paragraph at lines 11113--11118 [][][]\T1/zi4/m/it/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/it/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/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ it/10 write.table[][][][]\T1/ptm/m/n/10 ; [2225] Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/zi4/m/it/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/it/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] Underfull \hbox (badness 2469) in paragraph at lines 11663--11667 []\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 11663--11667 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2234] [2235] [2236] [2237] [2238] [2239] Underfull \hbox (badness 4060) in paragraph at lines 12087--12090 []\T1/ptm/m/n/10 If `[]\T1/zi4/m/it/10 --default-packages[]\T1/ptm/m/n/10 ' is not used, then []\T1/zi4/m/it/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron- ment vari-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 12110--12110 []\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 '[] [2240] [2241] [2242] [2243] Underfull \hbox (badness 2150) in paragraph at lines 12365--12367 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / www . gnu . org / software / emac s / manual / [2244] [2245] [2246] [2247] Underfull \hbox (badness 10000) in paragraph at lines 12585--12589 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/it/10 stylepath []\T1/ptm/m/n/10 is now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12618--12624 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2248] Underfull \hbox (badness 2762) in paragraph at lines 12633--12641 \T1/ptm/m/n/10 UTF-8 lo-cales (note that pdf-TeX as-sumes UTF-8 by de-fault sin ce 2018). 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If Underfull \hbox (badness 4779) in paragraph at lines 12852--12854 []\T1/ptm/m/n/10 The file `\T1/zi4/m/it/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI ([]\T1/zi4/m/it/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-do ws and [2251] Underfull \hbox (badness 1077) in paragraph at lines 12882--12889 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2252] [2253] [2254] [2255] [2256] [2257] [2258] Underfull \hbox (badness 3780) in paragraph at lines 13290--13294 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][][]\ T1/zi4/m/it/10 options[][][]("BioC_mirror")[]\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 13306--13309 []\T1/ptm/m/n/10 Repository `[]\T1/zi4/m/it/10 CRAN[]\T1/ptm/m/n/10 ' is treate d spe-cially: the value is taken from the cur-rent set-ting of [2259] [2260] [2261] Underfull \hbox (badness 2302) in paragraph at lines 13511--13513 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2262] [2263] [2264] [2265] [2266] Underfull \hbox (badness 10000) in paragraph at lines 13810--13815 []\T1/ptm/m/n/10 logical; if []\T1/zi4/m/it/10 TRUE []\T1/ptm/m/n/10 (de-fault) , [][][]\T1/zi4/m/it/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13819--13822 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2267] [2268] [2269] [2270] [2271] [2272] [2273] Underfull \hbox (badness 2932) in paragraph at lines 14252--14259 []\T1/ptm/m/n/10 If []\T1/zi4/m/it/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fa ult) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 and se-lected if their []\T1/zi4/m/it/10 extension []\T1/ptm/m/n /10 com-po-nent matches (as a reg-exp) the file name. Ob- [2274] [2275] [2276] Underfull \hbox (badness 1460) in paragraph at lines 14417--14425 \T1/ptm/m/n/10 drives can be in-cluded in filepaths). []\T1/zi4/m/it/10 Rtools []\T1/ptm/m/n/10 4 and ear-lier in-cluded a []\T1/zi4/m/it/10 tar []\T1/ptm/m/n /10 which used [2277] [2278] Underfull \hbox (badness 6510) in paragraph at lines 14567--14571 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/zi4/m/it/10 tar []\T1/ptm/m/n/10 is set to the com-mand []\T1/zi4/m/it/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 14574--14577 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 14574--14577 \T1/zi4/m/it/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2279] [2280] [2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288] Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 []\T1/ptm/m/n/10 Arguments such as []\T1/zi4/m/it/10 destdir []\T1/ptm/m/n/10 a nd []\T1/zi4/m/it/10 dependencies []\T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 15243--15248 [][][]\T1/zi4/m/it/10 install.packages[][][] []\T1/ptm/m/n/10 and []\T1/zi4/m/i t/10 ignore_repo_cache[]\T1/ptm/m/n/10 , []\T1/zi4/m/it/10 max_repo_cache_age [ ]\T1/ptm/m/n/10 and Underfull \hbox (badness 1052) in paragraph at lines 15249--15251 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. 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usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on fullrefman.pdf (2415 pages, 6535325 bytes). 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'/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' building package 'tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' building package 'compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/compiler' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tools' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' building package 'utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/utils' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[9]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[8]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src/cairo' make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grDevices' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' building package 'graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/graphics' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' building