RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep']
Forking launchpad-buildd slave process...
Kernel version: Linux lgw01-48 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64
Buildd toolchain package versions: launchpad-buildd_139 python-lpbuildd_139 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa8 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.5 git-build-recipe_0.3~git201603101733.90b6821~ubuntu14.04.2 git_1:1.9.1-1ubuntu0.3 dpkg-dev_1.17.5ubuntu5.6 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1 qemu-user-static_2.0.0+dfsg-2ubuntu1.22.
Syncing the system clock with the buildd NTP service...
 3 May 23:22:12 ntpdate[1664]: adjust time server 10.211.37.1 offset 0.002397 sec
RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-9686715', '/home/buildd/filecache-default/9af1b65e710cc0b334e8c9a330a1d817d2c021bb']
Unpacking chroot for build PACKAGEBUILD-9686715
RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-9686715']
Mounting chroot for build PACKAGEBUILD-9686715
RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-9686715', 'deb http://ftpmaster.internal/ubuntu yakkety main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-security main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-proposed main universe']
Overriding sources.list in build-PACKAGEBUILD-9686715
RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-9686715', 'i386']
Updating debian chroot for build PACKAGEBUILD-9686715
Get:1 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB]
Get:2 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB]
Get:3 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB]
Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed InRelease [95.7 kB]
Get:5 http://ftpmaster.internal/ubuntu yakkety/main i386 Packages [1198 kB]
Get:6 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [568 kB]
Get:7 http://ftpmaster.internal/ubuntu yakkety/universe i386 Packages [7601 kB]
Get:8 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4413 kB]
Get:9 http://ftpmaster.internal/ubuntu yakkety-security/main i386 Packages [64 B]
Get:10 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B]
Get:11 http://ftpmaster.internal/ubuntu yakkety-security/universe i386 Packages [64 B]
Get:12 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B]
Get:13 http://ftpmaster.internal/ubuntu yakkety-updates/main i386 Packages [64 B]
Get:14 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B]
Get:15 http://ftpmaster.internal/ubuntu yakkety-updates/universe i386 Packages [64 B]
Get:16 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B]
Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 Packages [60.4 kB]
Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main Translation-en [33.1 kB]
Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/universe i386 Packages [329 kB]
Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/universe Translation-en [179 kB]
Fetched 14.9 MB in 7s (2080 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following NEW packages will be installed:
  libpng16-16
The following packages will be upgraded:
  apt apt-transport-https bash binutils bzip2 cpp-5 debconf dmsetup dpkg
  dpkg-dev g++-5 gcc-5 gcc-5-base gcc-6-base grep hostname init
  init-system-helpers initscripts libapt-pkg5.0 libasan2 libatomic1 libbz2-1.0
  libcc1-0 libcilkrts5 libdevmapper1.02.1 libdpkg-perl libgcc-5-dev libgcc1
  libgcrypt20 libgomp1 libgpg-error0 libitm1 libmpx0 libperl5.22 libpng12-0
  libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1
  libsemanage-common libsemanage1 libsepol1 libslang2 libstdc++-5-dev
  libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4
  linux-libc-dev make optipng perl perl-base perl-modules-5.22
  policyrcd-script-zg2 systemd systemd-sysv sysv-rc sysvinit-utils tar tzdata
  zlib1g
66 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 95.1 MB of archives.
After this operation, 185 MB of additional disk space will be used.
Get:1 http://ftpmaster.internal/ubuntu yakkety/main i386 bash i386 4.3-14ubuntu2 [591 kB]
Get:2 http://ftpmaster.internal/ubuntu yakkety/main i386 dpkg i386 1.18.4ubuntu2 [2113 kB]
Get:3 http://ftpmaster.internal/ubuntu yakkety/main i386 grep i386 2.25-1 [157 kB]
Get:4 http://ftpmaster.internal/ubuntu yakkety/main i386 hostname i386 3.17ubuntu1 [11.9 kB]
Get:5 http://ftpmaster.internal/ubuntu yakkety/main i386 perl-modules-5.22 all 5.22.2-1 [2642 kB]
Get:6 http://ftpmaster.internal/ubuntu yakkety/main i386 libperl5.22 i386 5.22.2-1 [3014 kB]
Get:7 http://ftpmaster.internal/ubuntu yakkety/main i386 perl i386 5.22.2-1 [237 kB]
Get:8 http://ftpmaster.internal/ubuntu yakkety/main i386 perl-base i386 5.22.2-1 [1369 kB]
Get:9 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 bzip2 i386 1.0.6-8build1 [32.5 kB]
Get:10 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libbz2-1.0 i386 1.0.6-8build1 [30.9 kB]
Get:11 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 zlib1g i386 1:1.2.8.dfsg-2ubuntu5 [52.1 kB]
Get:12 http://ftpmaster.internal/ubuntu yakkety/main i386 init-system-helpers all 1.31ubuntu1 [31.9 kB]
Get:13 http://ftpmaster.internal/ubuntu yakkety/main i386 init i386 1.31ubuntu1 [4564 B]
Get:14 http://ftpmaster.internal/ubuntu yakkety/main i386 tar i386 1.28-2.2 [221 kB]
Get:15 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-6-base i386 6.1.1-0ubuntu12 [16.0 kB]
Get:16 http://ftpmaster.internal/ubuntu yakkety/main i386 libgcc1 i386 1:6.1.1-0ubuntu12 [46.9 kB]
Get:17 http://ftpmaster.internal/ubuntu yakkety/main i386 libstdc++6 i386 6.1.1-0ubuntu12 [433 kB]
Get:18 http://ftpmaster.internal/ubuntu yakkety/main i386 libapt-pkg5.0 i386 1.2.11 [736 kB]
Get:19 http://ftpmaster.internal/ubuntu yakkety/main i386 apt i386 1.2.11 [1054 kB]
Get:20 http://ftpmaster.internal/ubuntu yakkety/main i386 debconf all 1.5.59ubuntu1 [136 kB]
Get:21 http://ftpmaster.internal/ubuntu yakkety/main i386 sysvinit-utils i386 2.88dsf-59.3ubuntu5 [22.0 kB]
Get:22 http://ftpmaster.internal/ubuntu yakkety/main i386 sysv-rc all 2.88dsf-59.3ubuntu5 [18.2 kB]
Get:23 http://ftpmaster.internal/ubuntu yakkety/main i386 initscripts i386 2.88dsf-59.3ubuntu5 [24.5 kB]
Get:24 http://ftpmaster.internal/ubuntu yakkety/main i386 libgpg-error0 i386 1.22-1 [37.3 kB]
Get:25 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libselinux1 i386 2.5-2 [70.4 kB]
Get:26 http://ftpmaster.internal/ubuntu yakkety/main i386 libsystemd0 i386 229-5ubuntu1 [228 kB]
Get:27 http://ftpmaster.internal/ubuntu yakkety/main i386 systemd i386 229-5ubuntu1 [3682 kB]
Get:28 http://ftpmaster.internal/ubuntu yakkety/main i386 systemd-sysv i386 229-5ubuntu1 [17.7 kB]
Get:29 http://ftpmaster.internal/ubuntu yakkety/main i386 libudev1 i386 229-5ubuntu1 [63.5 kB]
Get:30 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libdevmapper1.02.1 i386 2:1.02.122-1ubuntu1 [154 kB]
Get:31 http://ftpmaster.internal/ubuntu yakkety/main i386 libgcrypt20 i386 1.7.0-2 [372 kB]
Get:32 http://ftpmaster.internal/ubuntu yakkety/main i386 libsepol1 i386 2.5-1 [236 kB]
Get:33 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsemanage-common all 2.5-1 [6800 B]
Get:34 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsemanage1 i386 2.5-1 [88.3 kB]
Get:35 http://ftpmaster.internal/ubuntu yakkety/main i386 libusb-0.1-4 i386 2:0.1.12-29 [17.7 kB]
Get:36 http://ftpmaster.internal/ubuntu yakkety/main i386 tzdata all 2016d-2 [168 kB]
Get:37 http://ftpmaster.internal/ubuntu yakkety/main i386 libslang2 i386 2.3.0-2.3ubuntu1 [416 kB]
Get:38 http://ftpmaster.internal/ubuntu yakkety/main i386 libtasn1-6 i386 4.8-1 [44.8 kB]
Get:39 http://ftpmaster.internal/ubuntu yakkety/main i386 apt-transport-https i386 1.2.11 [27.6 kB]
Get:40 http://ftpmaster.internal/ubuntu yakkety/main i386 libpng16-16 i386 1.6.21-4 [181 kB]
Get:41 http://ftpmaster.internal/ubuntu yakkety/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-1 [58.1 kB]
Get:42 http://ftpmaster.internal/ubuntu yakkety/main i386 libsasl2-modules-db i386 2.1.26.dfsg1-15 [15.4 kB]
Get:43 http://ftpmaster.internal/ubuntu yakkety/main i386 libsasl2-2 i386 2.1.26.dfsg1-15 [51.8 kB]
Get:44 http://ftpmaster.internal/ubuntu yakkety/main i386 binutils i386 2.26-8ubuntu3 [2482 kB]
Get:45 http://ftpmaster.internal/ubuntu yakkety/main i386 libgomp1 i386 6.1.1-0ubuntu12 [79.9 kB]
Get:46 http://ftpmaster.internal/ubuntu yakkety/main i386 libitm1 i386 6.1.1-0ubuntu12 [31.2 kB]
Get:47 http://ftpmaster.internal/ubuntu yakkety/main i386 libatomic1 i386 6.1.1-0ubuntu12 [9918 B]
Get:48 http://ftpmaster.internal/ubuntu yakkety/main i386 libasan2 i386 5.3.1-16ubuntu3 [271 kB]
Get:49 http://ftpmaster.internal/ubuntu yakkety/main i386 libubsan0 i386 6.1.1-0ubuntu12 [120 kB]
Get:50 http://ftpmaster.internal/ubuntu yakkety/main i386 libcilkrts5 i386 6.1.1-0ubuntu12 [45.8 kB]
Get:51 http://ftpmaster.internal/ubuntu yakkety/main i386 libmpx0 i386 5.3.1-16ubuntu3 [11.1 kB]
Get:52 http://ftpmaster.internal/ubuntu yakkety/main i386 libquadmath0 i386 6.1.1-0ubuntu12 [204 kB]
Get:53 http://ftpmaster.internal/ubuntu yakkety/main i386 g++-5 i386 5.3.1-16ubuntu3 [30.4 MB]
Get:54 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-5 i386 5.3.1-16ubuntu3 [8403 kB]
Get:55 http://ftpmaster.internal/ubuntu yakkety/main i386 libstdc++-5-dev i386 5.3.1-16ubuntu3 [1437 kB]
Get:56 http://ftpmaster.internal/ubuntu yakkety/main i386 libgcc-5-dev i386 5.3.1-16ubuntu3 [2242 kB]
Get:57 http://ftpmaster.internal/ubuntu yakkety/main i386 libcc1-0 i386 6.1.1-0ubuntu12 [33.0 kB]
Get:58 http://ftpmaster.internal/ubuntu yakkety/main i386 cpp-5 i386 5.3.1-16ubuntu3 [28.4 MB]
Get:59 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-5-base i386 5.3.1-16ubuntu3 [17.4 kB]
Get:60 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 dmsetup i386 2:1.02.122-1ubuntu1 [72.9 kB]
Get:61 http://ftpmaster.internal/ubuntu yakkety/main i386 dpkg-dev all 1.18.4ubuntu2 [584 kB]
Get:62 http://ftpmaster.internal/ubuntu yakkety/main i386 libdpkg-perl all 1.18.4ubuntu2 [195 kB]
Get:63 http://ftpmaster.internal/ubuntu yakkety/main i386 make i386 4.1-9 [154 kB]
Get:64 http://ftpmaster.internal/ubuntu yakkety/universe i386 libpng12-0 i386 1.2.54-6ubuntu1 [122 kB]
Get:65 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 linux-libc-dev i386 4.4.0-22.38 [840 kB]
Get:66 http://ftpmaster.internal/ubuntu yakkety/main i386 optipng i386 0.7.6-1build1 [86.3 kB]
Get:67 http://ftpmaster.internal/ubuntu yakkety/main i386 policyrcd-script-zg2 all 0.1-3 [5610 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 95.1 MB in 10s (9394 kB/s)
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Setting up bash (4.3-14ubuntu2) ...
update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
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Current default time zone: 'Etc/UTC'
Local time is now:      Tue May  3 23:23:03 UTC 2016.
Universal Time is now:  Tue May  3 23:23:03 UTC 2016.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-9686715', 'i386', 'yakkety-proposed', '-c', 'chroot:autobuild', '--arch=i386', '--dist=yakkety-proposed', '--purge=never', '--nolog', 'r-base_3.3.0-1.dsc']
Initiating build PACKAGEBUILD-9686715 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 i686
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lgw01-48.buildd

╔══════════════════════════════════════════════════════════════════════════════╗
║ r-base 3.3.0-1 (i386)                                      03 May 2016 23:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: r-base
Version: 3.3.0-1
Source Version: 3.3.0-1
Distribution: yakkety-proposed
Machine Architecture: amd64
Host Architecture: i386
Build Architecture: i386

I: NOTICE: Log filtering will replace 'build/r-base-asNdei/r-base-3.3.0' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-base-asNdei' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-9686715/chroot-autobuild' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘


Local sources
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r-base_3.3.0-1.dsc exists in .; copying to chroot

Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-kOMLHw/apt_archive/sbuild-build-depends-core-dummy.deb'.
Ign:1 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ InRelease
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Ign:3 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ Release.gpg
Get:4 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ Sources [208 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver)                         │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
  sbuild-build-depends-core-dummy
Authentication warning overridden.
Get:1 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
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Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk, mpack, bash-completion
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk, mpack, bash-completion
dpkg-deb: building package 'sbuild-build-depends-r-base-dummy' in '/«BUILDDIR»/resolver-IOnagW/apt_archive/sbuild-build-depends-r-base-dummy.deb'.
Ign:1 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ InRelease
Get:2 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ Release [2119 B]
Ign:3 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ Release.gpg
Get:4 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ Sources [685 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install r-base build dependencies (apt-based resolver)                       │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils
  ca-certificates-java debhelper default-jdk default-jdk-headless default-jre
  default-jre-headless dh-autoreconf dh-strip-nondeterminism file fontconfig
  fontconfig-config fonts-cabin fonts-comfortaa fonts-crosextra-caladea
  fonts-crosextra-carlito fonts-dejavu-core fonts-dejavu-extra
  fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome
  fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
  fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine
  fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto-hinted
  fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-stix
  gettext gettext-base gfortran gfortran-5 gir1.2-freedesktop gir1.2-glib-2.0
  gir1.2-pango-1.0 groff-base icu-devtools intltool-debian java-common
  libarchive-zip-perl libasound2 libasound2-data libasprintf0v5 libasyncns0
  libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data
  libavahi-common3 libbison-dev libblas-common libblas-dev libblas3 libbsd0
  libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2
  libcairo2-dev libcroco3 libcups2 libcupsfilters1 libcupsimage2 libcurl3
  libcurl4-openssl-dev libdatrie1 libdbus-1-3 libdrm-amdgpu1 libdrm-intel1
  libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1
  libexpat1-dev libfile-stripnondeterminism-perl libflac8 libfontconfig1
  libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev
  libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-5-dev libgfortran3
  libgif7 libgirepository-1.0-1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgraphite2-3
  libgraphite2-dev libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common
  libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
  libice-dev libice6 libicu-dev libicu57 libijs-0.35 libjbig-dev libjbig0
  libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
  libjpeg8-dev libjson-c3 libkpathsea6 liblapack-dev liblapack3 liblcms2-2
  libllvm3.8 liblzma-dev liblzo2-2 libmagic1 libncurses5-dev libnspr4 libnss3
  libnss3-nssdb libogg0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0
  libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpciaccess0
  libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1
  libpixman-1-0 libpixman-1-dev libpng-dev libpoppler58 libpotrace0
  libptexenc1 libpthread-stubs0-dev libpulse0 libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev
  libsigsegv2 libsm-dev libsm6 libsndfile1 libsynctex1 libtcl8.6 libtexlua52
  libtexluajit2 libtext-unidecode-perl libthai-data libthai0 libtiff5
  libtiff5-dev libtiffxx5 libtimedate-perl libtinfo-dev libtk8.6 libtool
  libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data
  libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0
  libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev
  libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb1 libxcb1-dev libxcomposite1
  libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
  libxfixes3 libxfont1 libxft-dev libxft2 libxi6 libxinerama1 libxkbfile1
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev
  libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6
  libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-8-jdk
  openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless pkg-config
  po-debconf poppler-data preview-latex-style python python-minimal python2.7
  python2.7-minimal shared-mime-info t1utils tcl8.6 tcl8.6-dev tex-common
  texinfo texlive-base texlive-binaries texlive-extra-utils
  texlive-fonts-extra texlive-fonts-recommended texlive-generic-recommended
  texlive-latex-base texlive-latex-extra texlive-latex-recommended
  texlive-pictures tk8.6 tk8.6-dev ttf-adf-accanthis ttf-adf-gillius
  ttf-adf-universalis ucf x11-common x11-xkb-utils x11proto-core-dev
  x11proto-input-dev x11proto-kb-dev x11proto-render-dev
  x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base
  xfonts-encodings xfonts-utils xkb-data xorg-sgml-doctools xserver-common
  xtrans-dev xvfb zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist
  whois vacation dh-make default-java-plugin fontforge gettext-doc
  gfortran-multilib gfortran-doc gfortran-5-multilib gfortran-5-doc
  libgfortran3-dbg groff libasound2-plugins alsa-utils liblapack-doc-man
  liblapack-doc libcairo2-doc cups-common libcurl4-doc libcurl3-dbg
  libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssl-dev libglib2.0-doc
  fonts-droid texlive-lang-cjk librsvg2-common gvfs libice-doc icu-doc
  liblcms2-utils liblzma-doc ncurses-doc imagemagick libpango1.0-doc pciutils
  pcscd pulseaudio readline-doc libsm-doc libtool-doc gcj-jdk libxcb-doc
  libxext-doc libxt-doc less www-browser mail-transport-agent inews
  openjdk-8-demo openjdk-8-source visualvm icedtea-8-plugin
  openjdk-8-jre-jamvm libnss-mdns fonts-ipafont-gothic fonts-ipafont-mincho
  ttf-wqy-microhei | ttf-wqy-zenhei fonts-indic libmail-box-perl poppler-utils
  ghostscript fonts-japanese-mincho | fonts-ipafont-mincho
  fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai
  fonts-arphic-uming fonts-nanum python-doc python-tk python2.7-doc
  binfmt-support tcl-tclreadline tcl8.6-doc texinfo-doc-nonfree perl-tk gv
  | postscript-viewer xpdf-reader | pdf-viewer dvipng dvidvi xindy fragmaster
  purifyeps lacheck chktex latexmk latexdiff cm-super python-pygments
  libfile-which-perl libspreadsheet-parseexcel-perl texlive-pstricks
  libtcltk-ruby dot2tex prerex tk8.6-doc gvfs-bin
Recommended packages:
  curl | wget | lynx-cur libasprintf-dev libgettextpo-dev bzip2-doc dbus
  libtxc-dxtn-s2tc0 | libtxc-dxtn0 xdg-user-dirs hicolor-icon-theme
  libgtk2.0-bin libpng-tools libltdl-dev tcpd libx11-doc libxml-sax-expat-perl
  xml-core libgnome-2-0 libgnomevfs2-0 libgconf-2-4 libmail-sendmail-perl
  lmodern ruby wish libyaml-tiny-perl ghostscript libfile-homedir-perl ruby
  | ruby-interpreter texlive-fonts-extra-doc texlive-fonts-recommended-doc
  tipa tex-gyre texlive-latex-base-doc texlive-latex-extra-doc prosper
  texlive-latex-recommended-doc texlive-pictures-doc tk xterm
  | x-terminal-emulator libfile-mimeinfo-perl libnet-dbus-perl
  libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils
  ca-certificates-java debhelper default-jdk default-jdk-headless default-jre
  default-jre-headless dh-autoreconf dh-strip-nondeterminism file fontconfig
  fontconfig-config fonts-cabin fonts-comfortaa fonts-crosextra-caladea
  fonts-crosextra-carlito fonts-dejavu-core fonts-dejavu-extra
  fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome
  fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
  fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine
  fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto-hinted
  fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-stix
  gettext gettext-base gfortran gfortran-5 gir1.2-freedesktop gir1.2-glib-2.0
  gir1.2-pango-1.0 groff-base icu-devtools intltool-debian java-common
  libarchive-zip-perl libasound2 libasound2-data libasprintf0v5 libasyncns0
  libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data
  libavahi-common3 libbison-dev libblas-common libblas-dev libblas3 libbsd0
  libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2
  libcairo2-dev libcroco3 libcups2 libcupsfilters1 libcupsimage2 libcurl3
  libcurl4-openssl-dev libdatrie1 libdbus-1-3 libdrm-amdgpu1 libdrm-intel1
  libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1
  libexpat1-dev libfile-stripnondeterminism-perl libflac8 libfontconfig1
  libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev
  libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-5-dev libgfortran3
  libgif7 libgirepository-1.0-1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgraphite2-3
  libgraphite2-dev libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common
  libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
  libice-dev libice6 libicu-dev libicu57 libijs-0.35 libjbig-dev libjbig0
  libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
  libjpeg8-dev libjson-c3 libkpathsea6 liblapack-dev liblapack3 liblcms2-2
  libllvm3.8 liblzma-dev liblzo2-2 libmagic1 libncurses5-dev libnspr4 libnss3
  libnss3-nssdb libogg0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0
  libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpciaccess0
  libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1
  libpixman-1-0 libpixman-1-dev libpng-dev libpoppler58 libpotrace0
  libptexenc1 libpthread-stubs0-dev libpulse0 libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev
  libsigsegv2 libsm-dev libsm6 libsndfile1 libsynctex1 libtcl8.6 libtexlua52
  libtexluajit2 libtext-unidecode-perl libthai-data libthai0 libtiff5
  libtiff5-dev libtiffxx5 libtimedate-perl libtinfo-dev libtk8.6 libtool
  libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data
  libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0
  libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev
  libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb1 libxcb1-dev libxcomposite1
  libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
  libxfixes3 libxfont1 libxft-dev libxft2 libxi6 libxinerama1 libxkbfile1
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev
  libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6
  libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-8-jdk
  openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless pkg-config
  po-debconf poppler-data preview-latex-style python python-minimal python2.7
  python2.7-minimal sbuild-build-depends-r-base-dummy shared-mime-info t1utils
  tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries
  texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended
  texlive-generic-recommended texlive-latex-base texlive-latex-extra
  texlive-latex-recommended texlive-pictures tk8.6 tk8.6-dev ttf-adf-accanthis
  ttf-adf-gillius ttf-adf-universalis ucf x11-common x11-xkb-utils
  x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev
  x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base
  xfonts-encodings xfonts-utils xkb-data xorg-sgml-doctools xserver-common
  xtrans-dev xvfb zlib1g-dev
0 upgraded, 309 newly installed, 0 to remove and 0 not upgraded.
Need to get 503 MB of archives.
After this operation, 1735 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
  sbuild-build-depends-r-base-dummy
Authentication warning overridden.
Get:1 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ sbuild-build-depends-r-base-dummy 0.invalid.0 [1180 B]
Get:2 http://ftpmaster.internal/ubuntu yakkety/main i386 bash-completion all 1:2.1-4.2ubuntu2 [152 kB]
Get:3 http://ftpmaster.internal/ubuntu yakkety/main i386 libxau6 i386 1:1.0.8-1 [8352 B]
Get:4 http://ftpmaster.internal/ubuntu yakkety/main i386 libxdmcp6 i386 1:1.1.2-1.1 [11.4 kB]
Get:5 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb1 i386 1.11.1-1ubuntu1 [44.1 kB]
Get:6 http://ftpmaster.internal/ubuntu yakkety/main i386 libx11-data all 2:1.6.3-1ubuntu2 [113 kB]
Get:7 http://ftpmaster.internal/ubuntu yakkety/main i386 libx11-6 i386 2:1.6.3-1ubuntu2 [592 kB]
Get:8 http://ftpmaster.internal/ubuntu yakkety/main i386 libxext6 i386 2:1.3.3-1 [31.6 kB]
Get:9 http://ftpmaster.internal/ubuntu yakkety/main i386 groff-base i386 1.22.3-7 [1160 kB]
Get:10 http://ftpmaster.internal/ubuntu yakkety/main i386 bsdmainutils i386 9.0.6ubuntu3 [175 kB]
Get:11 http://ftpmaster.internal/ubuntu yakkety/main i386 libpipeline1 i386 1.4.1-2 [26.5 kB]
Get:12 http://ftpmaster.internal/ubuntu yakkety/main i386 man-db i386 2.7.5-1 [865 kB]
Get:13 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-dejavu-core all 2.35-1 [1039 kB]
Get:14 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-freefont-ttf all 20120503-4 [4140 kB]
Get:15 http://ftpmaster.internal/ubuntu yakkety/main i386 ucf all 3.0036 [52.9 kB]
Get:16 http://ftpmaster.internal/ubuntu yakkety/main i386 fontconfig-config all 2.11.94-0ubuntu1 [49.9 kB]
Get:17 http://ftpmaster.internal/ubuntu yakkety/main i386 libexpat1 i386 2.1.1-1 [74.3 kB]
Get:18 http://ftpmaster.internal/ubuntu yakkety/main i386 libfreetype6 i386 2.6.3-3ubuntu1 [335 kB]
Get:19 http://ftpmaster.internal/ubuntu yakkety/main i386 libfontconfig1 i386 2.11.94-0ubuntu1 [140 kB]
Get:20 http://ftpmaster.internal/ubuntu yakkety/main i386 fontconfig i386 2.11.94-0ubuntu1 [177 kB]
Get:21 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-lato all 2.0-1 [2693 kB]
Get:22 http://ftpmaster.internal/ubuntu yakkety/main i386 libasyncns0 i386 0.8-5build1 [12.7 kB]
Get:23 http://ftpmaster.internal/ubuntu yakkety/main i386 x11-common all 1:7.7+13ubuntu3 [22.4 kB]
Get:24 http://ftpmaster.internal/ubuntu yakkety/main i386 libice6 i386 2:1.0.9-1 [38.2 kB]
Get:25 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg-turbo8 i386 1.4.2-0ubuntu3 [117 kB]
Get:26 http://ftpmaster.internal/ubuntu yakkety/main i386 liblcms2-2 i386 2.6-3ubuntu2 [147 kB]
Get:27 http://ftpmaster.internal/ubuntu yakkety/main i386 liblzo2-2 i386 2.08-1.2 [52.7 kB]
Get:28 http://ftpmaster.internal/ubuntu yakkety/main i386 libogg0 i386 1.3.2-1 [16.2 kB]
Get:29 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcrecpp0v5 i386 2:8.38-3.1 [16.0 kB]
Get:30 http://ftpmaster.internal/ubuntu yakkety/main i386 libsm6 i386 2:1.2.2-1 [14.8 kB]
Get:31 http://ftpmaster.internal/ubuntu yakkety/main i386 libunistring0 i386 0.9.3-5.2ubuntu1 [277 kB]
Get:32 http://ftpmaster.internal/ubuntu yakkety/main i386 libwrap0 i386 7.6.q-25 [45.8 kB]
Get:33 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcomposite1 i386 1:0.4.4-1 [7594 B]
Get:34 http://ftpmaster.internal/ubuntu yakkety/main i386 libxfixes3 i386 1:5.0.1-2 [11.4 kB]
Get:35 http://ftpmaster.internal/ubuntu yakkety/main i386 libxrender1 i386 1:0.9.9-0ubuntu1 [19.2 kB]
Get:36 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcursor1 i386 1:1.1.14-1 [22.8 kB]
Get:37 http://ftpmaster.internal/ubuntu yakkety/main i386 libxdamage1 i386 1:1.1.4-2 [6812 B]
Get:38 http://ftpmaster.internal/ubuntu yakkety/main i386 libfontenc1 i386 1:1.1.3-1 [14.0 kB]
Get:39 http://ftpmaster.internal/ubuntu yakkety/main i386 libxfont1 i386 1:1.5.1-1 [97.3 kB]
Get:40 http://ftpmaster.internal/ubuntu yakkety/main i386 libxft2 i386 2.3.2-1 [35.5 kB]
Get:41 http://ftpmaster.internal/ubuntu yakkety/main i386 libxinerama1 i386 2:1.1.3-1 [7900 B]
Get:42 http://ftpmaster.internal/ubuntu yakkety/main i386 libxpm4 i386 1:3.5.11-1 [32.1 kB]
Get:43 http://ftpmaster.internal/ubuntu yakkety/main i386 libxshmfence1 i386 1.2-1 [5164 B]
Get:44 http://ftpmaster.internal/ubuntu yakkety/main i386 libxss1 i386 1:1.2.2-1 [8566 B]
Get:45 http://ftpmaster.internal/ubuntu yakkety/main i386 libxtst6 i386 2:1.2.2-1 [13.8 kB]
Get:46 http://ftpmaster.internal/ubuntu yakkety/main i386 libxxf86vm1 i386 1:1.1.4-1 [11.3 kB]
Get:47 http://ftpmaster.internal/ubuntu yakkety/main i386 libzzip-0-13 i386 0.13.62-3 [27.5 kB]
Get:48 http://ftpmaster.internal/ubuntu yakkety/main i386 java-common all 0.56ubuntu2 [7742 B]
Get:49 http://ftpmaster.internal/ubuntu yakkety/main i386 default-jre-headless i386 2:1.8-56ubuntu2 [4376 B]
Get:50 http://ftpmaster.internal/ubuntu yakkety/main i386 libnspr4 i386 2:4.11-1ubuntu1 [121 kB]
Get:51 http://ftpmaster.internal/ubuntu yakkety/main i386 libnss3-nssdb all 2:3.21-1ubuntu4 [10.6 kB]
Get:52 http://ftpmaster.internal/ubuntu yakkety/main i386 libnss3 i386 2:3.21-1ubuntu4 [1187 kB]
Get:53 http://ftpmaster.internal/ubuntu yakkety/main i386 ca-certificates-java all 20160321 [12.9 kB]
Get:54 http://ftpmaster.internal/ubuntu yakkety/main i386 libavahi-common-data i386 0.6.32~rc+dfsg-1ubuntu2 [21.7 kB]
Get:55 http://ftpmaster.internal/ubuntu yakkety/main i386 libavahi-common3 i386 0.6.32~rc+dfsg-1ubuntu2 [23.5 kB]
Get:56 http://ftpmaster.internal/ubuntu yakkety/main i386 libdbus-1-3 i386 1.10.6-1ubuntu3 [173 kB]
Get:57 http://ftpmaster.internal/ubuntu yakkety/main i386 libavahi-client3 i386 0.6.32~rc+dfsg-1ubuntu2 [27.1 kB]
Get:58 http://ftpmaster.internal/ubuntu yakkety/main i386 libcups2 i386 2.1.3-5 [212 kB]
Get:59 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg8 i386 8c-2ubuntu8 [2188 B]
Get:60 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcsclite1 i386 1.8.14-1ubuntu1 [22.9 kB]
Get:61 http://ftpmaster.internal/ubuntu yakkety/main i386 libxi6 i386 2:1.7.6-1 [31.3 kB]
Get:62 http://ftpmaster.internal/ubuntu yakkety/main i386 openjdk-8-jre-headless i386 8u91-b14-2ubuntu1 [26.5 MB]
Get:63 http://ftpmaster.internal/ubuntu yakkety/main i386 poppler-data all 0.4.7-7 [1495 kB]
Get:64 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpython2.7-minimal i386 2.7.11-8 [336 kB]
Get:65 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 python2.7-minimal i386 2.7.11-8 [1357 kB]
Get:66 http://ftpmaster.internal/ubuntu yakkety/main i386 python-minimal i386 2.7.11-1 [28.2 kB]
Get:67 http://ftpmaster.internal/ubuntu yakkety/main i386 mime-support all 3.59ubuntu1 [31.0 kB]
Get:68 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpython2.7-stdlib i386 2.7.11-8 [1873 kB]
Get:69 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 python2.7 i386 2.7.11-8 [220 kB]
Get:70 http://ftpmaster.internal/ubuntu yakkety/main i386 libpython-stdlib i386 2.7.11-1 [7664 B]
Get:71 http://ftpmaster.internal/ubuntu yakkety/main i386 python i386 2.7.11-1 [137 kB]
Get:72 http://ftpmaster.internal/ubuntu yakkety/main i386 libjbig0 i386 2.1-3.1 [27.0 kB]
Get:73 http://ftpmaster.internal/ubuntu yakkety/main i386 libmagic1 i386 1:5.25-2ubuntu1 [222 kB]
Get:74 http://ftpmaster.internal/ubuntu yakkety/main i386 file i386 1:5.25-2ubuntu1 [21.1 kB]
Get:75 http://ftpmaster.internal/ubuntu yakkety/main i386 libbsd0 i386 0.8.2-1 [45.2 kB]
Get:76 http://ftpmaster.internal/ubuntu yakkety/main i386 xkb-data all 2.16-1ubuntu1 [305 kB]
Get:77 http://ftpmaster.internal/ubuntu yakkety/main i386 libasprintf0v5 i386 0.19.7-2ubuntu3 [6462 B]
Get:78 http://ftpmaster.internal/ubuntu yakkety/main i386 gettext-base i386 0.19.7-2ubuntu3 [48.8 kB]
Get:79 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-0 i386 2.48.0-1ubuntu4 [1183 kB]
Get:80 http://ftpmaster.internal/ubuntu yakkety/main i386 libgirepository-1.0-1 i386 1.46.0-3ubuntu1 [97.4 kB]
Get:81 http://ftpmaster.internal/ubuntu yakkety/main i386 gir1.2-glib-2.0 i386 1.46.0-3ubuntu1 [127 kB]
Get:82 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm2 i386 2.4.67-1 [30.8 kB]
Get:83 http://ftpmaster.internal/ubuntu yakkety/main i386 libedit2 i386 3.1-20150325-1ubuntu2 [80.9 kB]
Get:84 http://ftpmaster.internal/ubuntu yakkety/main i386 libelf1 i386 0.165-3ubuntu1 [48.7 kB]
Get:85 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-data all 2.48.0-1ubuntu4 [131 kB]
Get:86 http://ftpmaster.internal/ubuntu yakkety/main i386 libicu57 i386 57.1-1 [7806 kB]
Get:87 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml2 i386 2.9.3+dfsg1-1build1 [729 kB]
Get:88 http://ftpmaster.internal/ubuntu yakkety/main i386 libxmuu1 i386 2:1.1.2-2 [9988 B]
Get:89 http://ftpmaster.internal/ubuntu yakkety/main i386 shared-mime-info i386 1.6-1 [406 kB]
Get:90 http://ftpmaster.internal/ubuntu yakkety/main i386 xauth i386 1:1.0.9-1ubuntu2 [23.0 kB]
Get:91 http://ftpmaster.internal/ubuntu yakkety/main i386 libsigsegv2 i386 2.10-5 [14.3 kB]
Get:92 http://ftpmaster.internal/ubuntu yakkety/main i386 m4 i386 1.4.17-5 [195 kB]
Get:93 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 autoconf all 2.69-10 [321 kB]
Get:94 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 autotools-dev all 20160430.1 [39.6 kB]
Get:95 http://ftpmaster.internal/ubuntu yakkety/main i386 automake all 1:1.15-4ubuntu1 [510 kB]
Get:96 http://ftpmaster.internal/ubuntu yakkety/main i386 autopoint all 0.19.7-2ubuntu3 [406 kB]
Get:97 http://ftpmaster.internal/ubuntu yakkety/main i386 libbison-dev i386 2:3.0.4.dfsg-1 [338 kB]
Get:98 http://ftpmaster.internal/ubuntu yakkety/main i386 bison i386 2:3.0.4.dfsg-1 [256 kB]
Get:99 http://ftpmaster.internal/ubuntu yakkety/main i386 libcroco3 i386 0.6.11-1 [87.8 kB]
Get:100 http://ftpmaster.internal/ubuntu yakkety/main i386 gettext i386 0.19.7-2ubuntu3 [1085 kB]
Get:101 http://ftpmaster.internal/ubuntu yakkety/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB]
Get:102 http://ftpmaster.internal/ubuntu yakkety/main i386 po-debconf all 1.0.19 [234 kB]
Get:103 http://ftpmaster.internal/ubuntu yakkety/main i386 libarchive-zip-perl all 1.57-1 [84.0 kB]
Get:104 http://ftpmaster.internal/ubuntu yakkety/main i386 libfile-stripnondeterminism-perl all 0.016-1 [11.0 kB]
Get:105 http://ftpmaster.internal/ubuntu yakkety/main i386 libtimedate-perl all 2.3000-2 [37.5 kB]
Get:106 http://ftpmaster.internal/ubuntu yakkety/main i386 dh-strip-nondeterminism all 0.016-1 [4858 B]
Get:107 http://ftpmaster.internal/ubuntu yakkety/main i386 libtool all 2.4.6-0.1 [193 kB]
Get:108 http://ftpmaster.internal/ubuntu yakkety/main i386 dh-autoreconf all 12 [15.8 kB]
Get:109 http://ftpmaster.internal/ubuntu yakkety/main i386 debhelper all 9.20160403ubuntu1 [711 kB]
Get:110 http://ftpmaster.internal/ubuntu yakkety/main i386 libgtk2.0-common all 2.24.30-1ubuntu1 [123 kB]
Get:111 http://ftpmaster.internal/ubuntu yakkety/main i386 libatk1.0-data all 2.20.0-1 [17.5 kB]
Get:112 http://ftpmaster.internal/ubuntu yakkety/main i386 libatk1.0-0 i386 2.20.0-1 [58.1 kB]
Get:113 http://ftpmaster.internal/ubuntu yakkety/main i386 libpixman-1-0 i386 0.33.6-1 [237 kB]
Get:114 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-render0 i386 1.11.1-1ubuntu1 [12.2 kB]
Get:115 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-shm0 i386 1.11.1-1ubuntu1 [5754 B]
Get:116 http://ftpmaster.internal/ubuntu yakkety/main i386 libcairo2 i386 1.14.6-1build1 [613 kB]
Get:117 http://ftpmaster.internal/ubuntu yakkety/main i386 libtiff5 i386 4.0.6-1 [154 kB]
Get:118 http://ftpmaster.internal/ubuntu yakkety/main i386 libgdk-pixbuf2.0-common all 2.34.0-1ubuntu1 [10.3 kB]
Get:119 http://ftpmaster.internal/ubuntu yakkety/main i386 libgdk-pixbuf2.0-0 i386 2.34.0-1ubuntu1 [170 kB]
Get:120 http://ftpmaster.internal/ubuntu yakkety/main i386 libthai-data all 0.1.24-2 [131 kB]
Get:121 http://ftpmaster.internal/ubuntu yakkety/main i386 libdatrie1 i386 0.2.10-2 [18.8 kB]
Get:122 http://ftpmaster.internal/ubuntu yakkety/main i386 libthai0 i386 0.1.24-2 [18.5 kB]
Get:123 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpango-1.0-0 i386 1.40.1-1 [155 kB]
Get:124 http://ftpmaster.internal/ubuntu yakkety/main i386 libgraphite2-3 i386 1.3.6-1ubuntu1 [73.3 kB]
Get:125 http://ftpmaster.internal/ubuntu yakkety/main i386 libharfbuzz0b i386 1.2.6-2 [188 kB]
Get:126 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpangoft2-1.0-0 i386 1.40.1-1 [36.3 kB]
Get:127 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpangocairo-1.0-0 i386 1.40.1-1 [22.5 kB]
Get:128 http://ftpmaster.internal/ubuntu yakkety/main i386 libxrandr2 i386 2:1.5.0-1 [19.1 kB]
Get:129 http://ftpmaster.internal/ubuntu yakkety/main i386 libgtk2.0-0 i386 2.24.30-1ubuntu1 [1904 kB]
Get:130 http://ftpmaster.internal/ubuntu yakkety/main i386 libglapi-mesa i386 11.2.1-1ubuntu1 [23.0 kB]
Get:131 http://ftpmaster.internal/ubuntu yakkety/main i386 libx11-xcb1 i386 2:1.6.3-1ubuntu2 [8944 B]
Get:132 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-dri2-0 i386 1.11.1-1ubuntu1 [7292 B]
Get:133 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-dri3-0 i386 1.11.1-1ubuntu1 [5392 B]
Get:134 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-glx0 i386 1.11.1-1ubuntu1 [22.3 kB]
Get:135 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-present0 i386 1.11.1-1ubuntu1 [5396 B]
Get:136 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-sync1 i386 1.11.1-1ubuntu1 [8702 B]
Get:137 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm-amdgpu1 i386 2.4.67-1 [19.5 kB]
Get:138 http://ftpmaster.internal/ubuntu yakkety/main i386 libpciaccess0 i386 0.13.4-1 [20.3 kB]
Get:139 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm-intel1 i386 2.4.67-1 [59.7 kB]
Get:140 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm-nouveau2 i386 2.4.67-1 [18.2 kB]
Get:141 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm-radeon1 i386 2.4.67-1 [23.1 kB]
Get:142 http://ftpmaster.internal/ubuntu yakkety/main i386 libllvm3.8 i386 1:3.8-2ubuntu3 [11.5 MB]
Get:143 http://ftpmaster.internal/ubuntu yakkety/main i386 libgl1-mesa-dri i386 11.2.1-1ubuntu1 [4950 kB]
Get:144 http://ftpmaster.internal/ubuntu yakkety/main i386 libgl1-mesa-glx i386 11.2.1-1ubuntu1 [135 kB]
Get:145 http://ftpmaster.internal/ubuntu yakkety/main i386 libasound2-data all 1.1.0-1 [29.9 kB]
Get:146 http://ftpmaster.internal/ubuntu yakkety/main i386 libasound2 i386 1.1.0-1 [371 kB]
Get:147 http://ftpmaster.internal/ubuntu yakkety/main i386 libgif7 i386 5.1.4-0.1 [31.9 kB]
Get:148 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libjson-c3 i386 0.12-3 [23.5 kB]
Get:149 http://ftpmaster.internal/ubuntu yakkety/main i386 libflac8 i386 1.3.1-4 [154 kB]
Get:150 http://ftpmaster.internal/ubuntu yakkety/main i386 libvorbis0a i386 1.3.5-3 [85.7 kB]
Get:151 http://ftpmaster.internal/ubuntu yakkety/main i386 libvorbisenc2 i386 1.3.5-3 [64.5 kB]
Get:152 http://ftpmaster.internal/ubuntu yakkety/main i386 libsndfile1 i386 1.0.25-10 [157 kB]
Get:153 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpulse0 i386 1:8.0-2ubuntu1 [252 kB]
Get:154 http://ftpmaster.internal/ubuntu yakkety/main i386 openjdk-8-jre i386 8u91-b14-2ubuntu1 [70.8 kB]
Get:155 http://ftpmaster.internal/ubuntu yakkety/main i386 default-jre i386 2:1.8-56ubuntu2 [980 B]
Get:156 http://ftpmaster.internal/ubuntu yakkety/main i386 openjdk-8-jdk-headless i386 8u91-b14-2ubuntu1 [8167 kB]
Get:157 http://ftpmaster.internal/ubuntu yakkety/main i386 default-jdk-headless i386 2:1.8-56ubuntu2 [976 B]
Get:158 http://ftpmaster.internal/ubuntu yakkety/main i386 openjdk-8-jdk i386 8u91-b14-2ubuntu1 [429 kB]
Get:159 http://ftpmaster.internal/ubuntu yakkety/main i386 default-jdk i386 2:1.8-56ubuntu2 [962 B]
Get:160 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-cabin all 1.5-2 [140 kB]
Get:161 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-comfortaa all 2.003-1 [131 kB]
Get:162 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-crosextra-caladea all 20130214-1 [82.3 kB]
Get:163 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-crosextra-carlito all 20130920-1 [742 kB]
Get:164 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-dejavu-extra all 2.35-1 [1749 kB]
Get:165 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-ebgaramond all 0.015+git20130628-3 [651 kB]
Get:166 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-ebgaramond-extra all 0.015+git20130628-3 [933 kB]
Get:167 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-font-awesome all 4.6.1~dfsg-1 [541 kB]
Get:168 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-freefont-otf all 20120503-4 [3068 kB]
Get:169 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-artemisia all 1.1-5 [260 kB]
Get:170 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-complutum all 1.1-6 [41.6 kB]
Get:171 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-didot all 1.1-6 [278 kB]
Get:172 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-neohellenic all 1.1-6 [215 kB]
Get:173 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-olga all 1.1-5 [33.4 kB]
Get:174 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-solomos all 1.1-5 [40.7 kB]
Get:175 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-junicode all 0.7.8-2 [642 kB]
Get:176 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-linuxlibertine all 5.3.0-2 [1688 kB]
Get:177 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-lobster all 2.0-2 [38.7 kB]
Get:178 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-lobstertwo all 2.0-2 [92.7 kB]
Get:179 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-oflb-asana-math all 000.907-6 [246 kB]
Get:180 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-roboto-hinted all 2:0~20160106-1 [2942 kB]
Get:181 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-sil-gentium all 20081126:1.03-1 [247 kB]
Get:182 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-sil-gentium-basic all 1.1-7 [379 kB]
Get:183 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-sil-gentiumplus all 5.000-1 [2805 kB]
Get:184 http://ftpmaster.internal/ubuntu yakkety/main i386 libgfortran3 i386 6.1.1-0ubuntu12 [263 kB]
Get:185 http://ftpmaster.internal/ubuntu yakkety/main i386 libgfortran-5-dev i386 5.3.1-16ubuntu3 [277 kB]
Get:186 http://ftpmaster.internal/ubuntu yakkety/main i386 gfortran-5 i386 5.3.1-16ubuntu3 [29.2 MB]
Get:187 http://ftpmaster.internal/ubuntu yakkety/main i386 gfortran i386 4:5.3.1-1ubuntu1 [1282 B]
Get:188 http://ftpmaster.internal/ubuntu yakkety/main i386 gir1.2-freedesktop i386 1.46.0-3ubuntu1 [5732 B]
Get:189 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpangoxft-1.0-0 i386 1.40.1-1 [16.0 kB]
Get:190 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 gir1.2-pango-1.0 i386 1.40.1-1 [21.4 kB]
Get:191 http://ftpmaster.internal/ubuntu yakkety/main i386 icu-devtools i386 57.1-1 [165 kB]
Get:192 http://ftpmaster.internal/ubuntu yakkety/main i386 libblas-common i386 3.6.0-2ubuntu2 [5338 B]
Get:193 http://ftpmaster.internal/ubuntu yakkety/main i386 libblas3 i386 3.6.0-2ubuntu2 [130 kB]
Get:194 http://ftpmaster.internal/ubuntu yakkety/main i386 libblas-dev i386 3.6.0-2ubuntu2 [129 kB]
Get:195 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libbz2-dev i386 1.0.6-8build1 [28.6 kB]
Get:196 http://ftpmaster.internal/ubuntu yakkety/main i386 libcairo-gobject2 i386 1.14.6-1build1 [16.7 kB]
Get:197 http://ftpmaster.internal/ubuntu yakkety/main i386 libcairo-script-interpreter2 i386 1.14.6-1build1 [58.5 kB]
Get:198 http://ftpmaster.internal/ubuntu yakkety/main i386 libexpat1-dev i386 2.1.1-1 [116 kB]
Get:199 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 zlib1g-dev i386 1:1.2.8.dfsg-2ubuntu5 [167 kB]
Get:200 http://ftpmaster.internal/ubuntu yakkety/main i386 libpng-dev i386 1.6.21-4 [143 kB]
Get:201 http://ftpmaster.internal/ubuntu yakkety/main i386 libfreetype6-dev i386 2.6.3-3ubuntu1 [5185 kB]
Get:202 http://ftpmaster.internal/ubuntu yakkety/main i386 pkg-config i386 0.29.1-0ubuntu1 [45.8 kB]
Get:203 http://ftpmaster.internal/ubuntu yakkety/main i386 libfontconfig1-dev i386 2.11.94-0ubuntu1 [662 kB]
Get:204 http://ftpmaster.internal/ubuntu yakkety/main i386 xorg-sgml-doctools all 1:1.11-1 [12.9 kB]
Get:205 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-core-dev all 7.0.28-2ubuntu1 [254 kB]
Get:206 http://ftpmaster.internal/ubuntu yakkety/main i386 libxau-dev i386 1:1.0.8-1 [10.2 kB]
Get:207 http://ftpmaster.internal/ubuntu yakkety/main i386 libxdmcp-dev i386 1:1.1.2-1.1 [25.0 kB]
Get:208 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-input-dev all 2.3.1-1 [118 kB]
Get:209 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-kb-dev all 1.0.7-0ubuntu1 [224 kB]
Get:210 http://ftpmaster.internal/ubuntu yakkety/main i386 xtrans-dev all 1.3.5-1 [70.5 kB]
Get:211 http://ftpmaster.internal/ubuntu yakkety/main i386 libpthread-stubs0-dev i386 0.3-4 [4054 B]
Get:212 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb1-dev i386 1.11.1-1ubuntu1 [76.3 kB]
Get:213 http://ftpmaster.internal/ubuntu yakkety/main i386 libx11-dev i386 2:1.6.3-1ubuntu2 [663 kB]
Get:214 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-render-dev all 2:0.11.1-2 [20.1 kB]
Get:215 http://ftpmaster.internal/ubuntu yakkety/main i386 libxrender-dev i386 1:0.9.9-0ubuntu1 [24.9 kB]
Get:216 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:217 http://ftpmaster.internal/ubuntu yakkety/main i386 libxext-dev i386 2:1.3.3-1 [82.8 kB]
Get:218 http://ftpmaster.internal/ubuntu yakkety/main i386 libice-dev i386 2:1.0.9-1 [42.4 kB]
Get:219 http://ftpmaster.internal/ubuntu yakkety/main i386 libsm-dev i386 2:1.2.2-1 [15.1 kB]
Get:220 http://ftpmaster.internal/ubuntu yakkety/main i386 libpixman-1-dev i386 0.33.6-1 [261 kB]
Get:221 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-render0-dev i386 1.11.1-1ubuntu1 [15.6 kB]
Get:222 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-shm0-dev i386 1.11.1-1ubuntu1 [6628 B]
Get:223 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-bin i386 2.48.0-1ubuntu4 [41.1 kB]
Get:224 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcre16-3 i386 2:8.38-3.1 [144 kB]
Get:225 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcre32-3 i386 2:8.38-3.1 [136 kB]
Get:226 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcre3-dev i386 2:8.38-3.1 [530 kB]
Get:227 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-dev i386 2.48.0-1ubuntu4 [1422 kB]
Get:228 http://ftpmaster.internal/ubuntu yakkety/main i386 libcairo2-dev i386 1.14.6-1build1 [629 kB]
Get:229 http://ftpmaster.internal/ubuntu yakkety/main i386 libcupsfilters1 i386 1.8.3-2ubuntu4 [84.2 kB]
Get:230 http://ftpmaster.internal/ubuntu yakkety/main i386 libcupsimage2 i386 2.1.3-5 [16.8 kB]
Get:231 http://ftpmaster.internal/ubuntu yakkety/main i386 libcurl3 i386 7.47.0-1ubuntu2 [207 kB]
Get:232 http://ftpmaster.internal/ubuntu yakkety/main i386 libcurl4-openssl-dev i386 7.47.0-1ubuntu2 [291 kB]
Get:233 http://ftpmaster.internal/ubuntu yakkety/main i386 libgraphite2-dev i386 1.3.6-1ubuntu1 [14.6 kB]
Get:234 http://ftpmaster.internal/ubuntu yakkety/main i386 libijs-0.35 i386 0.35-12 [16.0 kB]
Get:235 http://ftpmaster.internal/ubuntu yakkety/main i386 libjbig2dec0 i386 0.12+20150918-1build1 [58.0 kB]
Get:236 http://ftpmaster.internal/ubuntu yakkety/main i386 libpaper1 i386 1.1.24+nmu4ubuntu1 [13.8 kB]
Get:237 http://ftpmaster.internal/ubuntu yakkety/main i386 libgs9-common all 9.18~dfsg~0-0ubuntu5 [2982 kB]
Get:238 http://ftpmaster.internal/ubuntu yakkety/main i386 libgs9 i386 9.18~dfsg~0-0ubuntu5 [2154 kB]
Get:239 http://ftpmaster.internal/ubuntu yakkety/main i386 libharfbuzz-icu0 i386 1.2.6-2 [5378 B]
Get:240 http://ftpmaster.internal/ubuntu yakkety/main i386 libharfbuzz-gobject0 i386 1.2.6-2 [10.3 kB]
Get:241 http://ftpmaster.internal/ubuntu yakkety/main i386 libicu-dev i386 57.1-1 [15.3 MB]
Get:242 http://ftpmaster.internal/ubuntu yakkety/main i386 libharfbuzz-dev i386 1.2.6-2 [240 kB]
Get:243 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg-turbo8-dev i386 1.4.2-0ubuntu3 [263 kB]
Get:244 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg8-dev i386 8c-2ubuntu8 [1546 B]
Get:245 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg-dev i386 8c-2ubuntu8 [1544 B]
Get:246 http://ftpmaster.internal/ubuntu yakkety/main i386 libkpathsea6 i386 2015.20160222.37495-1build1 [58.6 kB]
Get:247 http://ftpmaster.internal/ubuntu yakkety/main i386 liblapack3 i386 3.6.0-2ubuntu2 [1764 kB]
Get:248 http://ftpmaster.internal/ubuntu yakkety/main i386 liblapack-dev i386 3.6.0-2ubuntu2 [1691 kB]
Get:249 http://ftpmaster.internal/ubuntu yakkety/main i386 libtinfo-dev i386 6.0+20160213-1ubuntu1 [76.4 kB]
Get:250 http://ftpmaster.internal/ubuntu yakkety/main i386 libncurses5-dev i386 6.0+20160213-1ubuntu1 [177 kB]
Get:251 http://ftpmaster.internal/ubuntu yakkety/main i386 libxft-dev i386 2.3.2-1 [43.6 kB]
Get:252 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpango1.0-dev i386 1.40.1-1 [284 kB]
Get:253 http://ftpmaster.internal/ubuntu yakkety/main i386 libpaper-utils i386 1.1.24+nmu4ubuntu1 [8298 B]
Get:254 http://ftpmaster.internal/ubuntu yakkety/main i386 libpoppler58 i386 0.41.0-0ubuntu2 [790 kB]
Get:255 http://ftpmaster.internal/ubuntu yakkety/main i386 libpotrace0 i386 1.13-2 [16.8 kB]
Get:256 http://ftpmaster.internal/ubuntu yakkety/main i386 libptexenc1 i386 2015.20160222.37495-1build1 [35.1 kB]
Get:257 http://ftpmaster.internal/ubuntu yakkety/main i386 libreadline6-dev i386 6.3-8ubuntu2 [126 kB]
Get:258 http://ftpmaster.internal/ubuntu yakkety/main i386 libreadline-dev i386 6.3-8ubuntu2 [988 B]
Get:259 http://ftpmaster.internal/ubuntu yakkety/main i386 libsynctex1 i386 2015.20160222.37495-1build1 [43.7 kB]
Get:260 http://ftpmaster.internal/ubuntu yakkety/main i386 libtcl8.6 i386 8.6.5+dfsg-2 [932 kB]
Get:261 http://ftpmaster.internal/ubuntu yakkety/main i386 libtexlua52 i386 2015.20160222.37495-1build1 [99.8 kB]
Get:262 http://ftpmaster.internal/ubuntu yakkety/main i386 libtexluajit2 i386 2015.20160222.37495-1build1 [226 kB]
Get:263 http://ftpmaster.internal/ubuntu yakkety/universe i386 libtext-unidecode-perl all 1.27-1 [103 kB]
Get:264 http://ftpmaster.internal/ubuntu yakkety/main i386 libjbig-dev i386 2.1-3.1 [24.1 kB]
Get:265 http://ftpmaster.internal/ubuntu yakkety/main i386 liblzma-dev i386 5.1.1alpha+20120614-2ubuntu2 [139 kB]
Get:266 http://ftpmaster.internal/ubuntu yakkety/main i386 libtiffxx5 i386 4.0.6-1 [6208 B]
Get:267 http://ftpmaster.internal/ubuntu yakkety/main i386 libtiff5-dev i386 4.0.6-1 [284 kB]
Get:268 http://ftpmaster.internal/ubuntu yakkety/main i386 libtk8.6 i386 8.6.5-1 [729 kB]
Get:269 http://ftpmaster.internal/ubuntu yakkety/main i386 libxt6 i386 1:1.1.5-0ubuntu1 [164 kB]
Get:270 http://ftpmaster.internal/ubuntu yakkety/main i386 libxmu6 i386 2:1.1.2-2 [48.4 kB]
Get:271 http://ftpmaster.internal/ubuntu yakkety/main i386 libxaw7 i386 2:1.0.13-1 [182 kB]
Get:272 http://ftpmaster.internal/ubuntu yakkety/main i386 libxkbfile1 i386 1:1.0.9-0ubuntu1 [68.8 kB]
Get:273 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml-namespacesupport-perl all 1.11-1 [13.2 kB]
Get:274 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml-sax-base-perl all 1.07-1 [21.5 kB]
Get:275 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml-sax-perl all 0.99+dfsg-2ubuntu1 [64.6 kB]
Get:276 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml-libxml-perl i386 2.0123+dfsg-1build1 [332 kB]
Get:277 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-scrnsaver-dev all 1.2.2-1 [25.0 kB]
Get:278 http://ftpmaster.internal/ubuntu yakkety/main i386 libxss-dev i386 1:1.2.2-1 [12.7 kB]
Get:279 http://ftpmaster.internal/ubuntu yakkety/main i386 libxt-dev i386 1:1.1.5-0ubuntu1 [395 kB]
Get:280 http://ftpmaster.internal/ubuntu yakkety/universe i386 mpack i386 1.6-8 [39.3 kB]
Get:281 http://ftpmaster.internal/ubuntu yakkety/main i386 tex-common all 6.05 [545 kB]
Get:282 http://ftpmaster.internal/ubuntu yakkety/main i386 preview-latex-style all 11.88-1.1ubuntu1 [184 kB]
Get:283 http://ftpmaster.internal/ubuntu yakkety/main i386 t1utils i386 1.39-2 [54.6 kB]
Get:284 http://ftpmaster.internal/ubuntu yakkety/main i386 tcl8.6 i386 8.6.5+dfsg-2 [14.3 kB]
Get:285 http://ftpmaster.internal/ubuntu yakkety/main i386 tcl8.6-dev i386 8.6.5+dfsg-2 [963 kB]
Get:286 http://ftpmaster.internal/ubuntu yakkety/universe i386 texinfo i386 6.1.0.dfsg.1-6 [743 kB]
Get:287 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-binaries i386 2015.20160222.37495-1build1 [7552 kB]
Get:288 http://ftpmaster.internal/ubuntu yakkety/main i386 xdg-utils all 1.1.1-1ubuntu1 [59.9 kB]
Get:289 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-base all 2015.20160320-1 [18.2 MB]
Get:290 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-latex-base all 2015.20160320-1 [849 kB]
Get:291 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-extra-utils all 2015.20160320-1 [11.9 MB]
Get:292 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-stix all 1.1.1-4 [591 kB]
Get:293 http://ftpmaster.internal/ubuntu yakkety/universe i386 ttf-adf-gillius all 0.20090423-2 [400 kB]
Get:294 http://ftpmaster.internal/ubuntu yakkety/universe i386 ttf-adf-universalis all 0.20090423-2 [221 kB]
Get:295 http://ftpmaster.internal/ubuntu yakkety/universe i386 ttf-adf-accanthis all 0.20090423-2 [401 kB]
Get:296 http://ftpmaster.internal/ubuntu yakkety/universe i386 texlive-fonts-extra all 2015.20160320-1 [233 MB]
Get:297 http://ftpmaster.internal/ubuntu yakkety/universe i386 texlive-fonts-recommended all 2015.20160320-1 [5695 kB]
Get:298 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-generic-recommended all 2015.20160320-1 [2860 kB]
Get:299 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-latex-recommended all 2015.20160320-1 [13.0 MB]
Get:300 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-pictures all 2015.20160320-1 [3737 kB]
Get:301 http://ftpmaster.internal/ubuntu yakkety/universe i386 texlive-latex-extra all 2015.20160320-1 [10.3 MB]
Get:302 http://ftpmaster.internal/ubuntu yakkety/main i386 tk8.6 i386 8.6.5-1 [12.2 kB]
Get:303 http://ftpmaster.internal/ubuntu yakkety/main i386 tk8.6-dev i386 8.6.5-1 [755 kB]
Get:304 http://ftpmaster.internal/ubuntu yakkety/main i386 x11-xkb-utils i386 7.7+2 [157 kB]
Get:305 http://ftpmaster.internal/ubuntu yakkety/main i386 xfonts-encodings all 1:1.0.4-2 [573 kB]
Get:306 http://ftpmaster.internal/ubuntu yakkety/main i386 xfonts-utils i386 1:7.7+3 [75.2 kB]
Get:307 http://ftpmaster.internal/ubuntu yakkety/main i386 xfonts-base all 1:1.0.4+nmu1 [5914 kB]
Get:308 http://ftpmaster.internal/ubuntu yakkety/main i386 xserver-common all 2:1.18.3-1ubuntu3 [26.5 kB]
Get:309 http://ftpmaster.internal/ubuntu yakkety/universe i386 xvfb i386 2:1.18.3-1ubuntu3 [828 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libxdmcp6:i386 (1:1.1.2-1.1) ...
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Unpacking groff-base (1.22.3-7) ...
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Unpacking libpipeline1:i386 (1.4.1-2) ...
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Selecting previously unselected package ucf.
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Selecting previously unselected package libnss3-nssdb.
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Processing triggers for libc-bin (2.23-0ubuntu3) ...
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Setting up libice-dev:i386 (2:1.0.9-1) ...
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Setting up libpaper1:i386 (1.1.24+nmu4ubuntu1) ...