package 'stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' building package 'datasets' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/datasets' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' building package 'methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/methods' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' building package 'grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/grid' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' building package 'splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/splines' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' building package 'stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/stats4' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk/src' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/tcltk' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' building package 'parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[6]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[7]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[6]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel/src' make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/parallel' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' building/updating vignettes for package 'grid' ... building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... building/updating vignettes for package 'stats' ... processing 'reshape.Rnw' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' touch make-indep-stamp fakeroot debian/rules binary *** check *** xvfb-run make check-all make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 7432,7433c7432,7433 < Fisher's Exact Test for Count Data hybrid using asym.chisq. iff < (exp=5, perc=80, Emin=1) --- > Fisher's Exact Test for Count Data hybrid using asym.chisq. iff (exp=5, > perc=80, Emin=1) 14066,14067c14066 < 4-sample test for equality of proportions without continuity < correction --- > 4-sample test for equality of proportions without continuity correction 14096,14097c14095 < 4-sample test for equality of proportions without continuity < correction --- > 4-sample test for equality of proportions without continuity correction 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/reproducible-path/r-base-4.2.2.20221110/tests/Examples' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running strict specific tests make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 'structure.R' ... OK comparing 'structure.Rout' to './structure.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/reproducible-path/r-base-4.2.2.20221110/tests' running sloppy specific tests make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'print-tests.R' ... OK comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK running code in 'lapack.R' ... OK comparing 'lapack.Rout' to './lapack.Rout.save' ...246,250c246,250 < [1,] -0.4659 -0.04141 -0.8795 -8.440e-02 -0.02379 < [2,] -0.3931 0.15031 0.2249 -1.824e-05 -0.87881 < [3,] -0.3811 0.62205 0.2170 -5.570e-01 0.33239 < [4,] -0.5166 0.14296 0.1852 7.659e-01 0.30290 < [5,] -0.4652 -0.75386 0.3073 -3.097e-01 0.15780 --- > [1,] -0.4659 -0.04141 -0.8795 8.440e-02 0.02379 > [2,] -0.3931 0.15031 0.2249 1.824e-05 0.87881 > [3,] -0.3811 0.62205 0.2170 5.570e-01 -0.33239 > [4,] -0.5166 0.14296 0.1852 -7.659e-01 -0.30290 > [5,] -0.4652 -0.75386 0.3073 3.097e-01 -0.15780 254,258c254,258 < [1,] -0.4831 -0.3264 0.47567 0.1955 -0.6289 < [2,] -0.3627 0.3731 0.53450 -0.5920 0.3051 < [3,] -0.3995 0.4779 -0.59210 -0.2252 -0.4590 < [4,] -0.3983 -0.6985 -0.36298 -0.3821 0.2752 < [5,] -0.5628 0.1948 -0.07549 0.6439 0.4743 --- > [1,] -0.4831 -0.3264 0.47567 -0.1955 0.6289 > [2,] -0.3627 0.3731 0.53450 0.5920 -0.3051 > [3,] -0.3995 0.4779 -0.59210 0.2252 0.4590 > [4,] -0.3983 -0.6985 -0.36298 0.3821 -0.2752 > [5,] -0.5628 0.1948 -0.07549 -0.6439 -0.4743 266,270c266,270 < [1,] -0.4659 -0.04141 -0.8795 -8.440e-02 -0.02379 < [2,] -0.3931 0.15031 0.2249 -1.824e-05 -0.87881 < [3,] -0.3811 0.62205 0.2170 -5.570e-01 0.33239 < [4,] -0.5166 0.14296 0.1852 7.659e-01 0.30290 < [5,] -0.4652 -0.75386 0.3073 -3.097e-01 0.15780 --- > [1,] -0.4659 -0.04141 -0.8795 8.440e-02 0.02379 > [2,] -0.3931 0.15031 0.2249 1.824e-05 0.87881 > [3,] -0.3811 0.62205 0.2170 5.570e-01 -0.33239 > [4,] -0.5166 0.14296 0.1852 -7.659e-01 -0.30290 > [5,] -0.4652 -0.75386 0.3073 3.097e-01 -0.15780 277,278c277,278 < [4,] 0.1955 -0.5920 -0.2252 -0.3821 0.64390 < [5,] -0.6289 0.3051 -0.4590 0.2752 0.47430 --- > [4,] -0.1955 0.5920 0.2252 0.3821 -0.64390 > [5,] 0.6289 -0.3051 0.4590 -0.2752 -0.47430 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/reproducible-path/r-base-4.2.2.20221110/tests' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' checking Sys.timezone ... make[5]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'timezone.R' ... OK make[5]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running regression tests ... make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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 'd-p-q-r-tst-2.