Creating config file /etc/papersize with new version
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Setting up libsynctex1:i386 (2015.20160222.37495-1build1) ...
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Setting up libxt6:i386 (1:1.1.5-0ubuntu1) ...
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Setting up libxaw7:i386 (2:1.0.13-1) ...
Setting up libxkbfile1:i386 (1:1.0.9-0ubuntu1) ...
Setting up libxml-namespacesupport-perl (1.11-1) ...
Setting up libxml-sax-base-perl (1.07-1) ...
Setting up libxml-sax-perl (0.99+dfsg-2ubuntu1) ...
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 libxml-libxml-perl (2.0123+dfsg-1build1) ...
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 x11proto-scrnsaver-dev (1.2.2-1) ...
Setting up libxss-dev:i386 (1:1.2.2-1) ...
Setting up libxt-dev:i386 (1:1.1.5-0ubuntu1) ...
Setting up mpack (1.6-8) ...
Setting up tex-common (6.05) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up preview-latex-style (11.88-1.1ubuntu1) ...
Setting up t1utils (1.39-2) ...
Setting up tcl8.6 (8.6.5+dfsg-2) ...
Setting up tcl8.6-dev:i386 (8.6.5+dfsg-2) ...
Setting up texinfo (6.1.0.dfsg.1-6) ...
Running mktexlsr. This may take some time. ... done.
Setting up texlive-binaries (2015.20160222.37495-1build1) ...
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 xdg-utils (1.1.1-1ubuntu1) ...
Setting up fonts-stix (1.1.1-4) ...
Setting up ttf-adf-gillius (0.20090423-2) ...
Setting up ttf-adf-universalis (0.20090423-2) ...
Setting up ttf-adf-accanthis (0.20090423-2) ...
Setting up tk8.6 (8.6.5-1) ...
Setting up tk8.6-dev:i386 (8.6.5-1) ...
Setting up x11-xkb-utils (7.7+2) ...
Setting up xfonts-encodings (1:1.0.4-2) ...
Setting up xfonts-utils (1:7.7+3) ...
Setting up xfonts-base (1:1.0.4+nmu1) ...
Setting up xserver-common (2:1.18.3-1ubuntu3) ...
Setting up xvfb (2:1.18.3-1ubuntu3) ...
Processing triggers for tex-common (6.05) ...
update-language: texlive-base not installed and configured, doing nothing!
texlive-base is not ready, skipping fmtutil --all call
Setting up texlive-base (2015.20160320-1) ...
/usr/bin/tl-paper: setting paper size for dvips to a4.
/usr/bin/tl-paper: setting paper size for dvipdfmx to a4.
/usr/bin/tl-paper: setting paper size for xdvi to a4.
/usr/bin/tl-paper: setting paper size for pdftex to a4.
Processing triggers for tex-common (6.05) ...
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.
Setting up texlive-fonts-extra (2015.20160320-1) ...
Setting up texlive-fonts-recommended (2015.20160320-1) ...
Setting up texlive-generic-recommended (2015.20160320-1) ...
Setting up texlive-latex-base (2015.20160320-1) ...
Processing triggers for tex-common (6.05) ...
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.
Setting up texlive-latex-recommended (2015.20160320-1) ...
Setting up texlive-pictures (2015.20160320-1) ...
Setting up texlive-extra-utils (2015.20160320-1) ...
Processing triggers for tex-common (6.05) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-latex-extra (2015.20160320-1) ...
Processing triggers for tex-common (6.05) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up libnss3-nssdb (2:3.21-1ubuntu4) ...
Setting up dh-autoreconf (12) ...
Setting up libnss3:i386 (2:3.21-1ubuntu4) ...
Setting up openjdk-8-jre-headless:i386 (8u91-b14-2ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
OpenJDK Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Setting up ca-certificates-java (20160321) ...
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:NetLock_Business_=Class_B=_Root.pem
Adding debian:Sonera_Class_1_Root_CA.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:ComSign_CA.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:GeoTrust_Global_CA_2.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Certigna.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:RSA_Security_2048_v3.pem
Adding debian:StartCom_Certification_Authority_G2.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:EC-ACC.pem
Adding debian:ApplicationCA_-_Japanese_Government.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Certification_Authority_of_WoSign_G2.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem
Adding debian:Juur-SK.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:Camerfirma_Global_Chambersign_Root.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:StartCom_Certification_Authority.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:NetLock_Notary_=Class_A=_Root.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:Swisscom_Root_CA_2.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
Adding debian:Equifax_Secure_Global_eBusiness_CA.pem
Adding debian:NetLock_Express_=Class_C=_Root.pem
Adding debian:WoSign_China.pem
Adding debian:AddTrust_Low-Value_Services_Root.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
Adding debian:Security_Communication_EV_RootCA1.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:TC_TrustCenter_Class_3_CA_II.pem
Adding debian:ACEDICOM_Root.pem
Adding debian:AddTrust_Qualified_Certificates_Root.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:CNNIC_ROOT.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:PSCProcert.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:ACCVRAIZ1.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:Visa_eCommerce_Root.pem
Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem
Adding debian:UTN_USERFirst_Hardware_Root_CA.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:AC_Raíz_Certicámara_S.A..pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:NetLock_Qualified_=Class_QA=_Root.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:DST_ACES_CA_X6.pem
Adding debian:Secure_Global_CA.pem
Adding debian:S-TRUST_Universal_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:CA_Disig_Root_R1.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:Root_CA_Generalitat_Valenciana.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:Comodo_Trusted_Services_root.pem
Adding debian:Certum_Root_CA.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem
Adding debian:IGC_A.pem
Adding debian:SwissSign_Platinum_CA_-_G2.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:StartCom_Certification_Authority_2.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:Certinomis_-_Autorité_Racine.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:CA_WoSign_ECC_Root.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:UTN_USERFirst_Email_Root_CA.pem
Adding debian:EE_Certification_Centre_Root_CA.pem
Adding debian:Comodo_Secure_Services_root.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:Equifax_Secure_eBusiness_CA_1.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem
Adding debian:Equifax_Secure_CA.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem
Adding debian:CA_Disig.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:SecureTrust_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:Swisscom_Root_EV_CA_2.pem
Adding debian:Buypass_Class_2_CA_1.pem
Adding debian:AddTrust_Public_Services_Root.pem
Adding debian:Staat_der_Nederlanden_Root_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:Microsec_e-Szigno_Root_CA.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:Swisscom_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:WoSign.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:QuoVadis_Root_CA.pem
done.
Setting up default-jre-headless (2:1.8-56ubuntu2) ...
Setting up debhelper (9.20160403ubuntu1) ...
Setting up openjdk-8-jre:i386 (8u91-b14-2ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode
Setting up default-jre (2:1.8-56ubuntu2) ...
Setting up openjdk-8-jdk-headless:i386 (8u91-b14-2ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/javah to provide /usr/bin/javah (javah) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
Setting up default-jdk-headless (2:1.8-56ubuntu2) ...
Setting up openjdk-8-jdk:i386 (8u91-b14-2ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up default-jdk (2:1.8-56ubuntu2) ...
Setting up sbuild-build-depends-r-base-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.23-0ubuntu3) ...
Processing triggers for systemd (229-5ubuntu1) ...
Processing triggers for ca-certificates (20160104ubuntu1) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...

done.
done.

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 3.13.0-85-generic amd64 (i686)
Toolchain package versions: binutils_2.26-8ubuntu3 dpkg-dev_1.18.4ubuntu2 g++-5_5.3.1-16ubuntu3 gcc-5_5.3.1-16ubuntu3 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-16ubuntu3 libstdc++6_6.1.1-0ubuntu12 linux-libc-dev_4.4.0-22.38
Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.2.11 apt-transport-https_1.2.11 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.7-2ubuntu3 autotools-dev_20160430.1 base-files_9.6ubuntu1 base-passwd_3.5.39 bash_4.3-14ubuntu2 bash-completion_1:2.1-4.2ubuntu2 binutils_2.26-8ubuntu3 bison_2:3.0.4.dfsg-1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 ca-certificates-java_20160321 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-16ubuntu3 dash_0.5.8-2.1ubuntu2 debconf_1.5.59ubuntu1 debhelper_9.20160403ubuntu1 debianutils_4.7 default-jdk_2:1.8-56ubuntu2 default-jdk-headless_2:1.8-56ubuntu2 default-jre_2:1.8-56ubuntu2 default-jre-headless_2:1.8-56ubuntu2 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.122-1ubuntu1 dpkg_1.18.4ubuntu2 dpkg-dev_1.18.4ubuntu2 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.6.0+git+20160126-2 fontconfig_2.11.94-0ubuntu1 fontconfig-config_2.11.94-0ubuntu1 fonts-cabin_1.5-2 fonts-comfortaa_2.003-1 fonts-crosextra-caladea_20130214-1 fonts-crosextra-carlito_20130920-1 fonts-dejavu-core_2.35-1 fonts-dejavu-extra_2.35-1 fonts-ebgaramond_0.015+git20130628-3 fonts-ebgaramond-extra_0.015+git20130628-3 fonts-font-awesome_4.6.1~dfsg-1 fonts-freefont-otf_20120503-4 fonts-freefont-ttf_20120503-4 fonts-gfs-artemisia_1.1-5 fonts-gfs-complutum_1.1-6 fonts-gfs-didot_1.1-6 fonts-gfs-neohellenic_1.1-6 fonts-gfs-olga_1.1-5 fonts-gfs-solomos_1.1-5 fonts-junicode_0.7.8-2 fonts-lato_2.0-1 fonts-linuxlibertine_5.3.0-2 fonts-lobster_2.0-2 fonts-lobstertwo_2.0-2 fonts-oflb-asana-math_000.907-6 fonts-roboto-hinted_2:0~20160106-1 fonts-sil-gentium_20081126:1.03-1 fonts-sil-gentium-basic_1.1-7 fonts-sil-gentiumplus_5.000-1 fonts-stix_1.1.1-4 g++_4:5.3.1-1ubuntu1 g++-5_5.3.1-16ubuntu3 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-16ubuntu3 gcc-5-base_5.3.1-16ubuntu3 gcc-6-base_6.1.1-0ubuntu12 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gfortran_4:5.3.1-1ubuntu1 gfortran-5_5.3.1-16ubuntu3 gir1.2-freedesktop_1.46.0-3ubuntu1 gir1.2-glib-2.0_1.46.0-3ubuntu1 gir1.2-pango-1.0_1.40.1-1 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 hostname_3.17ubuntu1 icu-devtools_57.1-1 init_1.31ubuntu1 init-system-helpers_1.31ubuntu1 initscripts_2.88dsf-59.3ubuntu5 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 java-common_0.56ubuntu2 libacl1_2.2.52-3 libapparmor1_2.10.95-0ubuntu2 libapt-pkg5.0_1.2.11 libarchive-zip-perl_1.57-1 libasan2_5.3.1-16ubuntu3 libasn1-8-heimdal_1.7~git20150920+dfsg-4ubuntu1 libasound2_1.1.0-1 libasound2-data_1.1.0-1 libasprintf0v5_0.19.7-2ubuntu3 libasyncns0_0.8-5build1 libatk1.0-0_2.20.0-1 libatk1.0-data_2.20.0-1 libatomic1_6.1.1-0ubuntu12 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu2 libaudit1_1:2.4.5-1ubuntu2 libavahi-client3_0.6.32~rc+dfsg-1ubuntu2 libavahi-common-data_0.6.32~rc+dfsg-1ubuntu2 libavahi-common3_0.6.32~rc+dfsg-1ubuntu2 libbison-dev_2:3.0.4.dfsg-1 libblas-common_3.6.0-2ubuntu2 libblas-dev_3.6.0-2ubuntu2 libblas3_3.6.0-2ubuntu2 libblkid1_2.27.1-6ubuntu3 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8build1 libbz2-dev_1.0.6-8build1 libc-bin_2.23-0ubuntu3 libc-dev-bin_2.23-0ubuntu3 libc6_2.23-0ubuntu3 libc6-dev_2.23-0ubuntu3 libcairo-gobject2_1.14.6-1build1 libcairo-script-interpreter2_1.14.6-1build1 libcairo2_1.14.6-1build1 libcairo2-dev_1.14.6-1build1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_6.1.1-0ubuntu12 libcilkrts5_6.1.1-0ubuntu12 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcups2_2.1.3-5 libcupsfilters1_1.8.3-2ubuntu4 libcupsimage2_2.1.3-5 libcurl3_7.47.0-1ubuntu2 libcurl3-gnutls_7.47.0-1ubuntu2 libcurl4-openssl-dev_7.47.0-1ubuntu2 libdatrie1_0.2.10-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu3 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.122-1ubuntu1 libdpkg-perl_1.18.4ubuntu2 libdrm-amdgpu1_2.4.67-1 libdrm-intel1_2.4.67-1 libdrm-nouveau2_2.4.67-1 libdrm-radeon1_2.4.67-1 libdrm2_2.4.67-1 libedit2_3.1-20150325-1ubuntu2 libelf1_0.165-3ubuntu1 libexpat1_2.1.1-1 libexpat1-dev_2.1.1-1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-6ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libflac8_1.3.1-4 libfontconfig1_2.11.94-0ubuntu1 libfontconfig1-dev_2.11.94-0ubuntu1 libfontenc1_1:1.1.3-1 libfreetype6_2.6.3-3ubuntu1 libfreetype6-dev_2.6.3-3ubuntu1 libgcc-5-dev_5.3.1-16ubuntu3 libgcc1_1:6.1.1-0ubuntu12 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libgdk-pixbuf2.0-0_2.34.0-1ubuntu1 libgdk-pixbuf2.0-common_2.34.0-1ubuntu1 libgfortran-5-dev_5.3.1-16ubuntu3 libgfortran3_6.1.1-0ubuntu12 libgif7_5.1.4-0.1 libgirepository-1.0-1_1.46.0-3ubuntu1 libgl1-mesa-dri_11.2.1-1ubuntu1 libgl1-mesa-glx_11.2.1-1ubuntu1 libglapi-mesa_11.2.1-1ubuntu1 libglib2.0-0_2.48.0-1ubuntu4 libglib2.0-bin_2.48.0-1ubuntu4 libglib2.0-data_2.48.0-1ubuntu4 libglib2.0-dev_2.48.0-1ubuntu4 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.10-4ubuntu1 libgomp1_6.1.1-0ubuntu12 libgpg-error0_1.22-1 libgraphite2-3_1.3.6-1ubuntu1 libgraphite2-dev_1.3.6-1ubuntu1 libgs9_9.18~dfsg~0-0ubuntu5 libgs9-common_9.18~dfsg~0-0ubuntu5 libgssapi-krb5-2_1.13.2+dfsg-5 libgssapi3-heimdal_1.7~git20150920+dfsg-4ubuntu1 libgtk2.0-0_2.24.30-1ubuntu1 libgtk2.0-common_2.24.30-1ubuntu1 libharfbuzz-dev_1.2.6-2 libharfbuzz-gobject0_1.2.6-2 libharfbuzz-icu0_1.2.6-2 libharfbuzz0b_1.2.6-2 libhcrypto4-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimbase1-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimntlm0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhogweed4_3.2-1 libhx509-5-heimdal_1.7~git20150920+dfsg-4ubuntu1 libice-dev_2:1.0.9-1 libice6_2:1.0.9-1 libicu-dev_57.1-1 libicu57_57.1-1 libidn11_1.32-3ubuntu1 libijs-0.35_0.35-12 libisl15_0.16.1-1 libitm1_6.1.1-0ubuntu12 libjbig-dev_2.1-3.1 libjbig0_2.1-3.1 libjbig2dec0_0.12+20150918-1build1 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_1.4.2-0ubuntu3 libjpeg-turbo8-dev_1.4.2-0ubuntu3 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c3_0.12-3 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8ubuntu1 libkmod2_22-1ubuntu4 libkpathsea6_2015.20160222.37495-1build1 libkrb5-26-heimdal_1.7~git20150920+dfsg-4ubuntu1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 liblapack-dev_3.6.0-2ubuntu2 liblapack3_3.6.0-2ubuntu2 liblcms2-2_2.6-3ubuntu2 libldap-2.4-2_2.4.42+dfsg-2ubuntu3 libllvm3.8_1:3.8-2ubuntu3 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma-dev_5.1.1alpha+20120614-2ubuntu2 liblzma5_5.1.1alpha+20120614-2ubuntu2 liblzo2-2_2.08-1.2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-6ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libmpx0_5.3.1-16ubuntu3 libncurses5_6.0+20160213-1ubuntu1 libncurses5-dev_6.0+20160213-1ubuntu1 libncursesw5_6.0+20160213-1ubuntu1 libnettle6_3.2-1 libnspr4_2:4.11-1ubuntu1 libnss3_2:3.21-1ubuntu4 libnss3-nssdb_2:3.21-1ubuntu4 libogg0_1.3.2-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpango-1.0-0_1.40.1-1 libpango1.0-dev_1.40.1-1 libpangocairo-1.0-0_1.40.1-1 libpangoft2-1.0-0_1.40.1-1 libpangoxft-1.0-0_1.40.1-1 libpaper-utils_1.1.24+nmu4ubuntu1 libpaper1_1.1.24+nmu4ubuntu1 libpciaccess0_0.13.4-1 libpcre16-3_2:8.38-3.1 libpcre3_2:8.38-3.1 libpcre3-dev_2:8.38-3.1 libpcre32-3_2:8.38-3.1 libpcrecpp0v5_2:8.38-3.1 libpcsclite1_1.8.14-1ubuntu1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpixman-1-dev_0.33.6-1 libpng-dev_1.6.21-4 libpng12-0_1.2.54-6ubuntu1 libpng16-16_1.6.21-4 libpoppler58_0.41.0-0ubuntu2 libpotrace0_1.13-2 libprocps4_2:3.3.10-4ubuntu2 libptexenc1_2015.20160222.37495-1build1 libpthread-stubs0-dev_0.3-4 libpulse0_1:8.0-2ubuntu1 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-8 libpython2.7-stdlib_2.7.11-8 libquadmath0_6.1.1-0ubuntu12 libreadline-dev_6.3-8ubuntu2 libreadline6_6.3-8ubuntu2 libreadline6-dev_6.3-8ubuntu2 libroken18-heimdal_1.7~git20150920+dfsg-4ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.2.3-3ubuntu3 libselinux1_2.5-2 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsm-dev_2:1.2.2-1 libsm6_2:1.2.2-1 libsmartcols1_2.27.1-6ubuntu3 libsndfile1_1.0.25-10 libsqlite3-0_3.11.0-1ubuntu1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2g-1ubuntu4 libstdc++-5-dev_5.3.1-16ubuntu3 libstdc++6_6.1.1-0ubuntu12 libsynctex1_2015.20160222.37495-1build1 libsystemd0_229-5ubuntu1 libtasn1-6_4.8-1 libtcl8.6_8.6.5+dfsg-2 libtexlua52_2015.20160222.37495-1build1 libtexluajit2_2015.20160222.37495-1build1 libtext-unidecode-perl_1.27-1 libthai-data_0.1.24-2 libthai0_0.1.24-2 libtiff5_4.0.6-1 libtiff5-dev_4.0.6-1 libtiffxx5_4.0.6-1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160213-1ubuntu1 libtinfo5_6.0+20160213-1ubuntu1 libtk8.6_8.6.5-1 libtool_2.4.6-0.1 libubsan0_6.1.1-0ubuntu12 libudev1_229-5ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-29 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6ubuntu3 libvorbis0a_1.3.5-3 libvorbisenc2_1.3.5-3 libwind0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libwrap0_7.6.q-25 libx11-6_2:1.6.3-1ubuntu2 libx11-data_2:1.6.3-1ubuntu2 libx11-dev_2:1.6.3-1ubuntu2 libx11-xcb1_2:1.6.3-1ubuntu2 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-dri2-0_1.11.1-1ubuntu1 libxcb-dri3-0_1.11.1-1ubuntu1 libxcb-glx0_1.11.1-1ubuntu1 libxcb-present0_1.11.1-1ubuntu1 libxcb-render0_1.11.1-1ubuntu1 libxcb-render0-dev_1.11.1-1ubuntu1 libxcb-shm0_1.11.1-1ubuntu1 libxcb-shm0-dev_1.11.1-1ubuntu1 libxcb-sync1_1.11.1-1ubuntu1 libxcb1_1.11.1-1ubuntu1 libxcb1-dev_1.11.1-1ubuntu1 libxcomposite1_1:0.4.4-1 libxcursor1_1:1.1.14-1 libxdamage1_1:1.1.4-2 libxdmcp-dev_1:1.1.2-1.1 libxdmcp6_1:1.1.2-1.1 libxext-dev_2:1.3.3-1 libxext6_2:1.3.3-1 libxfixes3_1:5.0.1-2 libxfont1_1:1.5.1-1 libxft-dev_2.3.2-1 libxft2_2.3.2-1 libxi6_2:1.7.6-1 libxinerama1_2:1.1.3-1 libxkbfile1_1:1.0.9-0ubuntu1 libxml-libxml-perl_2.0123+dfsg-1build1 libxml-namespacesupport-perl_1.11-1 libxml-sax-base-perl_1.07-1 libxml-sax-perl_0.99+dfsg-2ubuntu1 libxml2_2.9.3+dfsg1-1build1 libxmu6_2:1.1.2-2 libxmuu1_2:1.1.2-2 libxpm4_1:3.5.11-1 libxrandr2_2:1.5.0-1 libxrender-dev_1:0.9.9-0ubuntu1 libxrender1_1:0.9.9-0ubuntu1 libxshmfence1_1.2-1 libxss-dev_1:1.2.2-1 libxss1_1:1.2.2-1 libxt-dev_1:1.1.5-0ubuntu1 libxt6_1:1.1.5-0ubuntu1 libxtst6_2:1.2.2-1 libxxf86vm1_1:1.1.4-1 libzzip-0-13_0.13.62-3 linux-libc-dev_4.4.0-22.38 lockfile-progs_0.1.17 login_1:4.2-3.1ubuntu5 lsb-base_9.20160110 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mime-support_3.59ubuntu1 mount_2.27.1-6ubuntu3 mpack_1.6-8 multiarch-support_2.23-0ubuntu3 ncurses-base_6.0+20160213-1ubuntu1 ncurses-bin_6.0+20160213-1ubuntu1 openjdk-8-jdk_8u91-b14-2ubuntu1 openjdk-8-jdk-headless_8u91-b14-2ubuntu1 openjdk-8-jre_8u91-b14-2ubuntu1 openjdk-8-jre-headless_8u91-b14-2ubuntu1 openssl_1.0.2g-1ubuntu4 optipng_0.7.6-1build1 passwd_1:4.2-3.1ubuntu5 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 pkg-config_0.29.1-0ubuntu1 pkg-create-dbgsym_0.72 pkgbinarymangler_129 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 poppler-data_0.4.7-7 preview-latex-style_11.88-1.1ubuntu1 procps_2:3.3.10-4ubuntu2 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-8 python2.7-minimal_2.7.11-8 readline-common_6.3-8ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-base-dummy_0.invalid.0 sed_4.2.2-7 sensible-utils_0.0.9 shared-mime-info_1.6-1 systemd_229-5ubuntu1 systemd-sysv_229-5ubuntu1 sysv-rc_2.88dsf-59.3ubuntu5 sysvinit-utils_2.88dsf-59.3ubuntu5 t1utils_1.39-2 tar_1.28-2.2 tcl8.6_8.6.5+dfsg-2 tcl8.6-dev_8.6.5+dfsg-2 tex-common_6.05 texinfo_6.1.0.dfsg.1-6 texlive-base_2015.20160320-1 texlive-binaries_2015.20160222.37495-1build1 texlive-extra-utils_2015.20160320-1 texlive-fonts-extra_2015.20160320-1 texlive-fonts-recommended_2015.20160320-1 texlive-generic-recommended_2015.20160320-1 texlive-latex-base_2015.20160320-1 texlive-latex-extra_2015.20160320-1 texlive-latex-recommended_2015.20160320-1 texlive-pictures_2015.20160320-1 tk8.6_8.6.5-1 tk8.6-dev_8.6.5-1 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 ttf-adf-universalis_0.20090423-2 tzdata_2016d-2 ubuntu-keyring_2012.05.19 ucf_3.0036 util-linux_2.27.1-6ubuntu3 x11-common_1:7.7+13ubuntu3 x11-xkb-utils_7.7+2 x11proto-core-dev_7.0.28-2ubuntu1 x11proto-input-dev_2.3.1-1 x11proto-kb-dev_1.0.7-0ubuntu1 x11proto-render-dev_2:0.11.1-2 x11proto-scrnsaver-dev_1.2.2-1 x11proto-xext-dev_7.3.0-1 xauth_1:1.0.9-1ubuntu2 xdg-utils_1.1.1-1ubuntu1 xfonts-base_1:1.0.4+nmu1 xfonts-encodings_1:1.0.4-2 xfonts-utils_1:7.7+3 xkb-data_2.16-1ubuntu1 xorg-sgml-doctools_1:1.11-1 xserver-common_2:1.18.3-1ubuntu3 xtrans-dev_1.3.5-1 xvfb_2:1.18.3-1ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build                                                                        │
└──────────────────────────────────────────────────────────────────────────────┘