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/reproducible-path/r-base-4.2.2.20221110/tests' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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' ...611c611 < skipping tests requiring the Matrix package --- > [ ]: .M.sub.i.logical() maybe inefficient 1257c1257,1280 < skipping tests requiring the Matrix package --- > > 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)) > > m2 <- matrix(c(0, 0, 2:0), 3, 5) > > (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"), m2), identical(as(c2, "matrix"), m2), identical(as(c3, > + "matrix"), m2)) > > invisible(lapply(c("Z", "C", "C2", "C3"), removeClass)) 1305c1328,1336 < skipping tests requiring the Matrix package --- > > sci <- names(getClass("integer")@contains) > > setClass("MyClass") > > ncl <- "NumOrMyClass" > > setClassUnion(ncl, c("numeric", "MyClass")) > > nsci <- names(getClass("integer")@contains) > > stopifnot(sci %in% nsci, identical(setdiff(nsci, sci), ncl)) > > setClassUnion("dMatrixOrMatrix", members = c("dMatrix", "matrix")) > > stopifnot("dMatrixOrMatrix" %in% names(getClass("dgCMatrix")@contains)) > > invisible(lapply(c("NumOrMyClass", "MyClass", "dMatrixOrMatrix"), removeClass)) OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests of Internet functions make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,145 < 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 > > > > 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 > > OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests of date-time printing expect platform-specific differences make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'datetime2.R' ... OK comparing 'datetime2.Rout' to './datetime2.Rout.save' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests of documentation examples make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'R-intro.R' ... OK comparing 'R-intro.Rout' to './R-intro.Rout.save' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' gcc -I"/build/reproducible-path/r-base-4.2.2.20221110/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R-exts.c -o R-exts.o gcc -shared -L/build/reproducible-path/r-base-4.2.2.20221110/lib -Wl,-z,relro -o R-exts.so R-exts.o -L/build/reproducible-path/r-base-4.2.2.20221110/lib -lR make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'R-exts.R' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests of consistency of as/is.* make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests of random deviate generation make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running demos from base and stats make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests of primitives make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'primitives.R' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running regexp regression tests make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests of translation make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'reg-translation.R' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running more Internet and socket tests make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'internet2.R' ... OK running code in 'libcurl.R' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests of CRAN tools (can be slow unless mirror is local) make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'CRANtools.R' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running tests to possibly trigger segfaults make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' creating 'no-segfault.R' running code in 'no-segfault.R' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' testing building standalone Rmath make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' check output can be found in src/nmath/standalone/check.log make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running unit tests for the condition system make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' running code in 'conditions.R' ... OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' building NEWS database [for news() example] make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[4]: 'NEWS.rds' is up to date. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' -rw-r--r-- 1 root root 190768 Jan 26 01:49 NEWS.rds make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' checking package 'base' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/base.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'base' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown packages 'round', 'date', 'chron', 'nnet' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking examples ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/base.Rcheck/00check.log' for details. checking package 'tools' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/tools.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'tools' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown package 'mathjaxr' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking R/sysdata.rda ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running 'QC.R' Running 'Rd.R' Running 'Rd2HTML.R' Running 'S3.R' Running 'undoc.R' OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/tools.Rcheck/00check.log' for details. checking package 'utils' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/utils.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'utils' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown packages 'knitr', 'nlme', 'MASS' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking R/sysdata.rda ... OK * checking compiled code ... OK * checking files in 'vignettes' ... OK * checking examples ... SKIPPED * checking tests ... Running 'Sweave-tst.R' Running 'charclass.R' ERROR Running the tests in 'tests/charclass.R' failed. Last 13 lines of output: + charClass(testCodepoints[["ASCII"]], "digit"))) + } > { + stopifnot(all.equal( + c(FALSE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE, TRUE), + charClass(testCodepoints[["ASCII"]], "alnum"))) + } > { + stopifnot(all.equal( + c(TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE), + charClass(testCodepoints[["Cyrillic"]], "alpha"))) + } Error: c(TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE) and charClass(testCodepoints[["Cyrillic"]], "alpha") are not equal: 4 element mismatches Execution halted * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'Sweave.Rnw'... OK OK * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/utils.Rcheck/00check.log' for details. checking package 'grDevices' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/grDevices.