Unpack source
─────────────

gpgv: Signature made Tue May  3 11:24:15 2016 UTC using RSA key ID AB99A21A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-base_3.3.0-1.dsc
dpkg-source: info: extracting r-base in r-base-3.3.0
dpkg-source: info: unpacking r-base_3.3.0.orig.tar.gz
dpkg-source: info: applying r-base_3.3.0-1.diff.gz

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

DEB_BUILD_OPTIONS=parallel=4
HOME=/home/buildd
LANG=C.UTF-8
LOGNAME=buildd
MAIL=/var/mail/buildd
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
PWD=/«PKGBUILDDIR»
SHELL=/bin/sh
SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env'
SUDO_GID=2501
SUDO_UID=2001
SUDO_USER=buildd
TERM=unknown
USER=buildd
USERNAME=root

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package r-base
dpkg-buildpackage: source version 3.3.0-1
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build r-base-3.3.0
dpkg-buildpackage: host architecture i386
 fakeroot debian/rules clean
*** clean ***
dh_testdir
dh_testroot
rm -f	configure-stamp \
	build-stamp build-indep-stamp build-arch-stamp \
	make-stamp make-arch-stamp make-indep-stamp \
	install-indep-stamp install-arch-stamp \
	check-stamp 
[ ! -f Makefile ] || /usr/bin/make distclean
rm -f `find . -name "*~"`
rm -rf debian/tmp debian/files* core debian/substvars
rm -f doc/html/function.html doc/html/packages.html
rm -f modules/*.so src/unix/Rscript
dh_clean
 debian/rules build-arch
*** configure ***
#automake
#autoconf
dh_testdir
R_TEXI2DVICMD=emulation				\
R_PAPERSIZE=letter				\
R_BROWSER=xdg-open				\
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				\
LIBnn=lib					\
AWK=/usr/bin/awk                                \
CC="gcc -std=gnu99"					\
CXX=g++						\
F77=gfortran					\
FC=gfortran					\
CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"				\
CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"				\
FFLAGS="-g -O2 -fstack-protector-strong"				\
FCFLAGS="-g -O2 -fstack-protector-strong"				\
CPPFLAGS=					\
LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro"				\
FLIBS=						\
rsharedir=/usr/share/R/share			\
rincludedir=/usr/share/R/include		\
rdocdir=/usr/share/R/doc			\
./configure --prefix=/usr			\
	    --with-cairo			\
	    --with-jpeglib			\
	    --with-readline			\
	    --with-tcltk			\
	    --with-system-bzlib			\
	    --with-system-pcre			\
	    --with-system-zlib			\
	    --mandir=/usr/share/man		\
	    --infodir=/usr/share/info		\
	    --datadir=/usr/share/R/share	\
	    --includedir=/usr/share/R/include	\
	    --with-blas		\
	    --with-lapack		\
	    --enable-R-profiling		\
	    --enable-R-shlib			\
	    --enable-memory-profiling		\
	    --without-recommended-packages	\
	    --build i686-linux-gnu
configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking whether ln -s works... yes
checking for bison... bison -y
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for /usr/bin/pager... /usr/bin/pager
checking for gtar... no
checking for gnutar... no
checking for 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 notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc -std=gnu99 needs -traditional... no
checking how to run the C preprocessor... gcc -std=gnu99 -E
defining F77 to be gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc -std=gnu99 accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether g++ can compile ObjC++... no
checking whether  can compile ObjC++... no
no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
checking how to convert i686-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 -std=gnu99 object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... yes
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (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) 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 readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking whether rl_completion_matches exists and is declared... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking dl.h usability... no
checking dl.h presence... no
checking for dl.h... no
checking for dlfcn.h... (cached) yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking features.h usability... yes
checking features.h presence... yes
checking for features.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking fpu_control.h usability... yes
checking fpu_control.h presence... yes
checking for fpu_control.h... yes
checking glob.h usability... yes
checking glob.h presence... yes
checking for glob.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for strings.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking stdalign.h usability... yes
checking stdalign.h presence... yes
checking for stdalign.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for gcc -std=gnu99 option to accept ISO C99... none needed
checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 4
checking size of long long... 8
checking size of double... 8
checking size of size_t... 4
checking size of long double... 12
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes
checking for gcc -std=gnu99 option to support OpenMP... -fopenmp
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran...  -L/usr/lib/gcc/i686-linux-gnu/5 -L/usr/lib/gcc/i686-linux-gnu/5/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/5/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/5/../../.. -lgfortran -lm -lquadmath
checking how to get verbose linking output from gcc -std=gnu99... -v
checking for C libraries of gcc -std=gnu99...  -L/usr/lib/gcc/i686-linux-gnu/5 -L/usr/lib/gcc/i686-linux-gnu/5/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/5/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/5/../../.. -lgcc_s
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking whether gfortran appends underscores to external names... yes
checking whether gfortran appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether gfortran and gcc -std=gnu99 agree on int and double... yes
checking whether gfortran and gcc -std=gnu99 agree on double complex... yes
checking for gfortran option to support OpenMP... -fopenmp
checking whether g++ accepts -M for generating dependencies... yes
checking for g++ option to support OpenMP... -fopenmp
checking whether we can compute ObjC Make dependencies... no
checking whether C runtime needs -D__NO_MATH_INLINES... no
checking for xmkmf... no
checking whether g++  supports C++11 features by default... no
checking whether g++  supports C++11 features with -std=c++11... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log1pl exists and is declared... yes
checking whether log2 exists and is declared... yes
checking whether log10 exists and is declared... yes
checking whether nearbyint exists and is declared... yes
checking whether nearbyintl exists and is declared... yes
checking whether powl exists and is declared... yes
checking whether rint exists and is declared... yes
checking whether rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
checking sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking for cospi in -lsunmath... no
checking for atanpi... no
checking for atan2pi... no
checking for cospi... no
checking for exp10... yes
checking for pown... no
checking for sinpi... no
checking for tanpi... no
checking for __cospi... no
checking for __sinpi... no
checking for __tanpi... no
checking for fseeko... yes
checking for ftello... yes
checking for matherr... yes
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether getline exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
checking whether gmtime_r exists and is declared... yes
checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... yes
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... yes
checking for realpath... yes
checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for __setfpucw... no
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... no
checking whether mktime works correctly outside 1902-2037... no
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_... no
checking for ATL_xerbla in -latlas... no
checking for dgemm_ in -lblas... yes
checking for dgemm_ in -ldgemm... no
checking for dgemm_ in -lblas... (cached) yes
checking for dgemm_ in -lessl... no
checking for dgemm_ in -lblas... (cached) yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
checking for dpstrf_... no
checking for dpstrf_ in -llapack... yes
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking for iconvlist... no
checking for iconv... yes
checking for iconv declaration... 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... yes
checking wctype.h presence... yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether iswblank exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking X11/Xmu/Atoms.h usability... no
checking X11/Xmu/Atoms.h presence... no
checking for X11/Xmu/Atoms.h... no
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories... /usr/lib/tcl8.6/tclConfig.sh
checking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories... /usr/lib/tk8.6/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking mmap support for zlib... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support suffices... no
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
checking for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... yes
checking pcre.h presence... yes
checking for pcre.h... yes
checking pcre/pcre.h usability... no
checking pcre/pcre.h presence... no
checking for pcre/pcre.h... no
checking if PCRE version >= 8.10, < 10.0 and has UTF-8 support... yes
checking if PCRE version >= 8.32... yes
checking whether PCRE support suffices... yes
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 7.47.0
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
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 jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for sys/time.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
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 whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for gfortran option to support OpenMP... -fopenmp
checking whether NLS is requested... yes

Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for 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... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) 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 argz.h usability... yes
checking argz.h presence... yes
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached) 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... bison
checking version of bison... 3.0.4, ok
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... yes
checking whether to use NLS... yes
checking where the gettext function comes from... libc
Finished configuring src/extra/intl directory

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

R is now configured for i686-pc-linux-gnu

  Source directory:          .
  Installation directory:    /usr

  C compiler:                gcc -std=gnu99  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  Fortran 77 compiler:       gfortran  -g -O2 -fstack-protector-strong

  C++ compiler:              g++  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  C++11 compiler:            g++  -std=c++11 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  Fortran 90/95 compiler:    gfortran -g -O2 -fstack-protector-strong
  Obj-C compiler:	      

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

  Capabilities skipped:      
  Options not enabled:       shared BLAS

  Recommended packages:      no

touch configure-stamp
*** make-arch ***
/usr/bin/make		CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"			\
		CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"			\
		FFLAGS="-g -O2 -fstack-protector-strong"			\
		FCFLAGS="-g -O2 -fstack-protector-strong"			\
		CC="gcc -std=gnu99"				\
		CXX=g++			\
		F77=gfortran			\
		LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro"			\
		PKG_BUILT_STAMP=""""	\
		R_GZIPCMD="/bin/gzip -n"		\
		R
make[1]: Entering directory '/«PKGBUILDDIR»'
make[2]: Entering directory '/«PKGBUILDDIR»/m4'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/m4'
make[2]: Entering directory '/«PKGBUILDDIR»/tools'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tools'
make[2]: Entering directory '/«PKGBUILDDIR»/doc'
make[3]: Entering directory '/«PKGBUILDDIR»/doc/html'
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html'
make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
make[2]: Leaving directory '/«PKGBUILDDIR»/doc'
make[2]: Entering directory '/«PKGBUILDDIR»/etc'
make[2]: Leaving directory '/«PKGBUILDDIR»/etc'
make[2]: Entering directory '/«PKGBUILDDIR»/share'
make[2]: Leaving directory '/«PKGBUILDDIR»/share'
make[2]: Entering directory '/«PKGBUILDDIR»/src'
make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts'
creating src/scripts/R.fe
make[4]: Entering directory '/«PKGBUILDDIR»/src/scripts'
mkdir -p -- ../../bin
make[4]: Leaving directory '/«PKGBUILDDIR»/src/scripts'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts'
make[3]: Entering directory '/«PKGBUILDDIR»/src/include'
mkdir -p -- ../../include
make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/include'
make[3]: Entering directory '/«PKGBUILDDIR»/src/extra'
make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/extra/tre'
make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regcomp.c -o regcomp.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regerror.c -o regerror.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regexec.c -o regexec.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-ast.c -o tre-ast.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-compile.c -o tre-compile.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-mem.c -o tre-mem.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-parse.c -o tre-parse.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-stack.c -o tre-stack.o
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c xmalloc.c -o xmalloc.o
ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o
ranlib libtre.a
make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra'
make[3]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/appl'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interv.c -o interv.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c maxcol.c -o maxcol.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pretty.c -o pretty.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uncmin.c -o uncmin.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dchdc.f -o dchdc.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dpbfa.f -o dpbfa.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dpbsl.f -o dpbsl.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dpoco.f -o dpoco.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dpodi.f -o dpodi.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dpofa.f -o dpofa.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dposl.f -o dposl.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dqrdc.f -o dqrdc.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dqrls.f -o dqrls.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dqrsl.f -o dqrsl.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dqrutl.f -o dqrutl.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dsvdc.f -o dsvdc.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c dtrco.f -o dtrco.o
gfortran  -fopenmp -fpic  -g -O2 -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 '/«PKGBUILDDIR»/src/appl'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl'
make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making expm1.d from expm1.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mlutils.c -o mlutils.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d1mach.c -o d1mach.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c i1mach.c -o i1mach.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmax2.c -o fmax2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmin2.c -o fmin2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fprec.c -o fprec.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fround.c -o fround.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ftrunc.c -o ftrunc.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sign.c -o sign.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fsign.c -o fsign.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imax2.c -o imax2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imin2.c -o imin2.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chebyshev.c -o chebyshev.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log1p.c -o log1p.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c expm1.c -o expm1.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgammacor.c -o lgammacor.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gammalims.c -o gammalims.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stirlerr.c -o stirlerr.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bd0.c -o bd0.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma.c -o gamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgamma.c -o lgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma_cody.c -o gamma_cody.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c beta.c -o beta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lbeta.c -o lbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c polygamma.c -o polygamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cospi.c -o cospi.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_i.c -o bessel_i.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_j.c -o bessel_j.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_k.c -o bessel_k.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_y.c -o bessel_y.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c choose.c -o choose.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c snorm.c -o snorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sexp.c -o sexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgamma.c -o dgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgamma.c -o pgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgamma.c -o qgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgamma.c -o rgamma.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbeta.c -o dbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbeta.c -o pbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbeta.c -o qbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbeta.c -o rbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dunif.c -o dunif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c punif.c -o punif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qunif.c -o qunif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c runif.c -o runif.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnorm.c -o dnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnorm.c -o pnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnorm.c -o qnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnorm.c -o rnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlnorm.c -o dlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plnorm.c -o plnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlnorm.c -o qlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlnorm.c -o rlnorm.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c df.c -o df.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pf.c -o pf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qf.c -o qf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rf.c -o rf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnf.c -o dnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dt.c -o dt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pt.c -o pt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qt.c -o qt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rt.c -o rt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnt.c -o dnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dchisq.c -o dchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pchisq.c -o pchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qchisq.c -o qchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rchisq.c -o rchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnchisq.c -o rnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbinom.c -o dbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbinom.c -o pbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbinom.c -o qbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbinom.c -o rbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rmultinom.c -o rmultinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcauchy.c -o dcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pcauchy.c -o pcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qcauchy.c -o qcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcauchy.c -o rcauchy.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dexp.c -o dexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pexp.c -o pexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qexp.c -o qexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rexp.c -o rexp.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgeom.c -o dgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgeom.c -o pgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgeom.c -o qgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgeom.c -o rgeom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dhyper.c -o dhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c phyper.c -o phyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qhyper.c -o qhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rhyper.c -o rhyper.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbinom.c -o dnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbinom.c -o pnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbinom.c -o qnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnbinom.c -o rnbinom.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dpois.c -o dpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ppois.c -o ppois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qpois.c -o qpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rpois.c -o rpois.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dweibull.c -o dweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pweibull.c -o pweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qweibull.c -o qweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rweibull.c -o rweibull.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlogis.c -o dlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plogis.c -o plogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlogis.c -o qlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlogis.c -o rlogis.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnchisq.c -o dnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnchisq.c -o pnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnchisq.c -o qnchisq.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbeta.c -o dnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbeta.c -o pnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbeta.c -o qnbeta.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnf.c -o pnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnt.c -o pnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnf.c -o qnf.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnt.c -o qnt.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptukey.c -o ptukey.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qtukey.c -o qtukey.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c toms708.c -o toms708.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wilcox.c -o wilcox.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signrank.c -o signrank.o
ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath'
make[3]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rembedded.c -o Rembedded.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dynload.c -o dynload.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c system.c -o system.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-unix.c -o sys-unix.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-std.c -o sys-std.o
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c X11.c -o X11.o
ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o
ranlib libunix.a
make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[4]: Entering directory '/«PKGBUILDDIR»/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Entering directory '/«PKGBUILDDIR»/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 apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making radixsort.d from radixsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making g_alab_her.d from g_alab_her.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making g_her_glyph.d from g_her_glyph.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CommandLineArgs.c -o CommandLineArgs.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rdynload.c -o Rdynload.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Renviron.c -o Renviron.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RNG.c -o RNG.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c agrep.c -o agrep.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c apply.c -o apply.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arithmetic.c -o arithmetic.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c array.c -o array.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attrib.c -o attrib.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bind.c -o bind.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c builtin.c -o builtin.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c character.c -o character.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coerce.c -o coerce.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complex.c -o complex.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connections.c -o connections.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c context.c -o context.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cum.c -o cum.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcf.c -o dcf.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c datetime.c -o datetime.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c debug.c -o debug.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deparse.c -o deparse.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dotcode.c -o dotcode.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dounzip.c -o dounzip.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dstruct.c -o dstruct.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c duplicate.c -o duplicate.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c edit.c -o edit.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c engine.c -o engine.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c errors.c -o errors.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c eval.c -o eval.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c format.c -o format.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gevents.c -o gevents.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram.c -o gram.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram-ex.c -o gram-ex.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grep.c -o grep.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c identical.c -o identical.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inlined.c -o inlined.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inspect.c -o inspect.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c internet.c -o internet.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c iosupport.c -o iosupport.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lapack.c -o lapack.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c list.c -o list.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c localecharset.c -o localecharset.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c logic.c -o logic.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c main.c -o main.o
main.c: In function ‘dummy_ii’:
main.c:1656:12: warning: function returns address of local variable [-Wreturn-local-addr]
     return (uintptr_t) &ii;
            ^
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mapply.c -o mapply.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match.c -o match.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c memory.c -o memory.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c names.c -o names.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c objects.c -o objects.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c options.c -o options.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c paste.c -o paste.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c platform.c -o platform.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plotmath.c -o plotmath.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c print.c -o print.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printarray.c -o printarray.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printvector.c -o printvector.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printutils.c -o printutils.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qsort.c -o qsort.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c radixsort.c -o radixsort.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raw.c -o raw.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c registration.c -o registration.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c relop.c -o relop.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlocale.c -o rlocale.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c saveload.c -o saveload.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scan.c -o scan.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c seq.c -o seq.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c serialize.c -o serialize.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sort.c -o sort.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c source.c -o source.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c split.c -o split.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sprintf.c -o sprintf.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c startup.c -o startup.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subassign.c -o subassign.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subscript.c -o subscript.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subset.c -o subset.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c summary.c -o summary.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sysutils.c -o sysutils.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c times.c -o times.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unique.c -o unique.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c version.c -o version.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_alab_her.c -o g_alab_her.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_cntrlify.c -o g_cntrlify.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_fontdb.c -o g_fontdb.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_her_glyph.c -o g_her_glyph.o
gfortran  -fopenmp -fpic  -g -O2 -fstack-protector-strong -c xxxpr.f -o xxxpr.o
gcc -std=gnu99 -shared -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro  -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o 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  -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
make[5]: Entering directory '/«PKGBUILDDIR»/src/main'
mkdir -p -- /«PKGBUILDDIR»/bin/exec
mkdir -p -- /«PKGBUILDDIR»/lib
make[5]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmain.c -o Rmain.o
gcc -std=gnu99 -Wl,--export-dynamic -fopenmp  -L../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R.bin Rmain.o  -lR 
make[5]: Entering directory '/«PKGBUILDDIR»/src/main'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Entering directory '/«PKGBUILDDIR»/src/modules'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
making Rhttpd.d from Rhttpd.c
making Rsock.d from Rsock.c
making internet.d from internet.c
making libcurl.d from libcurl.c
making nanoftp.d from nanoftp.c
making nanohttp.d from nanohttp.c
making sock.d from sock.c
making sockconn.d from sockconn.c
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c Rsock.c -o Rsock.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c internet.c -o internet.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c libcurl.c -o libcurl.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c nanoftp.c -o nanoftp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c nanohttp.c -o nanohttp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c sock.c -o sock.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c sockconn.c -o sockconn.o
gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -L/usr/lib/i386-linux-gnu -lcurl -lR  
make[6]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
mkdir -p -- /«PKGBUILDDIR»/modules
make[6]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
making Lapack.d from Lapack.c
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Lapack.c -o Lapack.o
gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o lapack.so  Lapack.o  -lR  -llapack -lblas -lgfortran -lm -lquadmath
make[6]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/modules/X11'
gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devX11.c -o devX11.o
gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rotated.c -o rotated.o
gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbitmap.c -o rbitmap.o
gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -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 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt  -lR -lm 
gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dataentry.c -o dataentry.o
gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt  -lR -lm 
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
mkdir -p -- ../../library
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
building package 'base'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base'
mkdir -p -- ../../../library/base/demo
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
mkdir -p -- ../../../library/tools/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
making signals.d from signals.c
making install.d from install.c
making getfmts.d from getfmts.c
making http.d from http.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c text.c -o text.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmd5.c -o Rmd5.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signals.c -o signals.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c install.c -o install.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getfmts.c -o getfmts.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http.c -o http.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramLatex.c -o gramLatex.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramRd.c -o gramRd.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
byte-compiling package 'compiler'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
byte-compiling package 'base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
byte-compiling package 'tools'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
mkdir -p -- ../../../library/utils/R
mkdir -p -- ../../../library/utils/Sweave
mkdir -p -- ../../../library/utils/misc
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src'
making init.d from init.c
making io.d from io.c
making size.d from size.c
making sock.d from sock.c
making stubs.d from stubs.c
making utils.d from utils.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c size.c -o size.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sock.c -o sock.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
byte-compiling package 'utils'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[5]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src'
making axis_scales.d from axis_scales.c
making chull.d from chull.c
making devices.d from devices.c
making init.d from init.c
making stubs.d from stubs.c
making colors.d from colors.c
making devCairo.d from devCairo.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
making devQuartz.d from devQuartz.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c axis_scales.c -o axis_scales.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chull.c -o chull.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devCairo.c -o devCairo.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPicTeX.c -o devPicTeX.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPS.c -o devPS.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devQuartz.c -o devQuartz.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
gcc -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../../../src/modules/X11  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cairoBM.c -o cairoBM.o
gcc -std=gnu99 -shared -L../../../../../lib -Wl,-Bsymbolic-functions -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 -lpng16 -lz -lcairo -L../../../../../lib -lR -lm 
make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
byte-compiling package 'grDevices'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src'
making init.d from init.c
making base.d from base.c
making graphics.d from graphics.c
making par.d from par.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making stem.d from stem.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base.c -o base.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c par.c -o par.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stem.c -o stem.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -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 '/«PKGBUILDDIR»/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
byte-compiling package 'graphics'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src'
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making dblcen.d from dblcen.c
making distance.d from distance.c
making hclust-utils.d from hclust-utils.c
making nls.d from nls.c
making rWishart.d from rWishart.c
making HoltWinters.d from HoltWinters.c
making PPsum.d from PPsum.c
making arima.d from arima.c
making burg.d from burg.c
making filter.d from filter.c
making mAR.d from mAR.c
making pacf.d from pacf.c
making starma.d from starma.c
making port.d from port.c
making family.d from family.c
making sbart.d from sbart.c
making approx.d from approx.c
making loglin.d from loglin.c
making lowess.d from lowess.c
making massdist.d from massdist.c
making splines.d from splines.c
making lm.d from lm.c
making complete_cases.d from complete_cases.c
making cov.d from cov.c
making deriv.d from deriv.c
making fft.d from fft.c
making fourier.d from fourier.c
making model.d from model.c
making optim.d from optim.c
making optimize.d from optimize.c
making integrate.d from integrate.c
making random.d from random.c
making distn.d from distn.c
making zeroin.d from zeroin.c
making rcont.d from rcont.c
making influence.d from influence.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kmeans.c -o kmeans.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ansari.c -o ansari.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bandwidths.c -o bandwidths.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chisqsim.c -o chisqsim.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d2x2xk.c -o d2x2xk.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fexact.c -o fexact.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kendall.c -o kendall.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ks.c -o ks.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c line.c -o line.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c smooth.c -o smooth.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prho.c -o prho.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c swilk.c -o swilk.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ksmooth.c -o ksmooth.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loessc.c -o loessc.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c monoSpl.c -o monoSpl.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c isoreg.c -o isoreg.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Srunmed.c -o Srunmed.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dblcen.c -o dblcen.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distance.c -o distance.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hclust-utils.c -o hclust-utils.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nls.c -o nls.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rWishart.c -o rWishart.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HoltWinters.c -o HoltWinters.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PPsum.c -o PPsum.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arima.c -o arima.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c burg.c -o burg.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filter.c -o filter.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mAR.c -o mAR.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pacf.c -o pacf.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c starma.c -o starma.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c port.c -o port.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c family.c -o family.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sbart.c -o sbart.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c approx.c -o approx.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loglin.c -o loglin.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowess.c -o lowess.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c massdist.c -o massdist.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complete_cases.c -o complete_cases.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cov.c -o cov.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deriv.c -o deriv.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fft.c -o fft.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fourier.c -o fourier.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c model.c -o model.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optimize.c -o optimize.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distn.c -o distn.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zeroin.c -o zeroin.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcont.c -o rcont.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fopenmp -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c influence.c -o influence.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c bsplvd.f -o bsplvd.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c bvalue.f -o bvalue.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c bvalus.f -o bvalus.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c loessf.f -o loessf.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c ppr.f -o ppr.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c qsbart.f -o qsbart.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c sgram.f -o sgram.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c sinerp.f -o sinerp.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c sslvrg.f -o sslvrg.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c stxwx.f -o stxwx.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c hclust.f -o hclust.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c kmns.f -o kmns.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c eureka.f -o eureka.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c stl.f -o stl.o
gfortran -fpic  -g -O2 -fstack-protector-strong -ffloat-store -c portsrc.f -o portsrc.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -c lminfl.f -o lminfl.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -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 '/«PKGBUILDDIR»/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
byte-compiling package 'stats'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
making utils.d from utils.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c do_substitute_direct.c -o do_substitute_direct.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c methods_list_dispatch.c -o methods_list_dispatch.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c slot.c -o slot.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c class_support.c -o class_support.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tests.c -o tests.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -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 '/«PKGBUILDDIR»/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
byte-compiling 'methods'
initializing class and method definitions ... done
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
mkdir -p -- ../../../library/grid/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src'
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making matrix.d from matrix.c
making register.d from register.c
making state.d from state.c
making unit.d from unit.c
making util.d from util.c
making viewport.d from viewport.c
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gpar.c -o gpar.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grid.c -o grid.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c just.c -o just.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c layout.c -o layout.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matrix.c -o matrix.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c register.c -o register.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c state.c -o state.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unit.c -o unit.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c viewport.c -o viewport.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
byte-compiling package 'grid'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
building package 'splines'
mkdir -p -- ../../../library/splines
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
mkdir -p -- ../../../library/splines/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src'
making splines.d from splines.c
gcc -std=gnu99 -I../../../../include -DNDEBUG     -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src'
mkdir -p -- ../../../../library/splines/libs
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
byte-compiling package 'splines'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
mkdir -p -- ../../../library/stats4/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
byte-compiling package 'stats4'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src'
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk.c -o tcltk.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk_unix.c -o tcltk_unix.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib/i386-linux-gnu -ltcl8.6 -L/usr/lib/i386-linux-gnu -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src'
mkdir -p -- ../../../../library/tcltk/libs
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
byte-compiling package 'tcltk'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
building package 'parallel'
mkdir -p -- ../../../library/parallel
mkdir -p -- ../../../library/parallel/doc
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
mkdir -p -- ../../../library/parallel/R
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src'
making init.d from init.c
making rngstream.d from rngstream.c
making fork.d from fork.c
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rngstream.c -o rngstream.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H    -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fork.c -o fork.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src'
mkdir -p -- ../../../../library/parallel/libs
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
byte-compiling package 'parallel'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
make[2]: Entering directory '/«PKGBUILDDIR»/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tests'
you should 'make docs' now ...
make[1]: Leaving directory '/«PKGBUILDDIR»'
(cd src/nmath/standalone;				\
	/usr/bin/make	CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"		\
		CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"	\
		FFLAGS="-g -O2 -fstack-protector-strong -D_REENTRANT"	\
		CC="gcc -std=gnu99"				\
		CXX=g++			\
		F77=gfortran			\
		R_GZIPCMD="/bin/gzip -n"		\
		libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.1 \
		shared static )
make[1]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone'
(cd ../../include; /usr/bin/make Rmath.h)
make[2]: Entering directory '/«PKGBUILDDIR»/src/include'
make[2]: 'Rmath.h' is up to date.
make[2]: Leaving directory '/«PKGBUILDDIR»/src/include'
Copying source files
make[2]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making expm1.d from expm1.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
making std_unif.d from std_unif.c
make[2]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone'
make[2]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c expm1.c -o expm1.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.lo
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.lo
gcc -std=gnu99 -shared -fopenmp -Wl,-Bsymbolic-functions -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 expm1.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm
make[2]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone'
make[2]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c expm1.c -o expm1.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.o
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./..  -DHAVE_CONFIG_H -DMATHLIB_STANDALONE  -fopenmp  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.o
ar -cr libRmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o
ranlib libRmath.a
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make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[4]: Entering directory '/«PKGBUILDDIR»/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Entering directory '/«PKGBUILDDIR»/src/main'
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
make[5]: Entering directory '/«PKGBUILDDIR»/src/main'
/«PKGBUILDDIR»/lib/libR.so is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
make[5]: Entering directory '/«PKGBUILDDIR»/src/main'
/«PKGBUILDDIR»/bin/exec/R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Entering directory '/«PKGBUILDDIR»/src/modules'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
make[5]: 'internet.so' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
make[5]: 'lapack.so' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
/«PKGBUILDDIR»/modules/R_X11.so is unchanged
/«PKGBUILDDIR»/modules/R_de.so is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile'
building system startup profile
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations'
building package 'translations'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
building package 'base'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
building package 'tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src'
../../../../library/tools/libs/tools.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
building package 'compiler'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
building package 'utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
all.R is unchanged
make[5]: Nothing to be done for 'iconvlist'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src'
../../../../library/utils/libs/utils.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
building package 'grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src'
../../../../library/grDevices/libs/grDevices.so is unchanged
make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[10]: 'cairo.so' is up to date.
make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
building package 'graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src'
../../../../library/graphics/libs/graphics.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
building package 'stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src'
../../../../library/stats/libs/stats.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets'
building package 'datasets'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
building package 'methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src'
../../../../library/methods/libs/methods.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Nothing to be done for 'RfilesLazy'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
building package 'grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src'
../../../../library/grid/libs/grid.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
building package 'splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src'
../../../../library/splines/libs/splines.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
building package 'stats4'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
building package 'tcltk'
all.R is unchanged
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src'
../../../../library/tcltk/libs/tcltk.so is unchanged
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
building package 'parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src'
../../../../library/parallel/libs/parallel.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
make[2]: Entering directory '/«PKGBUILDDIR»/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tests'
you should 'make docs' now ...
make[2]: Entering directory '/«PKGBUILDDIR»/doc'
creating NEWS
creating NEWS.pdf
make[3]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/doc/html'
make[4]: Leaving directory '/«PKGBUILDDIR»/doc/html'
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
make[2]: Leaving directory '/«PKGBUILDDIR»/doc'
make[2]: Entering directory '/«PKGBUILDDIR»/src/library'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
installing parsed Rd
make[4]: Entering directory '/«PKGBUILDDIR»/src/library'
  base
  stats
  utils
  methods
  graphics
  grDevices
  datasets
  grid
  tools
  tcltk
  splines
  stats4
  compiler
  parallel
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
building/updating package metadata ...
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
writing package indices
make[4]: Entering directory '/«PKGBUILDDIR»/src/library'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[2]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[1]: Leaving directory '/«PKGBUILDDIR»'
/usr/bin/make javaconf
make[1]: Entering directory '/«PKGBUILDDIR»'
make[2]: Entering directory '/«PKGBUILDDIR»/m4'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/m4'
make[2]: Entering directory '/«PKGBUILDDIR»/tools'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tools'
make[2]: Entering directory '/«PKGBUILDDIR»/doc'
make[3]: Entering directory '/«PKGBUILDDIR»/doc/html'
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html'
make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
make[2]: Leaving directory '/«PKGBUILDDIR»/doc'
make[2]: Entering directory '/«PKGBUILDDIR»/etc'
make[2]: Leaving directory '/«PKGBUILDDIR»/etc'
make[2]: Entering directory '/«PKGBUILDDIR»/share'
make[2]: Leaving directory '/«PKGBUILDDIR»/share'
make[2]: Entering directory '/«PKGBUILDDIR»/src'
make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts'
make[4]: Entering directory '/«PKGBUILDDIR»/src/scripts'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/scripts'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts'
make[3]: Entering directory '/«PKGBUILDDIR»/src/include'
make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext'
make[4]: Nothing to be done for 'R'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/include'
make[3]: Entering directory '/«PKGBUILDDIR»/src/extra'
make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: 'Makedeps' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: 'libtre.a' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra'
make[3]: Entering directory '/«PKGBUILDDIR»/src/appl'
make[4]: Entering directory '/«PKGBUILDDIR»/src/appl'
make[4]: 'libappl.a' is up to date.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/appl'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl'
make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath'
make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath'
make[4]: 'libnmath.a' is up to date.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath'
make[3]: Entering directory '/«PKGBUILDDIR»/src/unix'
make[4]: Entering directory '/«PKGBUILDDIR»/src/unix'
make[4]: 'libunix.a' is up to date.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[4]: Entering directory '/«PKGBUILDDIR»/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Entering directory '/«PKGBUILDDIR»/src/main'
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
make[5]: Entering directory '/«PKGBUILDDIR»/src/main'
/«PKGBUILDDIR»/lib/libR.so is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
make[5]: Entering directory '/«PKGBUILDDIR»/src/main'
/«PKGBUILDDIR»/bin/exec/R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Entering directory '/«PKGBUILDDIR»/src/modules'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
make[5]: 'internet.so' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
make[5]: 'lapack.so' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
/«PKGBUILDDIR»/modules/R_X11.so is unchanged
/«PKGBUILDDIR»/modules/R_de.so is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile'
building system startup profile
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations'
building package 'translations'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
building package 'base'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
building package 'tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src'
../../../../library/tools/libs/tools.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
building package 'compiler'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
building package 'utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
all.R is unchanged
make[5]: Nothing to be done for 'iconvlist'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src'
../../../../library/utils/libs/utils.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
building package 'grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src'
../../../../library/grDevices/libs/grDevices.so is unchanged
make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[10]: 'cairo.so' is up to date.
make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
building package 'graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src'
../../../../library/graphics/libs/graphics.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
building package 'stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src'
../../../../library/stats/libs/stats.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets'
building package 'datasets'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
building package 'methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src'
../../../../library/methods/libs/methods.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Nothing to be done for 'RfilesLazy'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
building package 'grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src'
../../../../library/grid/libs/grid.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
building package 'splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src'
../../../../library/splines/libs/splines.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
building package 'stats4'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
building package 'tcltk'
all.R is unchanged
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src'
../../../../library/tcltk/libs/tcltk.so is unchanged
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
building package 'parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src'
../../../../library/parallel/libs/parallel.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
make[2]: Entering directory '/«PKGBUILDDIR»/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tests'
make[2]: Entering directory '/«PKGBUILDDIR»'
configuring Java ...
Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
Java version     : 1.8.0_91
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: /usr/lib/jvm/default-java/bin/javah
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)/jre/lib/i386/server -ljvm
make[3]: Entering directory '/tmp/Rjavareconf.ibbW9O'
gcc -std=gnu99 -I/«PKGBUILDDIR»/include -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/«PKGBUILDDIR»/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/jre/lib/i386/server -ljvm -L/«PKGBUILDDIR»/lib -lR
make[3]: Leaving directory '/tmp/Rjavareconf.ibbW9O'


JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/jre/lib/i386/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/i386/server -ljvm
Updating Java configuration in /«PKGBUILDDIR»
Done.

make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
touch make-arch-stamp
*** make-indep ***
/usr/bin/make -k docs
make[1]: Entering directory '/«PKGBUILDDIR»'
make[2]: Entering directory '/«PKGBUILDDIR»/m4'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/m4'
make[2]: Entering directory '/«PKGBUILDDIR»/tools'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tools'
make[2]: Entering directory '/«PKGBUILDDIR»/doc'
make[3]: Entering directory '/«PKGBUILDDIR»/doc/html'
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html'
make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
make[2]: Leaving directory '/«PKGBUILDDIR»/doc'
make[2]: Entering directory '/«PKGBUILDDIR»/etc'
make[2]: Leaving directory '/«PKGBUILDDIR»/etc'
make[2]: Entering directory '/«PKGBUILDDIR»/share'
make[2]: Leaving directory '/«PKGBUILDDIR»/share'
make[2]: Entering directory '/«PKGBUILDDIR»/src'
make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts'
make[4]: Entering directory '/«PKGBUILDDIR»/src/scripts'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/scripts'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts'
make[3]: Entering directory '/«PKGBUILDDIR»/src/include'
make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext'
make[4]: Nothing to be done for 'R'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/include'
make[3]: Entering directory '/«PKGBUILDDIR»/src/extra'
make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: 'Makedeps' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
make[5]: 'libtre.a' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra'
make[3]: Entering directory '/«PKGBUILDDIR»/src/appl'
make[4]: Entering directory '/«PKGBUILDDIR»/src/appl'
make[4]: 'libappl.a' is up to date.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/appl'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl'
make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath'
make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath'
make[4]: 'libnmath.a' is up to date.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath'
make[3]: Entering directory '/«PKGBUILDDIR»/src/unix'
make[4]: Entering directory '/«PKGBUILDDIR»/src/unix'
make[4]: 'libunix.a' is up to date.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[4]: Entering directory '/«PKGBUILDDIR»/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Entering directory '/«PKGBUILDDIR»/src/main'
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
make[5]: Entering directory '/«PKGBUILDDIR»/src/main'
/«PKGBUILDDIR»/lib/libR.so is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
make[5]: Entering directory '/«PKGBUILDDIR»/src/main'
/«PKGBUILDDIR»/bin/exec/R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Entering directory '/«PKGBUILDDIR»/src/modules'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
make[5]: 'internet.so' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
make[5]: 'lapack.so' is up to date.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/modules/X11'
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installing parsed NAMESPACE files
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installing parsed Rd
make[4]: Entering directory '/«PKGBUILDDIR»/src/library'
  base
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writing package indices
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make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
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make[1]: Entering directory '/«PKGBUILDDIR»/doc/manual'
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Converting parsed Rd's to LaTeX 
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Converting parsed Rd's to LaTeX .
PDF/LaTeX documentation: reference index ...
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(/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}] [1] [2] (./base-pkg.tex
Chapter 1.
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Underfull \hbox (badness 4595) in paragraph at lines 40--43
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[1] [2]
Underfull \hbox (badness 1960) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
/ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 .

Underfull \hbox (badness 10000) in paragraph at lines 141--149
\T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if

Underfull \hbox (badness 10000) in paragraph at lines 141--149
\T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is

Underfull \hbox (badness 1668) in paragraph at lines 152--159
[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[3] [4] [5]
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[]\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]
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[]\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[7] [8]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ',
[9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
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[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[19] [20] [21] [22]
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[]\T1/zi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/zi4/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/zi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[23] [24] [25] [26] [27] [28] [29] [30]
Overfull \hbox (26.88089pt too wide) in paragraph at lines 1894--1894
 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
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[49] [50] [51] [52] [53] [54] [55] [56]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
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[72] [73] [74]
Underfull \hbox (badness 2521) in paragraph at lines 4782--4784
[]\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
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[90] [91] [92]
Overfull \hbox (7.0809pt too wide) in paragraph at lines 5909--5909
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[93] [94] [95]
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[]\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
[96] [97] [98]
Overfull \hbox (58.35893pt too wide) in paragraph at lines 6293--6295
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : 
[99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 6434--6437
[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
[101] [102]
Underfull \hbox (badness 1442) in paragraph at lines 6599--6605
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move a

Underfull \hbox (badness 1248) in paragraph at lines 6599--6605
\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-

Underfull \hbox (badness 2080) in paragraph at lines 6599--6605
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
[103]
Underfull \hbox (badness 3568) in paragraph at lines 6660--6667
\T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z
i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
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Underfull \hbox (badness 2096) in paragraph at lines 7298--7302
\T1/zi4/m/n/10 status _ codes$[][] \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 .
[114]
Underfull \hbox (badness 4595) in paragraph at lines 7355--7358
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[115]
Underfull \hbox (badness 3000) in paragraph at lines 7391--7393
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 
getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed 
for

Underfull \hbox (badness 2351) in paragraph at lines 7416--7419
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
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Underfull \hbox (badness 10000) in paragraph at lines 7671--7682
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[120] [121]
Underfull \hbox (badness 4479) in paragraph at lines 7743--7752
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),

Underfull \hbox (badness 2469) in paragraph at lines 7743--7752
[][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods,
 [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i
t/10 Group \T1/ptm/m/n/10 meth-ods for
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Underfull \hbox (badness 1394) in paragraph at lines 9355--9360
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[146] [147] [148] [149] [150]
Underfull \hbox (badness 1052) in paragraph at lines 9698--9703
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s
ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b
y \T1/zi4/m/n/10 R CMD check

Underfull \hbox (badness 1231) in paragraph at lines 9698--9703
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z
i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[151] [152]
Underfull \hbox (badness 1735) in paragraph at lines 9836--9840
\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
zi4/m/n/10 https : / / en . wikipedia .
[153] [154] [155] [156] [157] [158]
Underfull \hbox (badness 2150) in paragraph at lines 10240--10243
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
[159]
Underfull \hbox (badness 6396) in paragraph at lines 10254--10262
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 2409) in paragraph at lines 10295--10302
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 11341--11345
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
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[]\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-lowed

Underfull \hbox (badness 4341) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e
r-a-tions are those of
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[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 2253) in paragraph at lines 12939--12941
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[200]
Underfull \hbox (badness 1565) in paragraph at lines 13010--13014
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[201]
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[]\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
[202] [203]
Underfull \hbox (badness 1466) in paragraph at lines 13195--13198
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[204] [205]
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[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 13314--13317
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
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[]\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,
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[]\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
[222]
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[]\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[223]
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[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use

Underfull \hbox (badness 4156) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[224]
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Underfull \hbox (badness 2452) in paragraph at lines 15058--15062
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15058--15062
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
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[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
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\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[240] [241] [242] [243]
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[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
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[249]
Underfull \hbox (badness 3679) in paragraph at lines 16166--16168
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[250] [251] [252] [253] [254] [255] [256] [257]
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[]\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
[258] [259] [260] [261]
Underfull \hbox (badness 10000) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1442) in paragraph at lines 17527--17529
[]\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
[271]
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[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[272] [273] [274] [275] [276] [277] [278]
Underfull \hbox (badness 1248) in paragraph at lines 18033--18036
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[279] [280] [281] [282]
Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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[295] [296] [297] [298]
Underfull \hbox (badness 1360) in paragraph at lines 19249--19254
\T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS
SL used, but not all

Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /

Underfull \hbox (badness 1127) in paragraph at lines 19272--19278
\T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S
SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv
/m/n/10 R
[299]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory

Underfull \hbox (badness 2460) in paragraph at lines 19345--19349
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[300] [301]
Underfull \hbox (badness 1509) in paragraph at lines 19480--19487
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1354) in paragraph at lines 19480--19487
\T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta
in just the names of all avail-able pack-ages, and

Underfull \hbox (badness 1014) in paragraph at lines 19496--19501
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313]
Underfull \hbox (badness 1264) in paragraph at lines 20227--20232
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
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Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\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
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[337] [338] [339] [340]
Underfull \hbox (badness 1077) in paragraph at lines 21979--21985
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[341] [342] [343]
Underfull \hbox (badness 1484) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[344] [345] [346] [347]
Underfull \hbox (badness 2790) in paragraph at lines 22411--22414
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 22411--22414
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[348] [349] [350] [351]
Underfull \hbox (badness 1194) in paragraph at lines 22692--22695
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
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Underfull \hbox (badness 10000) in paragraph at lines 22898--22904
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 5862) in paragraph at lines 22898--22904
\T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE))
 \T1/ptm/m/n/10 which are also given by

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
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[368] [369]
Underfull \hbox (badness 10000) in paragraph at lines 23839--23841
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[370] [371] [372] [373]
Underfull \hbox (badness 1199) in paragraph at lines 24066--24072
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][] \T1/zi4/m/n/10 "numeric"

Underfull \hbox (badness 2027) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \
T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F
ALSE \T1/ptm/m/n/10 oth-er-wise. That is,
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Underfull \hbox (badness 1038) in paragraph at lines 24645--24653
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1881) in paragraph at lines 24654--24657
[]\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 24673--24675
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[382]
Underfull \hbox (badness 10000) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 2142) in paragraph at lines 24756--24762
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 24769--24774
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[383] [384]
Underfull \vbox (badness 10000) has occurred while \output is active [385]
Underfull \hbox (badness 10000) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[386]
Underfull \hbox (badness 10000) in paragraph at lines 25047--25050
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 25071--25073
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 1629) in paragraph at lines 25109--25120
\T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi
4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an
d

Underfull \hbox (badness 7203) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[387]
Underfull \hbox (badness 4084) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN OS X build),

Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
\T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric
ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C
RAN

Underfull \hbox (badness 7397) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m
/n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1082) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[388] [389] [390] [391] [392]
Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n
/10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
\T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[393] [394] [395] [396] [397]
Underfull \hbox (badness 1735) in paragraph at lines 25809--25813
[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\
T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu
e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which
[398] [399] [400] [401] [402] [403] [404] [405] [406]
Underfull \hbox (badness 2726) in paragraph at lines 26369--26372
[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
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[419]
Underfull \hbox (badness 1052) in paragraph at lines 27186--27191
[]\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1
0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide
d
[420] [421] [422] [423] [424]
Underfull \vbox (badness 10000) has occurred while \output is active [425]
[426] [427] [428] [429] [430] [431]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[432] [433] [434]
Underfull \hbox (badness 1163) in paragraph at lines 28157--28168
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446]
[447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 29676--29680
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 1221) in paragraph at lines 29676--29680
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[459] [460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 1655) in paragraph at lines 30246--30248
[]\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
[468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
[479] [480] [481]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 2980) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[482] [483] [484]
Underfull \hbox (badness 2261) in paragraph at lines 31310--31315
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[485]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
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[498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509]
[510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521]
[522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
Underfull \hbox (badness 1072) in paragraph at lines 34333--34337
[]\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 34338--34342
[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 3343) in paragraph at lines 34379--34386
\T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment 
vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 34379--34386
\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 34379--34386
\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
[532] [533] [534] [535] [536]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1152) in paragraph at lines 34670--34676
\T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c
om-po-nent which is
[537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548]
[549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560]
[561] [562] [563] [564] [565]
Underfull \hbox (badness 3333) in paragraph at lines 36500--36505
[]\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
[566] [567] [568] [569] [570] [571] [572] [573] [574] [575]
Underfull \hbox (badness 1472) in paragraph at lines 37120--37123
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586]
Underfull \hbox (badness 2671) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 10000) in paragraph at lines 38200--38203
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[593] [594]
Underfull \hbox (badness 10000) in paragraph at lines 38318--38322
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[595]
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[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
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[608] [609] [610] [611] [612] [613] [614] [615]
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[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 4846) in paragraph at lines 39706--39714
\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
[616] [617] [618] [619]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[620] [621] [622] [623]
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[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
[624] [625] [626] [627] [628] [629] [630] [631] [632] [633]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[634] [635]
Underfull \hbox (badness 2401) in paragraph at lines 40974--40978
[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
[636] [637]
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\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.
[638]
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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[639] [640] [641] [642] [643] [644] [645]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/zi4/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
[646]
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[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[647]
Underfull \hbox (badness 10000) in paragraph at lines 41757--41761
[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[648] [649]) (./compiler-pkg.tex [650]
Chapter 2.
[651] [652] [653] [654]) (./datasets-pkg.tex
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666]
[667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678]
[679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690]
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Underfull \hbox (badness 6658) in paragraph at lines 3940--3942
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h
ttp : / / www . ltrr . arizona . edu / ~hallman /
[722]
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[724] [725] [726]
Underfull \vbox (badness 10000) has occurred while \output is active [727]
Underfull \vbox (badness 10000) has occurred while \output is active [728]
[729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736]
Chapter 4.
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750] [751] [752] [753]
Underfull \hbox (badness 5175) in paragraph at lines 1071--1073
[]\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
[754] [755] [756] [757]
Underfull \hbox (badness 1852) in paragraph at lines 1268--1271
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[758] [759] [760]
Underfull \hbox (badness 1490) in paragraph at lines 1474--1479
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[761]
Underfull \hbox (badness 2698) in paragraph at lines 1528--1531
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[762]
Underfull \hbox (badness 10000) in paragraph at lines 1597--1601
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when
[763] [764] [765] [766]
Underfull \hbox (badness 1325) in paragraph at lines 1880--1890
\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[767] [768]
Underfull \hbox (badness 10000) in paragraph at lines 1985--1987
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[769] [770] [771]
Underfull \hbox (badness 6758) in paragraph at lines 2146--2149
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
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Underfull \hbox (badness 1152) in paragraph at lines 3150--3152
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[788] [789] [790] [791] [792]
Underfull \hbox (badness 2856) in paragraph at lines 3470--3473
[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

Underfull \hbox (badness 2662) in paragraph at lines 3484--3486
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[793] [794]
Underfull \hbox (badness 1173) in paragraph at lines 3600--3610
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\
T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to 
\T1/zi4/m/n/10 width \T1/ptm/m/n/10 by
[795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805]
Underfull \hbox (badness 1067) in paragraph at lines 4307--4314
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[806] [807]
Underfull \hbox (badness 3364) in paragraph at lines 4468--4470
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
[808]
Underfull \hbox (badness 1789) in paragraph at lines 4545--4547
[]\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[809]
Underfull \hbox (badness 1377) in paragraph at lines 4595--4600
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[810]
Underfull \hbox (badness 2671) in paragraph at lines 4622--4630
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as

Underfull \hbox (badness 1418) in paragraph at lines 4671--4678
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 2443) in paragraph at lines 4679--4688
\T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess
 to more char-ac-ters and

Underfull \hbox (badness 2653) in paragraph at lines 4679--4688
\T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes
e eas-ier to re-mem-ber,

Underfull \hbox (badness 1755) in paragraph at lines 4689--4691
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[811] [812]
Underfull \hbox (badness 1057) in paragraph at lines 4800--4805
[]\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
[813]
Underfull \hbox (badness 7344) in paragraph at lines 4860--4862
[]\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
[814] [815]
Underfull \hbox (badness 2035) in paragraph at lines 4984--4993
[]\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 4984--4993
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 4984--4993
\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[816]
Underfull \hbox (badness 10000) in paragraph at lines 5053--5060
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5053--5060
\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
[817] [818] [819]
Underfull \hbox (badness 1546) in paragraph at lines 5195--5203
[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
[820]
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[821] [822] [823] [824] [825] [826] [827]
Underfull \hbox (badness 10000) in paragraph at lines 5724--5727
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[828] [829] [830] [831] [832] [833]
Underfull \hbox (badness 1189) in paragraph at lines 6121--6123
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[834] [835]
Underfull \hbox (badness 10000) in paragraph at lines 6219--6221
[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[836] [837] [838] [839]
Underfull \hbox (badness 3780) in paragraph at lines 6510--6516
[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
[840] [841] [842]
Underfull \hbox (badness 2680) in paragraph at lines 6706--6708
[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[843] [844] [845]) (./graphics-pkg.tex [846]
Chapter 5.
[847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857]
Underfull \hbox (badness 10000) in paragraph at lines 683--690
[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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\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
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[911] [912] [913] [914] [915] [916] [917]
Underfull \hbox (badness 1924) in paragraph at lines 4359--4364
[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[918]
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[]\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
[919] [920] [921] [922] [923]
Underfull \hbox (badness 10000) in paragraph at lines 4740--4746
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

Underfull \hbox (badness 5908) in paragraph at lines 4740--4746
\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
[924]
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[925]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
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\T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i
s ex-ited by the com-mand
[965]
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po
int
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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l.8735 \HeaderA{units}{Graphical Units}{units}
                                               [989] [990] [991] [992])
(./grid-pkg.tex
Chapter 6.

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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[]\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
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104]
Chapter 7.
[1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115]
[1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124]
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

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\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in
[1144]
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\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
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[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1152] [1153] [1154] [1155] [1156]
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

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[]\T1/ptm/m/n/10 The
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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[]\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

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\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
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\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

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\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and

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[]\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
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[]\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
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[]\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z
i4/m/n/10 initialize \T1/ptm/m/n/10 and
[1190] [1191] [1192] [1193] [1194]
Underfull \hbox (badness 1675) in paragraph at lines 6345--6351
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1195] [1196] [1197] [1198]
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l.6828 \aliasA{S4}{S3Part}{S4}
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l.7102 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1205]
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[]\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
[1206] [1207] [1208]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219]
[1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230]
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[1242]
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[]\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.,
[1243] [1244] [1245] [1246]) (./parallel-pkg.tex
Chapter 8.

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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
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[1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1267] [1268]) (./splines-pkg.tex
Chapter 9.

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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279]
[1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284]
Chapter 10.
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[1296] [1297]
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305]
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[]\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 ,
[1306] [1307] [1308]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
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[1336] [1337]
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[]\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 ,
[1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348]
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[]\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 =
[1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367]
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[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

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[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1368] [1369] [1370] [1371]
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\T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is
 un-usual but avail-able for the sake of com-plete-ness.
[1372] [1373]
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[]\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 ,
[1374]
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[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1375] [1376] [1377] [1378] [1379] [1380] [1381]
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\T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa
me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node,
[1382] [1383] [1384] [1385] [1386]
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[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 10000) in paragraph at lines 6346--6348
[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1400] [1401]
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[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht
tps : / / cran . r-[]project . org / web / views /
[1402] [1403] [1404] [1405]
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[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
[1427]
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[]\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 ,
[1428] [1429] [1430] [1431] [1432]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443]
[1444] [1445] [1446] [1447]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1448] [1449] [1450] [1451]
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[]\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 ^^@
[1452]
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[]\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,
[1453]
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[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1454] [1455] [1456] [1457] [1458] [1459]
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to

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\T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th
e or-der-ing of the cor-re-
[1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 11300--11303
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
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                   \relax 
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[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
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Underfull \hbox (badness 4441) in paragraph at lines 12135--12137
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

Underfull \hbox (badness 10000) in paragraph at lines 12142--12144
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
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Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
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[1496]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface =

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[]\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
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[]\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 ,
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[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1
/ptm/m/n/10 and
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[1557] [1558] [1559]
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[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1560] [1561]
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[1575]
Underfull \hbox (badness 1377) in paragraph at lines 18069--18074
[]\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

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[]\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 1184) in paragraph at lines 18087--18091
\T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18095--18099
[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
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[]\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
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[1597] [1598]
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[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

Underfull \hbox (badness 1194) in paragraph at lines 19444--19447
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1599] [1600] [1601] [1602] [1603] [1604]
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[]\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 ,
[1605]
Underfull \hbox (badness 10000) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
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[1617] [1618] [1619] [1620] [1621]
Underfull \hbox (badness 10000) in paragraph at lines 20863--20869
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632]
[1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643]
[1644]
Underfull \hbox (badness 1337) in paragraph at lines 22198--22204
[]\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
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[1656] [1657]
Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666]
Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1667]
Underfull \hbox (badness 3690) in paragraph at lines 23619--23623
[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
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Underfull \hbox (badness 3439) in paragraph at lines 24089--24095
[][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO
rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1
0 ,
[1676] [1677] [1678]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1679]
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\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
[1680] [1681] [1682] [1683] [1684] [1685] [1686]
Underfull \hbox (badness 10000) in paragraph at lines 24757--24762
[]\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
[1687] [1688] [1689]
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Underfull \hbox (badness 3514) in paragraph at lines 25775--25780
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1703]
Underfull \hbox (badness 3514) in paragraph at lines 25837--25842
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
Underfull \hbox (badness 3514) in paragraph at lines 25894--25899
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1705]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1706] [1707] [1708] [1709]
Underfull \hbox (badness 3514) in paragraph at lines 26168--26173
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
Underfull \hbox (badness 3514) in paragraph at lines 26224--26229
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1711]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1712]
Underfull \hbox (badness 3514) in paragraph at lines 26336--26341
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1713]
Underfull \hbox (badness 6691) in paragraph at lines 26405--26410
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722]
Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732]
Underfull \hbox (badness 5431) in paragraph at lines 27535--27537
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1733] [1734] [1735]
Underfull \hbox (badness 5431) in paragraph at lines 27745--27748
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1736] [1737] [1738] [1739] [1740] [1741]
Underfull \hbox (badness 1337) in paragraph at lines 28057--28061
[]\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
[1742] [1743]
Underfull \hbox (badness 10000) in paragraph at lines 28174--28177
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1744] [1745]
Underfull \hbox (badness 1616) in paragraph at lines 28357--28360
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
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[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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[]\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
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[]\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]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
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[]\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or
[1786] [1787] [1788]) (./stats4-pkg.tex
Chapter 11.
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h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
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<to be read again> 
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l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1795] [1796] [1797]
[1798]) (./tcltk-pkg.tex
Chapter 12.
[1799] [1800] [1801] [1802] [1803] [1804] [1805]
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[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818]
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[][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1819]) (./tools-pkg.tex [1820]
Chapter 13.
[1821]

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[1822]
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[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1823] [1824]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

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\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

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\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

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\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1838]
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1839]
Underfull \hbox (badness 1014) in paragraph at lines 1148--1150
[]\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

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


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\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
[1840] [1841] [1842]
Underfull \hbox (badness 10000) in paragraph at lines 1348--1350
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1843] [1844] [1845]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

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[]\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
[1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1850]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from

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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
(Font)              using `T1/zi4/m/n' instead on input line 2660.

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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1881] [1882]
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR
UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10
 DependsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and
[1891] [1892] [1893] [1894]) (./utils-pkg.tex
Chapter 14.
[1895]
Underfull \hbox (badness 2556) in paragraph at lines 47--52
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1896] [1897]
Underfull \hbox (badness 1454) in paragraph at lines 197--200
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de-

Underfull \hbox (badness 1540) in paragraph at lines 213--216
[]\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the
 same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault
[1898] [1899] [1900] [1901] [1902] [1903]
Underfull \hbox (badness 10000) in paragraph at lines 543--549
[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1904]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

Underfull \hbox (badness 4229) in paragraph at lines 657--663
\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1905]
Underfull \hbox (badness 3861) in paragraph at lines 725--730
[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
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[1912] [1913] [1914] [1915]
Underfull \hbox (badness 1371) in paragraph at lines 1321--1323
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1916] [1917] [1918] [1919] [1920] [1921] [1922]
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[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1923] [1924]
Underfull \hbox (badness 10000) in paragraph at lines 1901--1903
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1925]
Underfull \hbox (badness 5189) in paragraph at lines 1991--1993
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1926] [1927] [1928] [1929]
Underfull \hbox (badness 1661) in paragraph at lines 2209--2216
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

Underfull \hbox (badness 1990) in paragraph at lines 2226--2229
[]\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1930] [1931] [1932] [1933] [1934] [1935]
Underfull \hbox (badness 10000) in paragraph at lines 2635--2639
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing
[1936]
Overfull \hbox (64.10922pt too wide) in paragraph at lines 2640--2643
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944]
Underfull \hbox (badness 1412) in paragraph at lines 3220--3225
[]\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/
10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1
0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the
[1945]
Underfull \hbox (badness 1430) in paragraph at lines 3246--3254
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the

Underfull \hbox (badness 1231) in paragraph at lines 3289--3295
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
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[1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.format}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4109 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.4109 ...mat Unordered and Ordered Lists}{format}
                                                   [1960] [1961] [1962]
[1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973]
[1974]
Underfull \hbox (badness 1371) in paragraph at lines 5062--5064
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1975]
Underfull \hbox (badness 1502) in paragraph at lines 5151--5156
[]\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 5151--5156
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1976] [1977] [1978]
Underfull \hbox (badness 10000) in paragraph at lines 5324--5333
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[1979]
Underfull \hbox (badness 2150) in paragraph at lines 5387--5390
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[1980] [1981]
Underfull \hbox (badness 3118) in paragraph at lines 5524--5526
[]\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
[1982]
Underfull \hbox (badness 2409) in paragraph at lines 5557--5561
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1983]
Underfull \hbox (badness 1325) in paragraph at lines 5665--5669
[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able
[1984]
Underfull \hbox (badness 10000) in paragraph at lines 5748--5751
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed

Underfull \hbox (badness 10000) in paragraph at lines 5748--5751
\T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac
k-age in-stall. E.g.,
[1985]
Underfull \hbox (badness 3219) in paragraph at lines 5821--5828
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/
10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-

Underfull \hbox (badness 5175) in paragraph at lines 5821--5828
\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 5821--5828
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1986]
Underfull \hbox (badness 10000) in paragraph at lines 5901--5906
[][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/
10 ,
[1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997]
[1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007]
Underfull \hbox (badness 10000) in paragraph at lines 7203--7205
[]\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
 al-low-ing things like

Underfull \hbox (badness 2310) in paragraph at lines 7208--7213
[]\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
 given pack-age is found and can suc-cess-fully be read,
[2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]
Underfull \hbox (badness 1789) in paragraph at lines 7758--7760
[]\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
[2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027]
[2028] [2029]
Underfull \hbox (badness 1097) in paragraph at lines 8583--8586
[]\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b
e used on Win-dows, in which case
[2030]
Underfull \hbox (badness 3000) in paragraph at lines 8719--8724
[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t
able[][][]\T1/ptm/m/n/10 ;
[2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039]
Underfull \hbox (badness 2134) in paragraph at lines 9302--9307
[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
table[][][]\T1/ptm/m/n/10 ;
[2040] [2041] [2042] [2043] [2044] [2045] [2046]
Underfull \hbox (badness 5077) in paragraph at lines 9727--9731
[]\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/
sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-

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\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see

Underfull \hbox (badness 2469) in paragraph at lines 9739--9743
[]\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 9739--9743
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2047] [2048] [2049] [2050] [2051] [2052]
Underfull \hbox (badness 10000) in paragraph at lines 10093--10095
[]\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][]
[]\T1/ptm/m/n/10 s are nicely viewed via
[2053] [2054] [2055]
Underfull \hbox (badness 2150) in paragraph at lines 10269--10271
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2056] [2057] [2058]
Underfull \hbox (badness 10000) in paragraph at lines 10447--10451
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n
ow taken from the en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 10478--10484
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2059] [2060]
Underfull \hbox (badness 2096) in paragraph at lines 10596--10599
[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether PNG fig-ures should be gen-er-ated. Ig-nored if

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[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether JPEG fig-ures should be gen-er-ated. Ig-nored if
[2061]
Underfull \hbox (badness 1009) in paragraph at lines 10666--10677
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[2062] [2063] [2064] [2065] [2066]
Underfull \hbox (badness 3780) in paragraph at lines 10965--10969
[]\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1
/zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via

Underfull \hbox (badness 2635) in paragraph at lines 10981--10984
[]\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp
e-cially: the value is taken from the cur-rent set-ting of
[2067] [2068] [2069] [2070] [2071] [2072]
Underfull \hbox (badness 5970) in paragraph at lines 11350--11353
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2073] [2074] [2075]
Underfull \hbox (badness 10000) in paragraph at lines 11529--11531
[]\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n
/10 ap-ply only to files pro-duced by
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Underfull \hbox (badness 10000) in paragraph at lines 11930--11933
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

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\T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9
2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX
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[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

Underfull \hbox (badness 1052) in paragraph at lines 12463--12465
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
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\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
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[][]\T1/ptm/m/n/10 .
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Underfull \hbox (badness 4595) in paragraph at lines 7355--7358
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[115]
Underfull \hbox (badness 3000) in paragraph at lines 7391--7393
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 
getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed 
for

Underfull \hbox (badness 2351) in paragraph at lines 7416--7419
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[116] [117] [118] [119]
Underfull \hbox (badness 10000) in paragraph at lines 7671--7682
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[120] [121]
Underfull \hbox (badness 4479) in paragraph at lines 7743--7752
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),

Underfull \hbox (badness 2469) in paragraph at lines 7743--7752
[][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods,
 [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i
t/10 Group \T1/ptm/m/n/10 meth-ods for
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[134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145]
Underfull \hbox (badness 1394) in paragraph at lines 9355--9360
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[146] [147] [148] [149] [150]
Underfull \hbox (badness 1052) in paragraph at lines 9698--9703
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s
ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b
y \T1/zi4/m/n/10 R CMD check

Underfull \hbox (badness 1231) in paragraph at lines 9698--9703
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z
i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[151] [152]
Underfull \hbox (badness 1735) in paragraph at lines 9836--9840
\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
zi4/m/n/10 https : / / en . wikipedia .
[153] [154] [155] [156] [157] [158]
Underfull \hbox (badness 2150) in paragraph at lines 10240--10243
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
[159]
Underfull \hbox (badness 6396) in paragraph at lines 10254--10262
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 2409) in paragraph at lines 10295--10302
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171]
[172] [173] [174] [175]
Underfull \hbox (badness 4569) in paragraph at lines 11341--11345
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 11341--11345
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[176] [177] [178] [179] [180] [181] [182] [183]
Underfull \hbox (badness 2698) in paragraph at lines 11917--11926
[]\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-lowed

Underfull \hbox (badness 4341) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e
r-a-tions are those of
[184] [185] [186] [187] [188] [189] [190] [191] [192] [193]
Underfull \hbox (badness 6236) in paragraph at lines 12561--12564
[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 2253) in paragraph at lines 12939--12941
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[200]
Underfull \hbox (badness 1565) in paragraph at lines 13010--13014
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[201]
Underfull \hbox (badness 10000) in paragraph at lines 13054--13056
[]\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
[202] [203]
Underfull \hbox (badness 1466) in paragraph at lines 13195--13198
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[204] [205]
Underfull \hbox (badness 10000) in paragraph at lines 13303--13307
[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 13314--13317
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[206] [207] [208] [209]
Underfull \hbox (badness 3965) in paragraph at lines 13577--13581
[]\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,
[210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221]
Underfull \hbox (badness 4429) in paragraph at lines 14338--14341
[]\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
[222]
Underfull \hbox (badness 10000) in paragraph at lines 14430--14432
[]\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[223]
Underfull \hbox (badness 10000) in paragraph at lines 14478--14482
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use

Underfull \hbox (badness 4156) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[224]
Underfull \vbox (badness 3803) has occurred while \output is active [225]
[226] [227] [228] [229] [230] [231] [232]
Underfull \hbox (badness 2452) in paragraph at lines 15058--15062
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15058--15062
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[233] [234] [235]
Underfull \hbox (badness 1092) in paragraph at lines 15231--15236
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[236] [237] [238] [239]
Underfull \hbox (badness 6741) in paragraph at lines 15479--15483
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[240] [241] [242] [243]
Underfull \hbox (badness 1867) in paragraph at lines 15785--15792
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[244] [245] [246] [247]
Underfull \vbox (badness 10000) has occurred while \output is active [248]
[249]
Underfull \hbox (badness 3679) in paragraph at lines 16166--16168
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[250] [251] [252] [253] [254] [255] [256] [257]
Underfull \hbox (badness 1478) in paragraph at lines 16711--16714
[]\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
[258] [259] [260] [261]
Underfull \hbox (badness 10000) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1442) in paragraph at lines 17527--17529
[]\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
[271]
Underfull \hbox (badness 2452) in paragraph at lines 17619--17635
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[272] [273] [274] [275] [276] [277] [278]
Underfull \hbox (badness 1248) in paragraph at lines 18033--18036
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[279] [280] [281] [282]
Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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[295] [296] [297] [298]
Underfull \hbox (badness 1360) in paragraph at lines 19249--19254
\T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS
SL used, but not all

Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /

Underfull \hbox (badness 1127) in paragraph at lines 19272--19278
\T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S
SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv
/m/n/10 R
[299]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory

Underfull \hbox (badness 2460) in paragraph at lines 19345--19349
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[300] [301]
Underfull \hbox (badness 1509) in paragraph at lines 19480--19487
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1354) in paragraph at lines 19480--19487
\T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta
in just the names of all avail-able pack-ages, and

Underfull \hbox (badness 1014) in paragraph at lines 19496--19501
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313]
Underfull \hbox (badness 1264) in paragraph at lines 20227--20232
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
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Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\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
[325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336]
[337] [338] [339] [340]
Underfull \hbox (badness 1077) in paragraph at lines 21979--21985
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[341] [342] [343]
Underfull \hbox (badness 1484) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[344] [345] [346] [347]
Underfull \hbox (badness 2790) in paragraph at lines 22411--22414
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 22411--22414
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[348] [349] [350] [351]
Underfull \hbox (badness 1194) in paragraph at lines 22692--22695
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
[352] [353] [354] [355]
Underfull \hbox (badness 10000) in paragraph at lines 22898--22904
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 5862) in paragraph at lines 22898--22904
\T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE))
 \T1/ptm/m/n/10 which are also given by

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
[356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367]
[368] [369]
Underfull \hbox (badness 10000) in paragraph at lines 23839--23841
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[370] [371] [372] [373]
Underfull \hbox (badness 1199) in paragraph at lines 24066--24072
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][] \T1/zi4/m/n/10 "numeric"

Underfull \hbox (badness 2027) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \
T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F
ALSE \T1/ptm/m/n/10 oth-er-wise. That is,
[374] [375] [376] [377] [378] [379] [380] [381]
Underfull \hbox (badness 1038) in paragraph at lines 24645--24653
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1881) in paragraph at lines 24654--24657
[]\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 24673--24675
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[382]
Underfull \hbox (badness 10000) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 2142) in paragraph at lines 24756--24762
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 24769--24774
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[383] [384]
Underfull \vbox (badness 10000) has occurred while \output is active [385]
Underfull \hbox (badness 10000) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[386]
Underfull \hbox (badness 10000) in paragraph at lines 25047--25050
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 25071--25073
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 1629) in paragraph at lines 25109--25120
\T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi
4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an
d

Underfull \hbox (badness 7203) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[387]
Underfull \hbox (badness 4084) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN OS X build),

Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
\T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric
ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C
RAN

Underfull \hbox (badness 7397) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m
/n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1082) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[388] [389] [390] [391] [392]
Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n
/10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
\T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[393] [394] [395] [396] [397]
Underfull \hbox (badness 1735) in paragraph at lines 25809--25813
[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\
T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu
e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which
[398] [399] [400] [401] [402] [403] [404] [405] [406]
Underfull \hbox (badness 2726) in paragraph at lines 26369--26372
[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418]
[419]
Underfull \hbox (badness 1052) in paragraph at lines 27186--27191
[]\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1
0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide
d
[420] [421] [422] [423] [424]
Underfull \vbox (badness 10000) has occurred while \output is active [425]
[426] [427] [428] [429] [430] [431]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[432] [433] [434]
Underfull \hbox (badness 1163) in paragraph at lines 28157--28168
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446]
[447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 29676--29680
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 1221) in paragraph at lines 29676--29680
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[459] [460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 1655) in paragraph at lines 30246--30248
[]\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
[468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
[479] [480] [481]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 2980) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[482] [483] [484]
Underfull \hbox (badness 2261) in paragraph at lines 31310--31315
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[485]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
[486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497]
[498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509]
[510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521]
[522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
Underfull \hbox (badness 1072) in paragraph at lines 34333--34337
[]\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 34338--34342
[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 3343) in paragraph at lines 34379--34386
\T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment 
vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 34379--34386
\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 34379--34386
\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
[532] [533] [534] [535] [536]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1152) in paragraph at lines 34670--34676
\T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c
om-po-nent which is
[537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548]
[549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560]
[561] [562] [563] [564] [565]
Underfull \hbox (badness 3333) in paragraph at lines 36500--36505
[]\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
[566] [567] [568] [569] [570] [571] [572] [573] [574] [575]
Underfull \hbox (badness 1472) in paragraph at lines 37120--37123
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586]
Underfull \hbox (badness 2671) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 10000) in paragraph at lines 38200--38203
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[593] [594]
Underfull \hbox (badness 10000) in paragraph at lines 38318--38322
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[595]
Underfull \hbox (badness 10000) in paragraph at lines 38380--38384
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607]
[608] [609] [610] [611] [612] [613] [614] [615]
Underfull \hbox (badness 1990) in paragraph at lines 39706--39714
[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 4846) in paragraph at lines 39706--39714
\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
[616] [617] [618] [619]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[620] [621] [622] [623]
Underfull \hbox (badness 1917) in paragraph at lines 40208--40215
[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
[624] [625] [626] [627] [628] [629] [630] [631] [632] [633]
Underfull \hbox (badness 3668) in paragraph at lines 40869--40871
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[634] [635]
Underfull \hbox (badness 2401) in paragraph at lines 40974--40978
[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
[636] [637]
Underfull \hbox (badness 2111) in paragraph at lines 41143--41148
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.
[638]
Underfull \hbox (badness 6542) in paragraph at lines 41159--41164
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[639] [640] [641] [642] [643] [644] [645]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/zi4/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
[646]
Underfull \hbox (badness 5417) in paragraph at lines 41696--41700
[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[647]
Underfull \hbox (badness 10000) in paragraph at lines 41757--41761
[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[648] [649]) (./compiler-pkg.tex [650]
Chapter 2.
[651] [652] [653] [654]) (./datasets-pkg.tex
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666]
[667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678]
[679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690]
[691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701]
Underfull \vbox (badness 1515) has occurred while \output is active [702]
[703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714]
[715] [716] [717] [718] [719] [720] [721]
Underfull \hbox (badness 6658) in paragraph at lines 3940--3942
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h
ttp : / / www . ltrr . arizona . edu / ~hallman /
[722]
Underfull \vbox (badness 10000) has occurred while \output is active [723]
[724] [725] [726]
Underfull \vbox (badness 10000) has occurred while \output is active [727]
Underfull \vbox (badness 10000) has occurred while \output is active [728]
[729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736]
Chapter 4.
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750] [751] [752] [753]
Underfull \hbox (badness 5175) in paragraph at lines 1071--1073
[]\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
[754] [755] [756] [757]
Underfull \hbox (badness 1852) in paragraph at lines 1268--1271
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[758] [759] [760]
Underfull \hbox (badness 1490) in paragraph at lines 1474--1479
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[761]
Underfull \hbox (badness 2698) in paragraph at lines 1528--1531
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[762]
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[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when
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\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
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[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\
T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to 
\T1/zi4/m/n/10 width \T1/ptm/m/n/10 by
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\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
[808]
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[809]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[810]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as

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\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

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\T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess
 to more char-ac-ters and

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\T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes
e eas-ier to re-mem-ber,

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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
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[]\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
[813]
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[]\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
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[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

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\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

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\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[816]
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[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

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\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
[817] [818] [819]
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[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[821] [822] [823] [824] [825] [826] [827]
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[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[828] [829] [830] [831] [832] [833]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
[840] [841] [842]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[843] [844] [845]) (./graphics-pkg.tex [846]
Chapter 5.
[847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857]
Underfull \hbox (badness 10000) in paragraph at lines 683--690
[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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\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
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[911] [912] [913] [914] [915] [916] [917]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
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[]\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
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
[924]
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[925]
</«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf, id=22
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
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[][] 
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\T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i
s ex-ited by the com-mand
[965]
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po
int
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
[988]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8735 \HeaderA{units}{Graphical Units}{units}
                                               [989] [990] [991] [992])
(./grid-pkg.tex
Chapter 6.

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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[]\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
[1066] [1067] [1068] [1069]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104]
Chapter 7.
[1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115]
[1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124]
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

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\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in
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\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
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[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1152] [1153] [1154] [1155] [1156]
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

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[]\T1/ptm/m/n/10 The
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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[]\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

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\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1171] [1172] [1173] [1174] [1175] [1176]
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\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

Underfull \hbox (badness 1117) in paragraph at lines 5281--5288
\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and

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[]\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
[1181] [1182] [1183] [1184] [1185]
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[]\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
[1186] [1187] [1188] [1189]
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[]\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z
i4/m/n/10 initialize \T1/ptm/m/n/10 and
[1190] [1191] [1192] [1193] [1194]
Underfull \hbox (badness 1675) in paragraph at lines 6345--6351
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
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                                                 [1205]
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[]\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
[1206] [1207] [1208]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219]
[1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230]
[1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241]
[1242]
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[]\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.,
[1243] [1244] [1245] [1246]) (./parallel-pkg.tex
Chapter 8.

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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]
[1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1267] [1268]) (./splines-pkg.tex
Chapter 9.

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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279]
[1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284]
Chapter 10.
[1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295]
[1296] [1297]
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305]
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[]\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 ,
[1306] [1307] [1308]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1320] [1321] [1322] [1323] [1324]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335]
[1336] [1337]
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[]\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 ,
[1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348]
[1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
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[]\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 =
[1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367]
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[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

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[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1368] [1369] [1370] [1371]
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\T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is
 un-usual but avail-able for the sake of com-plete-ness.
[1372] [1373]
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[]\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 ,
[1374]
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[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1375] [1376] [1377] [1378] [1379] [1380] [1381]
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\T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa
me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node,
[1382] [1383] [1384] [1385] [1386]
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[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

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[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1400] [1401]
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[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht
tps : / / cran . r-[]project . org / web / views /
[1402] [1403] [1404] [1405]
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[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
[1427]
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[]\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 ,
[1428] [1429] [1430] [1431] [1432]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443]
[1444] [1445] [1446] [1447]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1448] [1449] [1450] [1451]
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[]\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 ^^@
[1452]
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[]\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,
[1453]
Underfull \hbox (badness 1708) in paragraph at lines 10578--10582
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1454] [1455] [1456] [1457] [1458] [1459]
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to

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\T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th
e or-der-ing of the cor-re-
[1460] [1461] [1462] [1463] [1464]
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[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
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                                              [1468] [1469]
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[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478]
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[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

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[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1479] [1480] [1481] [1482] [1483] [1484]
Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495]
[1496]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505]
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1506] [1507] [1508]
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[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface =

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[]\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
[1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519]
[1520] [1521] [1522] [1523] [1524] [1525]
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[]\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 ,
[1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534]
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[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1
/ptm/m/n/10 and
[1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
[1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556]
[1557] [1558] [1559]
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[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1560] [1561]
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[1575]
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[]\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

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[]\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

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\T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

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[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
[1576] [1577] [1578]
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[1580] [1581] [1582] [1583] [1584] [1585]
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[]\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
[1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596]
[1597] [1598]
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[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

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[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1599] [1600] [1601] [1602] [1603] [1604]
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[]\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 ,
[1605]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616]
[1617] [1618] [1619] [1620] [1621]
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[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632]
[1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643]
[1644]
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[]\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
[1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655]
[1656] [1657]
Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666]
Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1667]
Underfull \hbox (badness 3690) in paragraph at lines 23619--23623
[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
[1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675]
Underfull \hbox (badness 3439) in paragraph at lines 24089--24095
[][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO
rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1
0 ,
[1676] [1677] [1678]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1679]
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\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
[1680] [1681] [1682] [1683] [1684] [1685] [1686]
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[]\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
[1687] [1688] [1689]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1703]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
Underfull \hbox (badness 3514) in paragraph at lines 25894--25899
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1705]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1706] [1707] [1708] [1709]
Underfull \hbox (badness 3514) in paragraph at lines 26168--26173
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1711]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1712]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1713]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722]
Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732]
Underfull \hbox (badness 5431) in paragraph at lines 27535--27537
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1733] [1734] [1735]
Underfull \hbox (badness 5431) in paragraph at lines 27745--27748
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1736] [1737] [1738] [1739] [1740] [1741]
Underfull \hbox (badness 1337) in paragraph at lines 28057--28061
[]\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
[1742] [1743]
Underfull \hbox (badness 10000) in paragraph at lines 28174--28177
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1744] [1745]
Underfull \hbox (badness 1616) in paragraph at lines 28357--28360
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756]
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Underfull \hbox (badness 10000) in paragraph at lines 29483--29487
[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
[1765] [1766] [1767]
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[1769] [1770]
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[]\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
[1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778]
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[]\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]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1780] [1781] [1782] [1783] [1784] [1785]
Underfull \hbox (badness 10000) in paragraph at lines 30788--30793
[]\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or
[1786] [1787] [1788]) (./stats4-pkg.tex
Chapter 11.
[1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
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<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1795] [1796] [1797]
[1798]) (./tcltk-pkg.tex
Chapter 12.
[1799] [1800] [1801] [1802] [1803] [1804] [1805]
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Underfull \vbox (badness 10000) has occurred while \output is active [1807]
Underfull \hbox (badness 1546) in paragraph at lines 664--671
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818]
Underfull \hbox (badness 3375) in paragraph at lines 1407--1410
[][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1819]) (./tools-pkg.tex [1820]
Chapter 13.
[1821]

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[1822]
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[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1823] [1824]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

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\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

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\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

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\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1825] [1826]
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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Underfull \hbox (badness 1635) in paragraph at lines 1050--1052
[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1838]
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1839]
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[]\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

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


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\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
[1840] [1841] [1842]
Underfull \hbox (badness 10000) in paragraph at lines 1348--1350
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1843] [1844] [1845]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

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[]\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
[1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1850]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from

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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1857] [1858] [1859] [1860]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1861] [1862] [1863] [1864]

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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
[1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879]
[1880]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1881] [1882]
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1883] [1884] [1885] [1886]
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
[1887] [1888]
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR
UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10
 DependsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
[1889] [1890]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and
[1891] [1892] [1893] [1894]) (./utils-pkg.tex
Chapter 14.
[1895]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1896] [1897]
Underfull \hbox (badness 1454) in paragraph at lines 197--200
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de-

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[]\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the
 same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault
[1898] [1899] [1900] [1901] [1902] [1903]
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[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1904]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

Underfull \hbox (badness 4229) in paragraph at lines 657--663
\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1905]
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[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1916] [1917] [1918] [1919] [1920] [1921] [1922]
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[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
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[]\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
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m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
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10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1
0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the
[1945]
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[1975]
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x,
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
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[]\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
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
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[1983]
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[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
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[1985]
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[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/
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 are source pack-ages

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[][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/
10 ,
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[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
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[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t
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rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
table[][][]\T1/ptm/m/n/10 ;
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[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia
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[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
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/sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][]
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s / manual /
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
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[]\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1
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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
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(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] [3]
[4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]
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Chapter 1.

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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[1] [2]
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[]\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 .

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\T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if

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\T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is

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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
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[]\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]
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[]\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[7] [8]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ',
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[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
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[]\T1/zi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/zi4/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/zi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
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 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
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[49] [50] [51] [52] [53] [54] [55] [56]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
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[72] [73] [74]
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[]\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
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[90] [91] [92]
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 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
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[]\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
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[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : 
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[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move a

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\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-

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\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
[103]
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\T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z
i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
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\T1/zi4/m/n/10 status _ codes$[][] \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 .
[114]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[115]
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 
getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed 
for

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[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
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[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
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[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),

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[][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods,
 [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i
t/10 Group \T1/ptm/m/n/10 meth-ods for
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[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s
ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b
y \T1/zi4/m/n/10 R CMD check

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\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z
i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
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\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
zi4/m/n/10 https : / / en . wikipedia .
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
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[159]
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[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

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[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
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\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
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[]\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-lowed

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\T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e
r-a-tions are those of
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[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
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[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[201]
Underfull \hbox (badness 10000) in paragraph at lines 13054--13056
[]\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
[202] [203]
Underfull \hbox (badness 1466) in paragraph at lines 13195--13198
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[204] [205]
Underfull \hbox (badness 10000) in paragraph at lines 13303--13307
[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 13314--13317
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[206] [207] [208] [209]
Underfull \hbox (badness 3965) in paragraph at lines 13577--13581
[]\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,
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Underfull \hbox (badness 4429) in paragraph at lines 14338--14341
[]\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
[222]
Underfull \hbox (badness 10000) in paragraph at lines 14430--14432
[]\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[223]
Underfull \hbox (badness 10000) in paragraph at lines 14478--14482
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use

Underfull \hbox (badness 4156) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[224]
Underfull \vbox (badness 3803) has occurred while \output is active [225]
[226] [227] [228] [229] [230] [231] [232]
Underfull \hbox (badness 2452) in paragraph at lines 15058--15062
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15058--15062
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[233] [234] [235]
Underfull \hbox (badness 1092) in paragraph at lines 15231--15236
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[236] [237] [238] [239]
Underfull \hbox (badness 6741) in paragraph at lines 15479--15483
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[240] [241] [242] [243]
Underfull \hbox (badness 1867) in paragraph at lines 15785--15792
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[244] [245] [246] [247]
Underfull \vbox (badness 10000) has occurred while \output is active [248]
[249]
Underfull \hbox (badness 3679) in paragraph at lines 16166--16168
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[250] [251] [252] [253] [254] [255] [256] [257]
Underfull \hbox (badness 1478) in paragraph at lines 16711--16714
[]\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
[258] [259] [260] [261]
Underfull \hbox (badness 10000) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1442) in paragraph at lines 17527--17529
[]\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
[271]
Underfull \hbox (badness 2452) in paragraph at lines 17619--17635
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[272] [273] [274] [275] [276] [277] [278]
Underfull \hbox (badness 1248) in paragraph at lines 18033--18036
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[279] [280] [281] [282]
Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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[295] [296] [297] [298]
Underfull \hbox (badness 1360) in paragraph at lines 19249--19254
\T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS
SL used, but not all

Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /

Underfull \hbox (badness 1127) in paragraph at lines 19272--19278
\T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S
SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv
/m/n/10 R
[299]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory

Underfull \hbox (badness 2460) in paragraph at lines 19345--19349
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[300] [301]
Underfull \hbox (badness 1509) in paragraph at lines 19480--19487
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1354) in paragraph at lines 19480--19487
\T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta
in just the names of all avail-able pack-ages, and

Underfull \hbox (badness 1014) in paragraph at lines 19496--19501
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313]
Underfull \hbox (badness 1264) in paragraph at lines 20227--20232
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324]
Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\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
[325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336]
[337] [338] [339] [340]
Underfull \hbox (badness 1077) in paragraph at lines 21979--21985
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[341] [342] [343]
Underfull \hbox (badness 1484) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[344] [345] [346] [347]
Underfull \hbox (badness 2790) in paragraph at lines 22411--22414
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 22411--22414
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[348] [349] [350] [351]
Underfull \hbox (badness 1194) in paragraph at lines 22692--22695
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
[352] [353] [354] [355]
Underfull \hbox (badness 10000) in paragraph at lines 22898--22904
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 5862) in paragraph at lines 22898--22904
\T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE))
 \T1/ptm/m/n/10 which are also given by

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
[356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367]
[368] [369]
Underfull \hbox (badness 10000) in paragraph at lines 23839--23841
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[370] [371] [372] [373]
Underfull \hbox (badness 1199) in paragraph at lines 24066--24072
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][] \T1/zi4/m/n/10 "numeric"

Underfull \hbox (badness 2027) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \
T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F
ALSE \T1/ptm/m/n/10 oth-er-wise. That is,
[374] [375] [376] [377] [378] [379] [380] [381]
Underfull \hbox (badness 1038) in paragraph at lines 24645--24653
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1881) in paragraph at lines 24654--24657
[]\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 24673--24675
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[382]
Underfull \hbox (badness 10000) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 2142) in paragraph at lines 24756--24762
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 24769--24774
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[383] [384]
Underfull \vbox (badness 10000) has occurred while \output is active [385]
Underfull \hbox (badness 10000) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[386]
Underfull \hbox (badness 10000) in paragraph at lines 25047--25050
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 25071--25073
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 1629) in paragraph at lines 25109--25120
\T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi
4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an
d

Underfull \hbox (badness 7203) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[387]
Underfull \hbox (badness 4084) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN OS X build),

Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
\T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric
ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C
RAN