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'grDevices' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown packages 'KernSmooth', 'MASS' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running 'convertColor-tests.R' Running 'ps-tests.R' Comparing 'ps-tests.Rout' to 'ps-tests.Rout.save' ... OK Running 'saved-recordPlot.R' Running 'xfig-tests.R' Comparing 'xfig-tests.Rout' to 'xfig-tests.Rout.save' ... OK OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/grDevices.Rcheck/00check.log' for details. checking package 'graphics' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/graphics.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'graphics' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown packages 'vcd', 'lattice', 'MASS', 'KernSmooth' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/graphics.Rcheck/00check.log' for details. checking package 'stats' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/stats.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'stats' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown packages 'multcomp', 'coin', 'nlme', 'cluster', 'MASS', 'rpart', 'Matrix', 'pcaPP', 'Kendall', 'SuppDists', 'pspearman', 'robustbase', 'survival' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking files in 'vignettes' ... OK * checking examples ... SKIPPED * checking tests ... Running 'NLSstClosest.R' Running 'arimaML.R' Running 'bandwidth.R' Comparing 'bandwidth.Rout' to 'bandwidth.Rout.save' ... OK Running 'cmdscale.R' Running 'drop1-polr.R' Running 'glm-etc.R' Running 'glm.R' Comparing 'glm.Rout' to 'glm.Rout.save' ... OK Running 'ig_glm.R' Running 'ks-test.R' Comparing 'ks-test.Rout' to 'ks-test.Rout.save' ... OK Running 'nafns.R' Running 'nlm.R' Running 'nls.R' Comparing 'nls.Rout' to 'nls.Rout.save' ...81c81,85 < skipping tests requiring the MASS package --- > Waiting for profiling to be done... > 2.5% 97.5% > a 1.00875 1.037847 > b 0.84138 0.914645 > c NA 0.042807 266a271,279 > Waiting for profiling to be done... > 2.5% 97.5% > Asym 2.14936 2.5724 > xmid 1.28535 1.6966 > scal 0.97526 1.1068 > Waiting for profiling to be done... > 2.5% 97.5% > xmid 1.2866 1.6949 > scal 0.9757 1.1063 295a309,311 > Waiting for profiling to be done... > 2.5% 97.5% > 0.68704 0.70281 303a320,322 > Waiting for profiling to be done... > 2.5% 97.5% > 0.68704 0.70281 309a329,332 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.49494 0.50893 > b 0.70019 0.74767 317a341,344 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.49494 0.50893 > b 0.70019 0.74767 323a351,355 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.35006 0.66057 > b 0.45107 0.91473 > logc -0.64627 0.40946 331a364,368 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.35006 0.66057 > b 0.45107 0.91473 > logc -0.64627 0.40946 338a376,380 > 2.5% 97.5% > 0.70019 0.74767 > 2.5% 97.5% > b 0.45105 0.91471 > logc -0.64625 0.40933 408a451,453 > 2.5% 97.5% > a 0.96 5.20 > b NA 1.07 459a505,508 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.907 NA > b NA 0.611 Running 'offsets.R' Running 'ppr.R' Running 'simulate.R' Comparing 'simulate.Rout' to 'simulate.Rout.save' ...366c366,399 < skipping tests requiring the MASS package --- > > > > ## gamma fit, from example(glm) > > clotting <- data.frame(u = c(5,10,15,20,30,40,60,80,100), > + lot1 = c(118,58,42,35,27,25,21,19,18)) > > fit7 <- glm(lot1 ~ log(u), data = clotting, family = Gamma) > > coef(summary(fit7)) > Estimate Std. Error t value Pr(>|t|) > (Intercept) -0.016554 0.00092755 -17.847 4.2791e-07 > log(u) 0.015343 0.00041496 36.975 2.7512e-09 > > set.seed(1) > > ( ys <- simulate(fit7, nsim = 3) ) > sim_1 sim_2 sim_3 > 1 119.451 118.552 123.140 > 2 56.310 51.798 48.747 > 3 42.193 39.456 40.843 > 4 34.581 33.905 35.580 > 5 26.208 26.971 27.210 > 6 25.476 25.840 24.437 > 7 22.287 22.151 21.375 > 8 20.206 20.503 19.626 > 9 18.224 19.094 17.952 > > for(i in seq_len(3)) > + print(coef(summary(update(fit7, ys[, i] ~ .)))) > Estimate Std. Error t value Pr(>|t|) > (Intercept) -0.016008 0.00077887 -20.553 1.6197e-07 > log(u) 0.015044 0.00034611 43.465 8.9084e-10 > Estimate Std. Error t value Pr(>|t|) > (Intercept) -0.015483 0.00050102 -30.903 9.5910e-09 > log(u) 0.014935 0.00021999 67.889 3.9547e-11 > Estimate Std. Error t value Pr(>|t|) > (Intercept) -0.016850 0.00075120 -22.431 8.8554e-08 > log(u) 0.015569 0.00033659 46.256 5.7704e-10 > > > > Running 'smooth.spline.R' Running 'table-margins.R' Running 'ts-tests.R' OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'reshape.Rnw'... OK OK * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/stats.Rcheck/00check.log' for details. checking package 'datasets' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/datasets.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'datasets' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking examples ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK checking package 'methods' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/methods.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'methods' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown package 'Matrix' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running 'S3.R' Running 'basicRefClass.R' Running 'duplicateClass.R' Running 'envRefClass.R' Running 'fieldAssignments.R' Running 'mixinInitialize.R' Running 'namesAndSlots.R' Running 'nextWithDots.R' Running 'refClassExample.R' Running 'testConditionalIs.R' Running 'testGroupGeneric.R' Running 'testIs.R' OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/methods.Rcheck/00check.log' for details. checking package 'grid' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/grid.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'grid' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown package 'lattice' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking files in 'vignettes' ... OK * checking examples ... SKIPPED * checking tests ... Running 'bugs.R' Running 'clippaths.R' Running 'compositing.R' Running 'coords.R' Running 'grep.R' Comparing 'grep.Rout' to 'grep.Rout.save' ... OK Running 'groups.R' Running 'masks.R' Running 'nesting.R' Running 'paths.R' Running 'patterns.R' Running 'reg.R' Running 'testls.R' Comparing 'testls.Rout' to 'testls.Rout.save' ... OK Running 'units.R' OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'displaylist.Rnw'... OK 'frame.Rnw'... OK 'grid.Rnw'... OK 'grobs.Rnw'... OK 'interactive.Rnw'... OK 'locndimn.Rnw'... OK 'moveline.Rnw'... OK 'nonfinite.Rnw'... OK 'plotexample.Rnw'... OK 'rotated.Rnw'... OK 'saveload.Rnw'... OK 'sharing.Rnw'... OK 'viewports.Rnw'... OK OK * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/grid.Rcheck/00check.log' for details. checking package 'splines' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/splines.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'splines' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown package 'Matrix' in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running 'sparse-tst.R' Running 'spline-tst.R' OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/build/reproducible-path/r-base-4.2.2.20221110/tests/splines.Rcheck/00check.log' for details. checking package 'stats4' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/stats4.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'stats4' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking examples ... SKIPPED * checking tests ... Running 'confint.R' OK * checking PDF version of manual ... OK * DONE Status: OK checking package 'tcltk' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/tcltk.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'tcltk' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK checking package 'compiler' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/compiler.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'compiler' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking examples ... SKIPPED * checking tests ... Running 'assign.R' Running 'basics.R' Running 'const.R' Running 'curexpr.R' Running 'envir.R' Running 'jit.R' Running 'loop.R' Running 'srcref.R' Running 'switch.R' Running 'vischk.R' OK * checking PDF version of manual ... OK * DONE Status: OK checking package 'parallel' * using log directory '/build/reproducible-path/r-base-4.2.2.20221110/tests/parallel.Rcheck' * using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-build-vignettes' * looks like 'parallel' is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking files in 'vignettes' ... OK * checking examples ... SKIPPED * checking tests ... Running 'Master.R' Running 'RSeed.R' OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'parallel.Rnw'... OK NONE * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' Recommended packages are not installed so cannot be tested make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' touch check-stamp *** install-arch *** dh_testdir dh_testroot dh_prep -a dh_installdirs -A /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core /usr/bin/make DESTDIR=/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core install make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/m4' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tools' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' installing doc ... mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/doc mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/man/man1 make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' installing doc/html ... mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/doc/html make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/html' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' installing doc/manual ... mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/doc/manual mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/doc/manual/images make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/etc installing etc ... make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/etc' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/share' installing share ... mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/R mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/dictionaries mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/encodings mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/java mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/licenses mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/make mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/Rd mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/Rd/macros mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/sh mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/texmf mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/texmf/tex/latex make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/share' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/bin make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/scripts' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/include/R_ext