Underfull \hbox (badness 7397) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m
/n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1082) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[388] [389] [390] [391] [392]
Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n
/10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
\T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[393] [394] [395] [396] [397]
Underfull \hbox (badness 1735) in paragraph at lines 25809--25813
[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\
T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu
e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which
[398] [399] [400] [401] [402] [403] [404] [405] [406]
Underfull \hbox (badness 2726) in paragraph at lines 26369--26372
[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418]
[419]
Underfull \hbox (badness 1052) in paragraph at lines 27186--27191
[]\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1
0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide
d
[420] [421] [422] [423] [424]
Underfull \vbox (badness 10000) has occurred while \output is active [425]
[426] [427] [428] [429] [430] [431]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[432] [433] [434]
Underfull \hbox (badness 1163) in paragraph at lines 28157--28168
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446]
[447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 29676--29680
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 1221) in paragraph at lines 29676--29680
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[459] [460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 1655) in paragraph at lines 30246--30248
[]\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
[468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
[479] [480] [481]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 2980) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[482] [483] [484]
Underfull \hbox (badness 2261) in paragraph at lines 31310--31315
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[485]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
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[498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509]
[510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521]
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Underfull \hbox (badness 1072) in paragraph at lines 34333--34337
[]\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 34338--34342
[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 3343) in paragraph at lines 34379--34386
\T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment 
vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 34379--34386
\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 34379--34386
\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
[532] [533] [534] [535] [536]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1152) in paragraph at lines 34670--34676
\T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c
om-po-nent which is
[537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548]
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[561] [562] [563] [564] [565]
Underfull \hbox (badness 3333) in paragraph at lines 36500--36505
[]\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
[566] [567] [568] [569] [570] [571] [572] [573] [574] [575]
Underfull \hbox (badness 1472) in paragraph at lines 37120--37123
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586]
Underfull \hbox (badness 2671) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 10000) in paragraph at lines 38200--38203
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[593] [594]
Underfull \hbox (badness 10000) in paragraph at lines 38318--38322
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[595]
Underfull \hbox (badness 10000) in paragraph at lines 38380--38384
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607]
[608] [609] [610] [611] [612] [613] [614] [615]
Underfull \hbox (badness 1990) in paragraph at lines 39706--39714
[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 4846) in paragraph at lines 39706--39714
\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
[616] [617] [618] [619]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[620] [621] [622] [623]
Underfull \hbox (badness 1917) in paragraph at lines 40208--40215
[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
[624] [625] [626] [627] [628] [629] [630] [631] [632] [633]
Underfull \hbox (badness 3668) in paragraph at lines 40869--40871
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[634] [635]
Underfull \hbox (badness 2401) in paragraph at lines 40974--40978
[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
[636] [637]
Underfull \hbox (badness 2111) in paragraph at lines 41143--41148
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.
[638]
Underfull \hbox (badness 6542) in paragraph at lines 41159--41164
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[639] [640] [641] [642] [643] [644] [645]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/zi4/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
[646]
Underfull \hbox (badness 5417) in paragraph at lines 41696--41700
[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[647]
Underfull \hbox (badness 10000) in paragraph at lines 41757--41761
[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[648] [649]) (./compiler-pkg.tex [650]
Chapter 2.
[651] [652] [653] [654]) (./datasets-pkg.tex
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666]
[667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678]
[679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690]
[691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701]
Underfull \vbox (badness 1515) has occurred while \output is active [702]
[703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714]
[715] [716] [717] [718] [719] [720] [721]
Underfull \hbox (badness 6658) in paragraph at lines 3940--3942
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h
ttp : / / www . ltrr . arizona . edu / ~hallman /
[722]
Underfull \vbox (badness 10000) has occurred while \output is active [723]
[724] [725] [726]
Underfull \vbox (badness 10000) has occurred while \output is active [727]
Underfull \vbox (badness 10000) has occurred while \output is active [728]
[729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736]
Chapter 4.
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750] [751] [752] [753]
Underfull \hbox (badness 5175) in paragraph at lines 1071--1073
[]\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
[754] [755] [756] [757]
Underfull \hbox (badness 1852) in paragraph at lines 1268--1271
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[758] [759] [760]
Underfull \hbox (badness 1490) in paragraph at lines 1474--1479
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[761]
Underfull \hbox (badness 2698) in paragraph at lines 1528--1531
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[762]
Underfull \hbox (badness 10000) in paragraph at lines 1597--1601
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when
[763] [764] [765] [766]
Underfull \hbox (badness 1325) in paragraph at lines 1880--1890
\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[767] [768]
Underfull \hbox (badness 10000) in paragraph at lines 1985--1987
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[769] [770] [771]
Underfull \hbox (badness 6758) in paragraph at lines 2146--2149
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[772] [773] [774] [775] [776] [777] [778] [779] [780]
Underfull \hbox (badness 10000) in paragraph at lines 2712--2713

[781] [782] [783] [784] [785] [786] [787]
Underfull \hbox (badness 1152) in paragraph at lines 3150--3152
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[788] [789] [790] [791] [792]
Underfull \hbox (badness 2856) in paragraph at lines 3470--3473
[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

Underfull \hbox (badness 2662) in paragraph at lines 3484--3486
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[793] [794]
Underfull \hbox (badness 1173) in paragraph at lines 3600--3610
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\
T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to 
\T1/zi4/m/n/10 width \T1/ptm/m/n/10 by
[795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805]
Underfull \hbox (badness 1067) in paragraph at lines 4307--4314
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[806] [807]
Underfull \hbox (badness 3364) in paragraph at lines 4468--4470
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
[808]
Underfull \hbox (badness 1789) in paragraph at lines 4545--4547
[]\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[809]
Underfull \hbox (badness 1377) in paragraph at lines 4595--4600
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[810]
Underfull \hbox (badness 2671) in paragraph at lines 4622--4630
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as

Underfull \hbox (badness 1418) in paragraph at lines 4671--4678
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 2443) in paragraph at lines 4679--4688
\T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess
 to more char-ac-ters and

Underfull \hbox (badness 2653) in paragraph at lines 4679--4688
\T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes
e eas-ier to re-mem-ber,

Underfull \hbox (badness 1755) in paragraph at lines 4689--4691
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[811] [812]
Underfull \hbox (badness 1057) in paragraph at lines 4800--4805
[]\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
[813]
Underfull \hbox (badness 7344) in paragraph at lines 4860--4862
[]\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
[814] [815]
Underfull \hbox (badness 2035) in paragraph at lines 4984--4993
[]\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 4984--4993
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

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\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[816]
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[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

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\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
[817] [818] [819]
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[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
[820]
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
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[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[843] [844] [845]) (./graphics-pkg.tex [846]
Chapter 5.
[847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857]
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[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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\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
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
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[]\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
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
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[925]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
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</«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf, id=22
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[][] 
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\T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i
s ex-ited by the com-mand
[965]
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po
int
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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l.8735 \HeaderA{units}{Graphical Units}{units}
                                               [989] [990] [991] [992])
(./grid-pkg.tex
Chapter 6.

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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[]\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
[1066] [1067] [1068] [1069]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104]
Chapter 7.
[1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115]
[1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124]
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

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\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in
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\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
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[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

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[]\T1/ptm/m/n/10 The
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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[]\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

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\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
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\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

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\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and

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[]\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
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[]\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
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[]\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z
i4/m/n/10 initialize \T1/ptm/m/n/10 and
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\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
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[]\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
[1206] [1207] [1208]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219]
[1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230]
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[1242]
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[]\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.,
[1243] [1244] [1245] [1246]) (./parallel-pkg.tex
Chapter 8.

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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]
[1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1267] [1268]) (./splines-pkg.tex
Chapter 9.

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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279]
[1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284]
Chapter 10.
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Underfull \hbox (badness 1412) in paragraph at lines 846--848
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
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Underfull \hbox (badness 2503) in paragraph at lines 1327--1330
[]\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 ,
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Underfull \hbox (badness 10000) in paragraph at lines 1506--1510
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
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Underfull \hbox (badness 3965) in paragraph at lines 2166--2168
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
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Underfull \hbox (badness 2503) in paragraph at lines 3325--3328
[]\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 ,
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Underfull \hbox (badness 3989) in paragraph at lines 4553--4560
[]\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 =
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Underfull \hbox (badness 2556) in paragraph at lines 5164--5167
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5181--5183
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
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Underfull \hbox (badness 1142) in paragraph at lines 5422--5434
\T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is
 un-usual but avail-able for the sake of com-plete-ness.
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Underfull \hbox (badness 2503) in paragraph at lines 5561--5565
[]\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 ,
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Underfull \hbox (badness 1168) in paragraph at lines 5622--5627
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
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Underfull \hbox (badness 8132) in paragraph at lines 6064--6069
\T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa
me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node,
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Underfull \hbox (badness 7081) in paragraph at lines 6342--6345
[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 10000) in paragraph at lines 6346--6348
[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
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Underfull \hbox (badness 10000) in paragraph at lines 7159--7162
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
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Underfull \hbox (badness 10000) in paragraph at lines 7296--7299
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht
tps : / / cran . r-[]project . org / web / views /
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Underfull \hbox (badness 2626) in paragraph at lines 8794--8797
[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
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Underfull \hbox (badness 2503) in paragraph at lines 8894--8898
[]\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 ,
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Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
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Underfull \hbox (badness 4518) in paragraph at lines 10155--10160
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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Underfull \hbox (badness 2142) in paragraph at lines 10497--10500
[]\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 ^^@
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Underfull \hbox (badness 1253) in paragraph at lines 10516--10519
[]\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,
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Underfull \hbox (badness 1708) in paragraph at lines 10578--10582
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
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Underfull \hbox (badness 1694) in paragraph at lines 10974--10977
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to

Underfull \hbox (badness 1867) in paragraph at lines 10993--11002
\T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th
e or-der-ing of the cor-re-
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Underfull \hbox (badness 10000) in paragraph at lines 11300--11303
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
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 (name{Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11454 \aliasA{hat}{influence.measures}{hat}
                                              [1468] [1469]
Underfull \hbox (badness 1484) in paragraph at lines 11577--11579
[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
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Underfull \hbox (badness 4441) in paragraph at lines 12135--12137
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

Underfull \hbox (badness 10000) in paragraph at lines 12142--12144
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
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Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
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Underfull \hbox (badness 4518) in paragraph at lines 13171--13176
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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Underfull \hbox (badness 4518) in paragraph at lines 13818--13823
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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Underfull \hbox (badness 10000) in paragraph at lines 13956--13960
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface =

Underfull \hbox (badness 1199) in paragraph at lines 13963--13965
[]\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
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Underfull \hbox (badness 2503) in paragraph at lines 15025--15029
[]\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 ,
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Underfull \hbox (badness 1418) in paragraph at lines 15534--15540
[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1
/ptm/m/n/10 and
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Underfull \hbox (badness 2359) in paragraph at lines 17158--17160
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
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Underfull \hbox (badness 1377) in paragraph at lines 18069--18074
[]\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 18074--18077
[]\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 1184) in paragraph at lines 18087--18091
\T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18095--18099
[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
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Underfull \hbox (badness 1337) in paragraph at lines 18711--18714
[]\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
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Underfull \hbox (badness 5563) in paragraph at lines 19441--19443
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

Underfull \hbox (badness 1194) in paragraph at lines 19444--19447
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
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Underfull \hbox (badness 2503) in paragraph at lines 19811--19814
[]\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 ,
[1605]
Underfull \hbox (badness 10000) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
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Underfull \hbox (badness 10000) in paragraph at lines 20863--20869
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
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[1644]
Underfull \hbox (badness 1337) in paragraph at lines 22198--22204
[]\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
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Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1667]
Underfull \hbox (badness 3690) in paragraph at lines 23619--23623
[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
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Underfull \hbox (badness 3439) in paragraph at lines 24089--24095
[][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO
rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1
0 ,
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Underfull \hbox (badness 1867) in paragraph at lines 24286--24288
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
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Underfull \hbox (badness 10000) in paragraph at lines 24299--24301
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
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Underfull \hbox (badness 10000) in paragraph at lines 24757--24762
[]\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
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Underfull \hbox (badness 3514) in paragraph at lines 25775--25780
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1703]
Underfull \hbox (badness 3514) in paragraph at lines 25837--25842
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
Underfull \hbox (badness 3514) in paragraph at lines 25894--25899
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1705]
Underfull \hbox (badness 3514) in paragraph at lines 25955--25961
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1706] [1707] [1708] [1709]
Underfull \hbox (badness 3514) in paragraph at lines 26168--26173
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
Underfull \hbox (badness 3514) in paragraph at lines 26224--26229
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1711]
Underfull \hbox (badness 3514) in paragraph at lines 26281--26286
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1712]
Underfull \hbox (badness 3514) in paragraph at lines 26336--26341
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1713]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

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\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1736] [1737] [1738] [1739] [1740] [1741]
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[]\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
[1742] [1743]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1744] [1745]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
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[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
[1765] [1766] [1767]
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[1769] [1770]
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[]\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
[1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778]
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[]\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]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1780] [1781] [1782] [1783] [1784] [1785]
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[]\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or
[1786] [1787] [1788]) (./stats4-pkg.tex
Chapter 11.
[1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
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l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1795] [1796] [1797]
[1798]) (./tcltk-pkg.tex
Chapter 12.
[1799] [1800] [1801] [1802] [1803] [1804] [1805]
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[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818]
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[][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1819]) (./tools-pkg.tex [1820]
Chapter 13.
[1821]

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[1822]
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[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1823] [1824]
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[]\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

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\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

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\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

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\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1838]
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1839]
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[]\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

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


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\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
[1840] [1841] [1842]
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1843] [1844] [1845]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

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[]\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
[1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
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l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1850]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from

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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
[1851] [1852] [1853] [1854] [1855] [1856]
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1857] [1858] [1859] [1860]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
[1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879]
[1880]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1881] [1882]
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1883] [1884] [1885] [1886]
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
[1887] [1888]
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR
UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10
 DependsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and
[1891] [1892] [1893] [1894]) (./utils-pkg.tex
Chapter 14.
[1895]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1896] [1897]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de-

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[]\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the
 same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault
[1898] [1899] [1900] [1901] [1902] [1903]
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[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1904]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

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\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1905]
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[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1916] [1917] [1918] [1919] [1920] [1921] [1922]
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[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1923] [1924]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1925]
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1926] [1927] [1928] [1929]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

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[]\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1930] [1931] [1932] [1933] [1934] [1935]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing
[1936]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944]
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[]\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/
10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1
0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the
[1945]
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[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the

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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956]
[1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier
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                                                   [1960] [1961] [1962]
[1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973]
[1974]
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1975]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-

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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1976] [1977] [1978]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[1979]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[1980] [1981]
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[]\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
[1982]
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1983]
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[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able
[1984]
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed

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\T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac
k-age in-stall. E.g.,
[1985]
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10 ,
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rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
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dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
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[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia
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/sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][]
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s / manual /
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[][][]@smallrm The in-staller as puts links to @smalltt R[] @smallrm and @small
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[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[27] [28] [29] [30] [31]
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 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i
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Chapter 7 [32] [33] [34] Chapter 8 [35] Chapter 9 [36] [37] [38] Appendix A
[39] [40]
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 []@texttt /configure --enable-utf --enable-unicode-properties --enable-jit --d
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[41] [42] [43] [44] [45] [46] [47]
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 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM
E@texttt /lib/libRblas.so[] 
[48] Appendix B [49] [50] [51] [52] [53] [54] Appendix C [55] [56] [57]
[58]
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[]@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % https:
//stat.ethz.ch/pipermail/r-
[59] [60] [61]
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[62]
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[]@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled
, run
[63]
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[64] [65]
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@texttt LDFLAGS=-L/usr/local/lib/sparcv9[] @textrm or @texttt LDFLAGS=-L/usr/lo
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onfig[] 

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 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s
olaris"[] 
[66] [67] [68] [69] [70] [71] Appendix D [72] [73] [74]
(Function and variable index) [75] (Concept index) [76]
(Environment variable index) [77] [78] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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(/«PKGBUILDDIR»/doc/manual/R-admin.toc) Chapter 1
(/«PKGBUILDDIR»/doc/manual/R-admin.aux) [1] Chapter 2
[2] [3] [4] [5] [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] [15]
[16] [17] [18] Chapter 4 [19]
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[][][]@smallrm The in-staller as puts links to @smalltt R[] @smallrm and @small
tt Rscript[] @smallrm in @smalltt /usr/bin[] @smallrm (Mav-er-icks, Yosemite) o
r
[20]
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@texttt org.r-project.R.x86_64.GUI.pkg[]@textrm , @texttt org.r-project.x86_64.
tcltk.x11[] @textrm and
[21] Chapter 5 [22] Chapter 6 [23]
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 []@texttt [1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "met
hods"[] 
[24] [25]
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[]@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age
s. No ad-di-
[26]
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[]@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R
.framework/Resources/etc/Makeconf[]
[27] [28] [29] [30] [31]
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tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] 

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 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i
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Chapter 7 [32] [33] [34] Chapter 8 [35] Chapter 9 [36] [37] [38] Appendix A
[39] [40]
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isable-cpp[] 
[41] [42] [43] [44] [45] [46] [47]
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E@texttt /lib/libRblas.so[] 
[48] Appendix B [49] [50] [51] [52] [53] [54] Appendix C [55] [56] [57]
[58]
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[]@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % https:
//stat.ethz.ch/pipermail/r-
[59] [60] [61]
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[62]
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[]@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled
, run
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[64] [65]
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onfig[] 

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 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s
olaris"[] 
[66] [67] [68] [69] [70] [71] Appendix D [72] [73] [74]
(Function and variable index) [75] (Concept index) [76]
(Environment variable index) [77] [78] )
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[1] [2] Chapter 1 [3] Cross reference values unknown; you must run TeX again.
[4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15]
[16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6
[25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32]
Appendix A [33] (Function and variable index) [34] (Concept index) [35]
[36] )
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ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
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[1] [2] Chapter 1 [3] [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13]
[14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23]
Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8
[31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35]
(Concept index) [36] [37] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
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lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
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[1] [2] Chapter 1 [3] [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13]
[14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23]
Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8
[31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35]
(Concept index) [36] [37] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
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onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1
[1] Cross reference values unknown; you must run TeX again. [2] [3] [4]
[5]
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23]
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LAGS)[] 
[24] [25] [26] [27]
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pp model/*/*.cpp model/*/*/*.cpp)[] 

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[28] [29] [30]
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e defined.[]  
[31] [32] [33]
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[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]
[49] [50] [51] [52] [53] [54] [55] [56] [57]
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 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@
euro"[] 
[58] [59] [60] [61] [62]
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[63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75]
[76] [77] [78] [79]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[80] [81] [82] [83]
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[84] [85] Chapter 3 [86] [87] [88] [89] [90] [91]
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[92] [93] [94] Chapter 4 [95] [96] [97]
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[98]
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e supply starting values[] 
[99]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
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[101] [102] [103] [104] [105]
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[106] [107]
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[108]
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[110] [111] Chapter 5 [112] [113] [114] [115] [116] [117] [118] [119] [120]
[121] [122] [123] [124] [125]
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[126] [127] [128] [129] [130] [131] [132] [133] [134]
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[135]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[136] [137] [138] [139] [140] [141]
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[142] [143]
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[144]
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a)));[] 

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 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 
[145] [146] [147]
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[148]
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[149] [150]
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 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety
pe_t;[] 
Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161]
[162] [163]
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 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na
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[164] Warning: unbalanced parentheses in @def... [165] [166] [167] [168]
[169] [170] Chapter 7 [171] [172] Chapter 8 [173] [174] [175]
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tatic libR[] 
[176]
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nst char *);[] 
[177] [178] [179] [180]
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 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan
ohttp.c[] @textrm and @texttt src/
[181] [182] [183] [184] [185]
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 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or

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(Function and variable index) [186] (Concept index) [187] [188] )
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ributes assigned to @textsl

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Output written on R-exts.pdf (191 pages, 845838 bytes).
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This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex)
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Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
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) localization, formatting, and turning on texinfo input format.)
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onts/map/pdftex/updmap/pdftex.map}] [2]
(/«PKGBUILDDIR»/doc/manual/R-exts.toc [-1] [-2] [-3]
[-4]) [-5] (/«PKGBUILDDIR»/doc/manual/R-exts.toc)
(/«PKGBUILDDIR»/doc/manual/R-exts.toc) (Acknowledgements)
(/«PKGBUILDDIR»/doc/manual/R-exts.aux) Chapter 1 [1]
[2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 494--497
[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23]
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 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF
LAGS)[] 
[24] [25] [26] [27]
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 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 

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 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[28] [29] [30]
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 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar
e defined.[]  
[31] [32] [33]
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[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]
[49] [50] [51] [52] [53] [54] [55] [56] [57]
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 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@
euro"[] 
[58] [59] [60] [61] [62]
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 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String
)[] 
[63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75]
[76] [77] [78] [79]
Underfull \hbox (badness 10000) in paragraph at lines 6119--6126
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[80] [81] [82] [83]
Underfull \hbox (badness 10000) in paragraph at lines 6438--6442
[]@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file
[84] [85] Chapter 3 [86] [87] [88] [89] [90] [91]
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 []                 @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1,
 28)))[] 
[92] [93] [94] Chapter 4 [95] [96] [97]
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 []@texttt evaluation nested too deeply: infinite recursion / options(expressio
ns=)?[] 
[98]
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 []@smalltt Message:  Error: no valid set of coefficients has been found: pleas
e supply starting values[] 
[99]
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 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star
t, etastart = etastart,[] 
[100]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g. @texttt debug(stats:::predict.Arima)[]@textrm .
[101] [102] [103] [104] [105]
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 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 

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[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -fsanitize=undefined,address[]
[106] [107]
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 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[108]
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 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl
assi,[] 

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 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t(
cu)),[] 
[109]
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 []@texttt #5  0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9
698f98,[] 
[110] [111] Chapter 5 [112] [113] [114] [115] [116] [117] [118] [119] [120]
[121] [122] [123] [124] [125]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[126] [127] [128] [129] [130] [131] [132] [133] [134]
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 []    @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL
SE");[] 
[135]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[136] [137] [138] [139] [140] [141]
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 []    @texttt // a version with (too) much PROTECT()ion .. "better safe than s
orry"[] 
[142] [143]
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 []    @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet
a)));[] 
[144]
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 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 

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 []    @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet
a)));[] 

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 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 
[145] [146] [147]
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 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one
xit);[] 
[148]
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 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[149] [150]
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 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety
pe_t;[] 
Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161]
[162] [163]
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 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na
.last, decreasing)[]@textrm .
[164] Warning: unbalanced parentheses in @def... [165] [166] [167] [168]
[169] [170] Chapter 7 [171] [172] Chapter 8 [173] [174] [175]
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 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[176]
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 []@texttt extern int  (*ptr_R_ReadConsole)(const char *, unsigned char *, int,
 int);[] 

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 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[177] [178] [179] [180]
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 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan
ohttp.c[] @textrm and @texttt src/
[181] [182] [183] [184] [185]
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 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [186] [187] [188] (Concept index) [189] [190]
[191] )
(see the transcript file for additional information)pdfTeX warning (\pdffontatt
r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att
ributes assigned to @textsl

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Output written on R-exts.pdf (198 pages, 903788 bytes).
Transcript written on R-exts.log.
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entering extended mode
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page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
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onts/map/pdftex/updmap/pdftex.map}] [2]
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[-4]) [-5] (/«PKGBUILDDIR»/doc/manual/R-exts.toc)
(/«PKGBUILDDIR»/doc/manual/R-exts.toc) (Acknowledgements)
(/«PKGBUILDDIR»/doc/manual/R-exts.aux) Chapter 1 [1]
[2] [3] [4] [5]
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23]
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 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF
LAGS)[] 
[24] [25] [26] [27]
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a07models.o $(SOURCES:.cpp=.o)[] 
[28] [29] [30]
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e defined.[]  
[31] [32] [33]
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[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]
[49] [50] [51] [52] [53] [54] [55] [56] [57]
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 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@
euro"[] 
[58] [59] [60] [61] [62]
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 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String
)[] 
[63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75]
[76] [77] [78] [79]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[80] [81] [82] [83]
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[]@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file
[84] [85] Chapter 3 [86] [87] [88] [89] [90] [91]
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[92] [93] [94] Chapter 4 [95] [96] [97]
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[98]
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e supply starting values[] 
[99]
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[100]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
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[101] [102] [103] [104] [105]
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[106] [107]
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[108]
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[109]
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 []@texttt #5  0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9
698f98,[] 
[110] [111] Chapter 5 [112] [113] [114] [115] [116] [117] [118] [119] [120]
[121] [122] [123] [124] [125]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[126] [127] [128] [129] [130] [131] [132] [133] [134]
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[135]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[136] [137] [138] [139] [140] [141]
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[142] [143]
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[144]
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[145] [146] [147]
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xit);[] 
[148]
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[149] [150]
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 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety
pe_t;[] 
Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161]
[162] [163]
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 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na
.last, decreasing)[]@textrm .
[164] Warning: unbalanced parentheses in @def... [165] [166] [167] [168]
[169] [170] Chapter 7 [171] [172] Chapter 8 [173] [174] [175]
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tatic libR[] 
[176]
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 int);[] 

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[177] [178] [179] [180]
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 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan
ohttp.c[] @textrm and @texttt src/
[181] [182] [183] [184] [185]
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 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [186] [187] [188] (Concept index) [189] [190]
[191] )
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[3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16]
[17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6
[26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
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[3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16]
[17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6
[26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
[39] [40] [41] [42]
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[3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16]
[17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6
[26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
[39] [40] [41] [42]
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onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface)
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[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] </«PKGBUILDDIR»/doc/manual/images/hist.pdf> <
/«PKGBUILDDIR»/doc/manual/images/ecdf.pdf> [38] </build/r-ba
se-asNdei/r-base-3.3.0/doc/manual/images/QQ.pdf> [39] </«BUILDDIR»/r-b
ase-3.3.0/doc/manual/images/ice.pdf> [40] [41] Chapter 9 [42] [43] Chapter 10
[44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56]
[57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69]
[70] [71]
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[78] [79] [80] [81] Chapter 13 [82]
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[83] Chapter 14 [84] [85]
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[86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95]
[96] [97] [98] Appendix C [99] [100] Appendix D [101] Appendix E [102]
Appendix F [103] [104] )
(see the transcript file for additional information) </home/buildd/.texmf-var/f
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[-4] (/«PKGBUILDDIR»/doc/manual/R-intro.toc)
(/«PKGBUILDDIR»/doc/manual/R-intro.toc) (Preface)
(/«PKGBUILDDIR»/doc/manual/R-intro.aux) Chapter 1 [1]
[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] </«PKGBUILDDIR»/doc/manual/images/h
ist.pdf> </«PKGBUILDDIR»/doc/manual/images/ecdf.pdf>
[38] </«PKGBUILDDIR»/doc/manual/images/QQ.pdf> [39] </build/
r-base-asNdei/r-base-3.3.0/doc/manual/images/ice.pdf> [40] [41] Chapter 9
[42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53]
Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66]
Chapter 12 [67] [68] [69] [70] [71]
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[72] [73] [74] [75] [76] </«PKGBUILDDIR»/doc/manual/images/f
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[78] [79] [80] [81] Chapter 13 [82]
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[83] Chapter 14 [84] [85]
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[86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95]
[96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E
[104] [105] Appendix F [106] [107] )
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[-4] (/«PKGBUILDDIR»/doc/manual/R-intro.toc)
(/«PKGBUILDDIR»/doc/manual/R-intro.toc) (Preface)
(/«PKGBUILDDIR»/doc/manual/R-intro.aux) Chapter 1 [1]
[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] </«PKGBUILDDIR»/doc/manual/images/h
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[38] </«PKGBUILDDIR»/doc/manual/images/QQ.pdf> [39] </build/
r-base-asNdei/r-base-3.3.0/doc/manual/images/ice.pdf> [40] [41] Chapter 9
[42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53]
Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66]
Chapter 12 [67] [68] [69] [70] [71]
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[72] [73] [74] [75] [76] </«PKGBUILDDIR»/doc/manual/images/f
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[78] [79] [80] [81] Chapter 13 [82]
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[83] Chapter 14 [84] [85]
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[86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95]
[96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E
[104] [105] Appendix F [106] [107] )
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onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 [1] [2] [3] [4] [5]
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] Chapter 2 [24] [25]
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[26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34]
Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
Chapter 7 [48]
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@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl
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[49] Chapter 8 [50] [51] [52] [53] [54]
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tchArgs = FALSE[] @textrm and
[55] [56] Chapter 9 [57] [58] Chapter 10 [59] Chapter 11 [60] Chapter 12
[61] [62] (Function and variable index) [63] [64] (Concept index) [65] [66] )
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(/«PKGBUILDDIR»/doc/manual/R-ints.toc) Chapter 1
(/«PKGBUILDDIR»/doc/manual/R-ints.aux) [1] [2] [3] [4]
[5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20]
[21] [22] [23] Chapter 2 [24] [25]
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[26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34]
Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
Chapter 7 [48]
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@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl
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[49] Chapter 8 [50] [51] [52] [53] [54]
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sed for

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LE_

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tchArgs = FALSE[] @textrm and
[55] [56] Chapter 9 [57] [58] Chapter 10 [59] Chapter 11 [60] Chapter 12
[61] [62] (Function and variable index) [63] [64] [65] (Concept index) [66]
[67] )
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ',
[9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
[12] [13] [14] [15] [16] [17] [18]
Underfull \hbox (badness 2671) in paragraph at lines 1135--1138
[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[19] [20] [21] [22]
Underfull \hbox (badness 4072) in paragraph at lines 1369--1375
[]\T1/zi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/zi4/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/zi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[23] [24] [25] [26] [27] [28] [29] [30]
Overfull \hbox (26.88089pt too wide) in paragraph at lines 1894--1894
 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
[31] [32] [33]
Underfull \hbox (badness 10000) in paragraph at lines 2079--2081
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]
[49] [50] [51] [52] [53] [54] [55] [56]
Underfull \hbox (badness 10000) in paragraph at lines 3580--3582
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71]
[72] [73] [74]
Underfull \hbox (badness 2521) in paragraph at lines 4782--4784
[]\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
[75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89]
[90] [91] [92]
Overfull \hbox (7.0809pt too wide) in paragraph at lines 5909--5909
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[93] [94] [95]
Underfull \hbox (badness 2096) in paragraph at lines 6090--6103
[]\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
[96] [97] [98]
Overfull \hbox (58.35893pt too wide) in paragraph at lines 6293--6295
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : 
[99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 6434--6437
[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
[101] [102]
Underfull \hbox (badness 1442) in paragraph at lines 6599--6605
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move a