make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include/R_ext' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/blas' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/blas' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tre' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tzone' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/tzone' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/xdr' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/xdr' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/intl' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra/intl' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/extra' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/appl' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/pkgconfig make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/bin/exec make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/lib make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/main' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/modules make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/internet' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/lapack' make[4]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[4]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules/X11' make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/modules' make[3]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/library installing packages ... building HTML index ... make[3]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/library' make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/tests' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' (cd src/unix; \ rm -vf Rscript /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/bin/Rscript; \ /usr/bin/make CFLAGS="`DEB_BUILD_MAINT_OPTIONS=optimize=-lto dpkg-buildflags --get CFLAGS` -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT" \ CXXFLAGS="`DEB_BUILD_MAINT_OPTIONS=optimize=-lto dpkg-buildflags --get CFLAGS` -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT" \ FFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110=. -fstack-protector-strong -D_REENTRANT" \ CC=gcc \ CXX=g++ \ F77=gfortran \ RHOME=/usr/lib/R \ DESTDIR=/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core \ install-Rscript ) removed 'Rscript' removed '/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/bin/Rscript' make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' gcc -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.2.2.20221110/src/unix=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D_REENTRANT -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/unix' #ls -ltr /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/bin/ #strings src/unix/Rscript cp -vax src/unix/Rscript /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/bin/ 'src/unix/Rscript' -> '/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/bin/Rscript' #ls -ltr /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/bin/ #strings /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/bin/Rscript (cd src/nmath/standalone; \ /usr/bin/make DESTDIR=/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core install ) make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/include' /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/src/nmath/standalone' chmod a+x /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/share/sh/echo.sh rm -v /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/COPYING removed '/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/COPYING' (cd /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/; \ ln -s ../../share/common-licenses/GPL-2 COPYING) rm -v /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/doc/COPYING removed '/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/doc/COPYING' (cd /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/doc; \ ln -s ../../../share/common-licenses/GPL-2 COPYING) (cd /build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr \ rdocdir=/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/R/doc \ install-pdf make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' installing R manuals in PDF format ... make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' make prefix=/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr \ infodir=/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info install-info make[1]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110' make[2]: Entering directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' mkdir -p -- /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info /usr/bin/install -c -m 644 "./dir" "/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info" installing R info pages ... updating '/build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/dir' ... you need to adjust /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/dir manually you need to adjust /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/dir manually make[2]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110/doc/manual' make[1]: Leaving directory '/build/reproducible-path/r-base-4.2.2.20221110' dh_movefiles --sourcedir=debian/r-base-core -pr-doc-pdf dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html gunzip -9v /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/*.gz /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-FAQ.info.gz: 67.2% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-FAQ.info /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-admin.info.gz: 68.3% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-admin.info /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-data.info.gz: 70.9% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-data.info /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-exts.info-1.gz: 66.8% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-exts.info-1 /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-exts.info-2.gz: 68.1% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-exts.info-2 /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-exts.info-3.gz: 77.8% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-exts.info-3 /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-exts.info.gz: 70.3% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-exts.info /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-intro.info.gz: 70.4% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-intro.info /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-ints.info.gz: 68.7% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-ints.info /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-lang.info.gz: 71.9% -- replaced with /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/info/R-lang.info dh_movefiles --sourcedir=debian/r-base-core -pr-doc-info rm -vf /build/reproducible-path/r-base-4.2.2.20221110/debian/r-doc-info/usr/share/info/dir \ /build/reproducible-path/r-base-4.2.2.20221110/debian/r-doc-info/usr/share/info/dir.old removed '/build/reproducible-path/r-base-4.2.2.20221110/debian/r-doc-info/usr/share/info/dir' touch install-indep-stamp 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/reproducible-path/r-base-4.2.2.20221110/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 2328 -rw-r--r-- 1 root root 1597100 Jan 26 02:17 libRmath.a -rwxr-xr-x 1 root root 783048 Jan 26 02:17 libRmath.so drwxr-xr-x 2 root root 60 Jan 26 02:18 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/reproducible-path/r-base-4.2.2.20221110/debian/r-mathlib/usr/include install -m 0644 debian/Rprofile.site /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/etc/R install -m 0644 debian/Renviron.site /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/etc/R (cd /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/etc; \ 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 . ) 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/reproducible-path/r-base-4.2.2.20221110/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/Rlogo.svg \ debian/r-base-core/usr/share/icons/hicolor/scalable/apps/rlogo_icon.svg 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_installexamples -pr-mathlib src/nmath/standalone/test.c #dh_installmenu -a # (cd /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .) (cd /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .) (cd /build/reproducible-path/r-base-4.2.2.20221110/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/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/share/lintian/overrides/r-base-core install -p -m 0644 debian/r-recommended.lintian \ /build/reproducible-path/r-base-4.2.2.20221110/debian/r-recommended/usr/share/lintian/overrides/r-recommended install -p -m 0644 debian/r-mathlib.lintian \ /build/reproducible-path/r-base-4.2.2.20221110/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib dh_installchangelogs -a -k doc/NEWS dh_strip -a dh_compress -a dh_fixperms -a dh_link -a dh_makeshlibs -a dh_installdeb -a dh_perl -a dh_shlibdeps -a -l /build/reproducible-path/r-base-4.2.2.20221110/debian/r-base-core/usr/lib/R/lib dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtcl8.6.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtk8.6.so' dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'r-base-core-dbgsym' in '../r-base-core-dbgsym_4.2.2.20221110-2_amd64.deb'. dpkg-deb: building package 'r-mathlib' in '../r-mathlib_4.2.2.20221110-2_amd64.deb'. dpkg-deb: building package 'r-mathlib-dbgsym' in '../r-mathlib-dbgsym_4.2.2.20221110-2_amd64.deb'. dpkg-deb: building package 'r-base-core' in '../r-base-core_4.2.2.20221110-2_amd64.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 -m0755 -d debian/r-doc-html/usr/share/doc-base/ install -p -m0644 debian/r-doc-html.doc-base.intro debian/r-doc-html/usr/share/doc-base/r-doc-html.r-intro install -p -m0644 debian/r-doc-html.doc-base.exts debian/r-doc-html/usr/share/doc-base/r-doc-html.r-extensions install -p -m0644 debian/r-doc-html.doc-base.faq debian/r-doc-html/usr/share/doc-base/r-doc-html.r-faq install -p -m0644 debian/r-doc-html.doc-base.ints debian/r-doc-html/usr/share/doc-base/r-doc-html.r-ints install -p -m0644 debian/r-doc-html.doc-base.admin debian/r-doc-html/usr/share/doc-base/r-doc-html.r-admin install -p -m0644 debian/r-doc-html.doc-base.lang debian/r-doc-html/usr/share/doc-base/r-doc-html.r-language install -p -m0644 debian/r-doc-html.doc-base.data debian/r-doc-html/usr/share/doc-base/r-doc-html.r-data dh_installchangelogs -i dh_installdirs -pr-base-dev usr/share/R/debian install -p -m 0755 debian/r-cran.mk \ /build/reproducible-path/r-base-4.2.2.20221110/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' in '../r-base_4.2.2.20221110-2_all.deb'. dpkg-deb: building package 'r-base-dev' in '../r-base-dev_4.2.2.20221110-2_all.deb'. dpkg-deb: building package 'r-base-html' in '../r-base-html_4.2.2.20221110-2_all.deb'. dpkg-deb: building package 'r-doc-pdf' in '../r-doc-pdf_4.2.2.20221110-2_all.deb'. dpkg-deb: building package 'r-doc-html' in '../r-doc-html_4.2.2.20221110-2_all.deb'. dpkg-deb: building package 'r-doc-info' in '../r-doc-info_4.2.2.20221110-2_all.deb'. dpkg-deb: building package 'r-recommended' in '../r-recommended_4.2.2.20221110-2_all.deb'. dpkg-genbuildinfo --build=binary -O../r-base_4.2.2.20221110-2_amd64.buildinfo dpkg-genchanges --build=binary -O../r-base_4.2.2.20221110-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload 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/478551 and its subdirectories I: Current time: Fri Jan 26 02:19:21 -12 2024 I: pbuilder-time-stamp: 1706278761