Underfull \hbox (badness 1248) in paragraph at lines 6599--6605
\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-

Underfull \hbox (badness 2080) in paragraph at lines 6599--6605
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
[103]
Underfull \hbox (badness 3568) in paragraph at lines 6660--6667
\T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z
i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
[104] [105]
Underfull \vbox (badness 10000) has occurred while \output is active [106]
[107] [108] [109] [110] [111] [112] [113]
Underfull \hbox (badness 2096) in paragraph at lines 7298--7302
\T1/zi4/m/n/10 status _ codes$[][] \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 .
[114]
Underfull \hbox (badness 4595) in paragraph at lines 7355--7358
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[115]
Underfull \hbox (badness 3000) in paragraph at lines 7391--7393
[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 
getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed 
for

Underfull \hbox (badness 2351) in paragraph at lines 7416--7419
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[116] [117] [118] [119]
Underfull \hbox (badness 10000) in paragraph at lines 7671--7682
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[120] [121]
Underfull \hbox (badness 4479) in paragraph at lines 7743--7752
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),

Underfull \hbox (badness 2469) in paragraph at lines 7743--7752
[][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods,
 [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i
t/10 Group \T1/ptm/m/n/10 meth-ods for
[122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133]
[134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145]
Underfull \hbox (badness 1394) in paragraph at lines 9355--9360
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[146] [147] [148] [149] [150]
Underfull \hbox (badness 1052) in paragraph at lines 9698--9703
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s
ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b
y \T1/zi4/m/n/10 R CMD check

Underfull \hbox (badness 1231) in paragraph at lines 9698--9703
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z
i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[151] [152]
Underfull \hbox (badness 1735) in paragraph at lines 9836--9840
\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
zi4/m/n/10 https : / / en . wikipedia .
[153] [154] [155] [156] [157] [158]
Underfull \hbox (badness 2150) in paragraph at lines 10240--10243
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
[159]
Underfull \hbox (badness 6396) in paragraph at lines 10254--10262
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 2409) in paragraph at lines 10295--10302
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171]
[172] [173] [174] [175]
Underfull \hbox (badness 4569) in paragraph at lines 11341--11345
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 11341--11345
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[176] [177] [178] [179] [180] [181] [182] [183]
Underfull \hbox (badness 2698) in paragraph at lines 11917--11926
[]\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-lowed

Underfull \hbox (badness 4341) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e
r-a-tions are those of
[184] [185] [186] [187] [188] [189] [190] [191] [192] [193]
Underfull \hbox (badness 6236) in paragraph at lines 12561--12564
[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 2253) in paragraph at lines 12939--12941
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[200]
Underfull \hbox (badness 1565) in paragraph at lines 13010--13014
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[201]
Underfull \hbox (badness 10000) in paragraph at lines 13054--13056
[]\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
[202] [203]
Underfull \hbox (badness 1466) in paragraph at lines 13195--13198
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[204] [205]
Underfull \hbox (badness 10000) in paragraph at lines 13303--13307
[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 13314--13317
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[206] [207] [208] [209]
Underfull \hbox (badness 3965) in paragraph at lines 13577--13581
[]\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,
[210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221]
Underfull \hbox (badness 4429) in paragraph at lines 14338--14341
[]\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
[222]
Underfull \hbox (badness 10000) in paragraph at lines 14430--14432
[]\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[223]
Underfull \hbox (badness 10000) in paragraph at lines 14478--14482
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use

Underfull \hbox (badness 4156) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[224]
Underfull \vbox (badness 3803) has occurred while \output is active [225]
[226] [227] [228] [229] [230] [231] [232]
Underfull \hbox (badness 2452) in paragraph at lines 15058--15062
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15058--15062
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[233] [234] [235]
Underfull \hbox (badness 1092) in paragraph at lines 15231--15236
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[236] [237] [238] [239]
Underfull \hbox (badness 6741) in paragraph at lines 15479--15483
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[240] [241] [242] [243]
Underfull \hbox (badness 1867) in paragraph at lines 15785--15792
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[244] [245] [246] [247]
Underfull \vbox (badness 10000) has occurred while \output is active [248]
[249]
Underfull \hbox (badness 3679) in paragraph at lines 16166--16168
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[250] [251] [252] [253] [254] [255] [256] [257]
Underfull \hbox (badness 1478) in paragraph at lines 16711--16714
[]\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
[258] [259] [260] [261]
Underfull \hbox (badness 10000) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1442) in paragraph at lines 17527--17529
[]\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
[271]
Underfull \hbox (badness 2452) in paragraph at lines 17619--17635
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[272] [273] [274] [275] [276] [277] [278]
Underfull \hbox (badness 1248) in paragraph at lines 18033--18036
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[279] [280] [281] [282]
Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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[295] [296] [297] [298]
Underfull \hbox (badness 1360) in paragraph at lines 19249--19254
\T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS
SL used, but not all

Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /

Underfull \hbox (badness 1127) in paragraph at lines 19272--19278
\T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S
SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv
/m/n/10 R
[299]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory

Underfull \hbox (badness 2460) in paragraph at lines 19345--19349
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[300] [301]
Underfull \hbox (badness 1509) in paragraph at lines 19480--19487
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1354) in paragraph at lines 19480--19487
\T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta
in just the names of all avail-able pack-ages, and

Underfull \hbox (badness 1014) in paragraph at lines 19496--19501
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313]
Underfull \hbox (badness 1264) in paragraph at lines 20227--20232
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324]
Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\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
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[337] [338] [339] [340]
Underfull \hbox (badness 1077) in paragraph at lines 21979--21985
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[341] [342] [343]
Underfull \hbox (badness 1484) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[344] [345] [346] [347]
Underfull \hbox (badness 2790) in paragraph at lines 22411--22414
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 22411--22414
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[348] [349] [350] [351]
Underfull \hbox (badness 1194) in paragraph at lines 22692--22695
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
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Underfull \hbox (badness 10000) in paragraph at lines 22898--22904
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 5862) in paragraph at lines 22898--22904
\T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE))
 \T1/ptm/m/n/10 which are also given by

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
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[368] [369]
Underfull \hbox (badness 10000) in paragraph at lines 23839--23841
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[370] [371] [372] [373]
Underfull \hbox (badness 1199) in paragraph at lines 24066--24072
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][] \T1/zi4/m/n/10 "numeric"

Underfull \hbox (badness 2027) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \
T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F
ALSE \T1/ptm/m/n/10 oth-er-wise. That is,
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Underfull \hbox (badness 1038) in paragraph at lines 24645--24653
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1881) in paragraph at lines 24654--24657
[]\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 24673--24675
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[382]
Underfull \hbox (badness 10000) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 2142) in paragraph at lines 24756--24762
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 24769--24774
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[383] [384]
Underfull \vbox (badness 10000) has occurred while \output is active [385]
Underfull \hbox (badness 10000) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[386]
Underfull \hbox (badness 10000) in paragraph at lines 25047--25050
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 25071--25073
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 1629) in paragraph at lines 25109--25120
\T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi
4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an
d

Underfull \hbox (badness 7203) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[387]
Underfull \hbox (badness 4084) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN OS X build),

Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
\T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric
ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C
RAN

Underfull \hbox (badness 7397) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m
/n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1082) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[388] [389] [390] [391] [392]
Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n
/10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
\T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[393] [394] [395] [396] [397]
Underfull \hbox (badness 1735) in paragraph at lines 25809--25813
[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\
T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu
e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which
[398] [399] [400] [401] [402] [403] [404] [405] [406]
Underfull \hbox (badness 2726) in paragraph at lines 26369--26372
[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418]
[419]
Underfull \hbox (badness 1052) in paragraph at lines 27186--27191
[]\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1
0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide
d
[420] [421] [422] [423] [424]
Underfull \vbox (badness 10000) has occurred while \output is active [425]
[426] [427] [428] [429] [430] [431]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[432] [433] [434]
Underfull \hbox (badness 1163) in paragraph at lines 28157--28168
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446]
[447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 29676--29680
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 1221) in paragraph at lines 29676--29680
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[459] [460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 1655) in paragraph at lines 30246--30248
[]\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
[468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
[479] [480] [481]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 2980) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[482] [483] [484]
Underfull \hbox (badness 2261) in paragraph at lines 31310--31315
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[485]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
[486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497]
[498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509]
[510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521]
[522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
Underfull \hbox (badness 1072) in paragraph at lines 34333--34337
[]\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 34338--34342
[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 3343) in paragraph at lines 34379--34386
\T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment 
vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 34379--34386
\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 34379--34386
\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
[532] [533] [534] [535] [536]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1152) in paragraph at lines 34670--34676
\T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c
om-po-nent which is
[537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548]
[549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560]
[561] [562] [563] [564] [565]
Underfull \hbox (badness 3333) in paragraph at lines 36500--36505
[]\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
[566] [567] [568] [569] [570] [571] [572] [573] [574] [575]
Underfull \hbox (badness 1472) in paragraph at lines 37120--37123
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586]
Underfull \hbox (badness 2671) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 10000) in paragraph at lines 38200--38203
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[593] [594]
Underfull \hbox (badness 10000) in paragraph at lines 38318--38322
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[595]
Underfull \hbox (badness 10000) in paragraph at lines 38380--38384
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607]
[608] [609] [610] [611] [612] [613] [614] [615]
Underfull \hbox (badness 1990) in paragraph at lines 39706--39714
[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 4846) in paragraph at lines 39706--39714
\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
[616] [617] [618] [619]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[620] [621] [622] [623]
Underfull \hbox (badness 1917) in paragraph at lines 40208--40215
[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
[624] [625] [626] [627] [628] [629] [630] [631] [632] [633]
Underfull \hbox (badness 3668) in paragraph at lines 40869--40871
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[634] [635]
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[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
[636] [637]
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\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.
[638]
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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[639] [640] [641] [642] [643] [644] [645]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/zi4/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
[646]
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[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[647]
Underfull \hbox (badness 10000) in paragraph at lines 41757--41761
[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[648] [649]) (./compiler-pkg.tex [650]
Chapter 2.
[651] [652] [653] [654]) (./datasets-pkg.tex
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666]
[667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678]
[679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690]
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Underfull \hbox (badness 6658) in paragraph at lines 3940--3942
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h
ttp : / / www . ltrr . arizona . edu / ~hallman /
[722]
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[724] [725] [726]
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Underfull \vbox (badness 10000) has occurred while \output is active [728]
[729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736]
Chapter 4.
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750] [751] [752] [753]
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[]\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
[754] [755] [756] [757]
Underfull \hbox (badness 1852) in paragraph at lines 1268--1271
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[758] [759] [760]
Underfull \hbox (badness 1490) in paragraph at lines 1474--1479
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[761]
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[762]
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[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when
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\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[767] [768]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
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[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[788] [789] [790] [791] [792]
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[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

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[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[793] [794]
Underfull \hbox (badness 1173) in paragraph at lines 3600--3610
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\
T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to 
\T1/zi4/m/n/10 width \T1/ptm/m/n/10 by
[795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805]
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\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[806] [807]
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
[808]
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[809]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[810]
Underfull \hbox (badness 2671) in paragraph at lines 4622--4630
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as

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\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

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\T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess
 to more char-ac-ters and

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\T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes
e eas-ier to re-mem-ber,

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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[811] [812]
Underfull \hbox (badness 1057) in paragraph at lines 4800--4805
[]\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
[813]
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[]\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
[814] [815]
Underfull \hbox (badness 2035) in paragraph at lines 4984--4993
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

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\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

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\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[816]
Underfull \hbox (badness 10000) in paragraph at lines 5053--5060
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

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\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
[817] [818] [819]
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[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
[820]
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[821] [822] [823] [824] [825] [826] [827]
Underfull \hbox (badness 10000) in paragraph at lines 5724--5727
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[828] [829] [830] [831] [832] [833]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[834] [835]
Underfull \hbox (badness 10000) in paragraph at lines 6219--6221
[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[836] [837] [838] [839]
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[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
[840] [841] [842]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[843] [844] [845]) (./graphics-pkg.tex [846]
Chapter 5.
[847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857]
Underfull \hbox (badness 10000) in paragraph at lines 683--690
[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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\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
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
[911] [912] [913] [914] [915] [916] [917]
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
[918]
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[]\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
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
[924]
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[925]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
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\T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i
s ex-ited by the com-mand
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po
int
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
[988]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8735 \HeaderA{units}{Graphical Units}{units}
                                               [989] [990] [991] [992])
(./grid-pkg.tex
Chapter 6.

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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
[1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019]
[1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030]
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[1064] [1065]
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[]\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
[1066] [1067] [1068] [1069]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080]
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099]
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104]
Chapter 7.
[1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115]
[1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124]
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
[1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133]
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

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\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1142] [1143]
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[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in
[1144]
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\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
[1145] [1146] [1147] [1148] [1149] [1150] [1151]
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[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1152] [1153] [1154] [1155] [1156]
Underfull \hbox (badness 10000) in paragraph at lines 3667--3672
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

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[]\T1/ptm/m/n/10 The
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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[]\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

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\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
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[1180]
Underfull \hbox (badness 1092) in paragraph at lines 5281--5288
\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

Underfull \hbox (badness 1117) in paragraph at lines 5281--5288
\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and

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[]\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
[1181] [1182] [1183] [1184] [1185]
Underfull \hbox (badness 1087) in paragraph at lines 5649--5654
[]\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
[1186] [1187] [1188] [1189]
Underfull \hbox (badness 2221) in paragraph at lines 5878--5883
[]\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z
i4/m/n/10 initialize \T1/ptm/m/n/10 and
[1190] [1191] [1192] [1193] [1194]
Underfull \hbox (badness 1675) in paragraph at lines 6345--6351
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1195] [1196] [1197] [1198]
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                   \relax 
l.6828 \aliasA{S4}{S3Part}{S4}
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l.7098 \aliasA{Logic}{S4groupGeneric}{Logic}
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l.7102 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1205]
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[]\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
[1206] [1207] [1208]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219]
[1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230]
[1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241]
[1242]
Underfull \hbox (badness 1852) in paragraph at lines 9765--9769
[]\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.,
[1243] [1244] [1245] [1246]) (./parallel-pkg.tex
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 15--17
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]
[1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
Underfull \hbox (badness 3386) in paragraph at lines 1254--1257
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1267] [1268]) (./splines-pkg.tex
Chapter 9.

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279]
[1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284]
Chapter 10.
[1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295]
[1296] [1297]
Underfull \hbox (badness 1412) in paragraph at lines 846--848
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305]
Underfull \hbox (badness 2503) in paragraph at lines 1327--1330
[]\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 ,
[1306] [1307] [1308]
Underfull \hbox (badness 10000) in paragraph at lines 1506--1510
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]
Underfull \hbox (badness 3965) in paragraph at lines 2166--2168
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1320] [1321] [1322] [1323] [1324]
Underfull \hbox (badness 3965) in paragraph at lines 2508--2510
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335]
[1336] [1337]
Underfull \hbox (badness 2503) in paragraph at lines 3325--3328
[]\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 ,
[1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348]
[1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
Underfull \hbox (badness 3989) in paragraph at lines 4553--4560
[]\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 =
[1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367]
Underfull \hbox (badness 2556) in paragraph at lines 5164--5167
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5181--5183
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1368] [1369] [1370] [1371]
Underfull \hbox (badness 1142) in paragraph at lines 5422--5434
\T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is
 un-usual but avail-able for the sake of com-plete-ness.
[1372] [1373]
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[]\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 ,
[1374]
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[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1375] [1376] [1377] [1378] [1379] [1380] [1381]
Underfull \hbox (badness 8132) in paragraph at lines 6064--6069
\T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa
me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node,
[1382] [1383] [1384] [1385] [1386]
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[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 10000) in paragraph at lines 6346--6348
[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
[1387] [1388] [1389] [1390] [1391]
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1400] [1401]
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[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht
tps : / / cran . r-[]project . org / web / views /
[1402] [1403] [1404] [1405]
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[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
[1427]
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[]\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 ,
[1428] [1429] [1430] [1431] [1432]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443]
[1444] [1445] [1446] [1447]
Underfull \hbox (badness 4518) in paragraph at lines 10155--10160
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1448] [1449] [1450] [1451]
Underfull \hbox (badness 2142) in paragraph at lines 10497--10500
[]\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 ^^@
[1452]
Underfull \hbox (badness 1253) in paragraph at lines 10516--10519
[]\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,
[1453]
Underfull \hbox (badness 1708) in paragraph at lines 10578--10582
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1454] [1455] [1456] [1457] [1458] [1459]
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[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to

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\T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th
e or-der-ing of the cor-re-
[1460] [1461] [1462] [1463] [1464]
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[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
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l.11454 \aliasA{hat}{influence.measures}{hat}
                                              [1468] [1469]
Underfull \hbox (badness 1484) in paragraph at lines 11577--11579
[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478]
Underfull \hbox (badness 4441) in paragraph at lines 12135--12137
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

Underfull \hbox (badness 10000) in paragraph at lines 12142--12144
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1479] [1480] [1481] [1482] [1483] [1484]
Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495]
[1496]
Underfull \hbox (badness 4518) in paragraph at lines 13171--13176
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1506] [1507] [1508]
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[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface =

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[]\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
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[]\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 ,
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[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1
/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
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[]\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

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[]\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

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\T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

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[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
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[]\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
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[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

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[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
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[]\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 ,
[1605]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
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Underfull \hbox (badness 10000) in paragraph at lines 20863--20869
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
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[1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643]
[1644]
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[]\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
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[1656] [1657]
Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666]
Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1667]
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[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
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Underfull \hbox (badness 3439) in paragraph at lines 24089--24095
[][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO
rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1
0 ,
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1679]
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\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
[1680] [1681] [1682] [1683] [1684] [1685] [1686]
Underfull \hbox (badness 10000) in paragraph at lines 24757--24762
[]\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
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Underfull \hbox (badness 3514) in paragraph at lines 25775--25780
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1703]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
Underfull \hbox (badness 3514) in paragraph at lines 25894--25899
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1705]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1706] [1707] [1708] [1709]
Underfull \hbox (badness 3514) in paragraph at lines 26168--26173
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1711]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1712]
Underfull \hbox (badness 3514) in paragraph at lines 26336--26341
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1713]
Underfull \hbox (badness 6691) in paragraph at lines 26405--26410
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722]
Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
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Underfull \hbox (badness 5431) in paragraph at lines 27535--27537
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1733] [1734] [1735]
Underfull \hbox (badness 5431) in paragraph at lines 27745--27748
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1736] [1737] [1738] [1739] [1740] [1741]
Underfull \hbox (badness 1337) in paragraph at lines 28057--28061
[]\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
[1742] [1743]
Underfull \hbox (badness 10000) in paragraph at lines 28174--28177
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1744] [1745]
Underfull \hbox (badness 1616) in paragraph at lines 28357--28360
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
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Underfull \hbox (badness 10000) in paragraph at lines 29483--29487
[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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[]\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
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[]\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]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
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[]\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or
[1786] [1787] [1788]) (./stats4-pkg.tex
Chapter 11.
[1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
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l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1795] [1796] [1797]
[1798]) (./tcltk-pkg.tex
Chapter 12.
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[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
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[][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1819]) (./tools-pkg.tex [1820]
Chapter 13.
[1821]

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[1822]
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[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1823] [1824]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

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\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

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\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

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\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1838]
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1839]
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[]\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

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


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\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
[1840] [1841] [1842]
Underfull \hbox (badness 10000) in paragraph at lines 1348--1350
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1843] [1844] [1845]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

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[]\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
[1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
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l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1850]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from

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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1857] [1858] [1859] [1860]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1861] [1862] [1863] [1864]

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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
[1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879]
[1880]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR
UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10
 DependsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
[1889] [1890]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and
[1891] [1892] [1893] [1894]) (./utils-pkg.tex
Chapter 14.
[1895]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1896] [1897]
Underfull \hbox (badness 1454) in paragraph at lines 197--200
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de-

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[]\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the
 same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault
[1898] [1899] [1900] [1901] [1902] [1903]
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[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1904]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

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\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1905]
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[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
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[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1923] [1924]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1925]
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

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[]\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1930] [1931] [1932] [1933] [1934] [1935]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing
[1936]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944]
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[]\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/
10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1
0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the
[1945]
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[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the

Underfull \hbox (badness 1231) in paragraph at lines 3289--3295
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
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[1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier
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<to be read again> 
                   \relax 
l.4109 ...mat Unordered and Ordered Lists}{format}
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                                                   [1960] [1961] [1962]
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[1974]
Underfull \hbox (badness 1371) in paragraph at lines 5062--5064
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1975]
Underfull \hbox (badness 1502) in paragraph at lines 5151--5156
[]\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 5151--5156
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1976] [1977] [1978]
Underfull \hbox (badness 10000) in paragraph at lines 5324--5333
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[1979]
Underfull \hbox (badness 2150) in paragraph at lines 5387--5390
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[1980] [1981]
Underfull \hbox (badness 3118) in paragraph at lines 5524--5526
[]\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
[1982]
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1983]
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[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able
[1984]
Underfull \hbox (badness 10000) in paragraph at lines 5748--5751
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed

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\T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac
k-age in-stall. E.g.,
[1985]
Underfull \hbox (badness 3219) in paragraph at lines 5821--5828
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/
10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-

Underfull \hbox (badness 5175) in paragraph at lines 5821--5828
\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 5821--5828
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1986]
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[][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/
10 ,
[1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997]
[1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007]
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[]\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
 al-low-ing things like

Underfull \hbox (badness 2310) in paragraph at lines 7208--7213
[]\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
 given pack-age is found and can suc-cess-fully be read,
[2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]
Underfull \hbox (badness 1789) in paragraph at lines 7758--7760
[]\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
[2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027]
[2028] [2029]
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[]\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b
e used on Win-dows, in which case
[2030]
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[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t
able[][][]\T1/ptm/m/n/10 ;
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[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
table[][][]\T1/ptm/m/n/10 ;
[2040] [2041] [2042] [2043] [2044] [2045] [2046]
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[]\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/
sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-

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\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see

Underfull \hbox (badness 2469) in paragraph at lines 9739--9743
[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia
, The Free En-cy-clo-pe-dia.

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[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2047] [2048] [2049] [2050] [2051] [2052]
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[]\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][]
[]\T1/ptm/m/n/10 s are nicely viewed via
[2053] [2054] [2055]
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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2056] [2057] [2058]
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[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n
ow taken from the en-vi-ron-ment vari-able

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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2059] [2060]
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[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether PNG fig-ures should be gen-er-ated. Ig-nored if

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[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether JPEG fig-ures should be gen-er-ated. Ig-nored if
[2061]
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[2062] [2063] [2064] [2065] [2066]
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[]\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1
/zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via

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[]\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp
e-cially: the value is taken from the cur-rent set-ting of
[2067] [2068] [2069] [2070] [2071] [2072]
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2073] [2074] [2075]
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[]\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n
/10 ap-ply only to files pro-duced by
[2076] [2077] [2078] [2079] [2080] [2081]
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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

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\T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9
2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX
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[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2091]
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[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see

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[][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av
ailable = NULL \T1/ptm/m/n/10 make a call to

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[][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package
s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n
/10 ,
[2092] [2093] [2094] [2095]
Overfull \hbox (25.86961pt too wide) in paragraph at lines 12764--12767
[][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi
-gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](<basename>, package = "<pkg
>")
[2096] [2097]
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[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[2098]
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
[2099] [2100] [2101]) [2102]
No file fullrefman.ind.
(./fullrefman.aux)

Package rerunfilecheck Warning: File `fullrefman.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Font Warning: Some font shapes were not available, defaults substituted.

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[72] [73] [74]
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move a

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\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
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[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[146] [147] [148] [149] [150]
Underfull \hbox (badness 1052) in paragraph at lines 9698--9703
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s
ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b
y \T1/zi4/m/n/10 R CMD check

Underfull \hbox (badness 1231) in paragraph at lines 9698--9703
\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z
i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[151] [152]
Underfull \hbox (badness 1735) in paragraph at lines 9836--9840
\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
zi4/m/n/10 https : / / en . wikipedia .
[153] [154] [155] [156] [157] [158]
Underfull \hbox (badness 2150) in paragraph at lines 10240--10243
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
[159]
Underfull \hbox (badness 6396) in paragraph at lines 10254--10262
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 2409) in paragraph at lines 10295--10302
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171]
[172] [173] [174] [175]
Underfull \hbox (badness 4569) in paragraph at lines 11341--11345
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 11341--11345
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[176] [177] [178] [179] [180] [181] [182] [183]
Underfull \hbox (badness 2698) in paragraph at lines 11917--11926
[]\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-lowed

Underfull \hbox (badness 4341) in paragraph at lines 11917--11926
\T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e
r-a-tions are those of
[184] [185] [186] [187] [188] [189] [190] [191] [192] [193]
Underfull \hbox (badness 6236) in paragraph at lines 12561--12564
[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
[194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 2253) in paragraph at lines 12939--12941
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[200]
Underfull \hbox (badness 1565) in paragraph at lines 13010--13014
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[201]
Underfull \hbox (badness 10000) in paragraph at lines 13054--13056
[]\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
[202] [203]
Underfull \hbox (badness 1466) in paragraph at lines 13195--13198
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[204] [205]
Underfull \hbox (badness 10000) in paragraph at lines 13303--13307
[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 13314--13317
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[206] [207] [208] [209]
Underfull \hbox (badness 3965) in paragraph at lines 13577--13581
[]\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,
[210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221]
Underfull \hbox (badness 4429) in paragraph at lines 14338--14341
[]\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
[222]
Underfull \hbox (badness 10000) in paragraph at lines 14430--14432
[]\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[223]
Underfull \hbox (badness 10000) in paragraph at lines 14478--14482
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use

Underfull \hbox (badness 4156) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[224]
Underfull \vbox (badness 3803) has occurred while \output is active [225]
[226] [227] [228] [229] [230] [231] [232]
Underfull \hbox (badness 2452) in paragraph at lines 15058--15062
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15058--15062
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[233] [234] [235]
Underfull \hbox (badness 1092) in paragraph at lines 15231--15236
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[236] [237] [238] [239]
Underfull \hbox (badness 6741) in paragraph at lines 15479--15483
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[240] [241] [242] [243]
Underfull \hbox (badness 1867) in paragraph at lines 15785--15792
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[244] [245] [246] [247]
Underfull \vbox (badness 10000) has occurred while \output is active [248]
[249]
Underfull \hbox (badness 3679) in paragraph at lines 16166--16168
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[250] [251] [252] [253] [254] [255] [256] [257]
Underfull \hbox (badness 1478) in paragraph at lines 16711--16714
[]\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
[258] [259] [260] [261]
Underfull \hbox (badness 10000) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1442) in paragraph at lines 17527--17529
[]\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
[271]
Underfull \hbox (badness 2452) in paragraph at lines 17619--17635
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[272] [273] [274] [275] [276] [277] [278]
Underfull \hbox (badness 1248) in paragraph at lines 18033--18036
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[279] [280] [281] [282]
Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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[295] [296] [297] [298]
Underfull \hbox (badness 1360) in paragraph at lines 19249--19254
\T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS
SL used, but not all

Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /

Underfull \hbox (badness 1127) in paragraph at lines 19272--19278
\T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S
SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv
/m/n/10 R
[299]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory

Underfull \hbox (badness 2460) in paragraph at lines 19345--19349
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[300] [301]
Underfull \hbox (badness 1509) in paragraph at lines 19480--19487
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1354) in paragraph at lines 19480--19487
\T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta
in just the names of all avail-able pack-ages, and

Underfull \hbox (badness 1014) in paragraph at lines 19496--19501
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313]
Underfull \hbox (badness 1264) in paragraph at lines 20227--20232
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
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Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\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
[325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336]
[337] [338] [339] [340]
Underfull \hbox (badness 1077) in paragraph at lines 21979--21985
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[341] [342] [343]
Underfull \hbox (badness 1484) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[344] [345] [346] [347]
Underfull \hbox (badness 2790) in paragraph at lines 22411--22414
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 22411--22414
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[348] [349] [350] [351]
Underfull \hbox (badness 1194) in paragraph at lines 22692--22695
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
[352] [353] [354] [355]
Underfull \hbox (badness 10000) in paragraph at lines 22898--22904
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 5862) in paragraph at lines 22898--22904
\T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE))
 \T1/ptm/m/n/10 which are also given by

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
[356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367]
[368] [369]
Underfull \hbox (badness 10000) in paragraph at lines 23839--23841
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[370] [371] [372] [373]
Underfull \hbox (badness 1199) in paragraph at lines 24066--24072
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][] \T1/zi4/m/n/10 "numeric"

Underfull \hbox (badness 2027) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \
T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F
ALSE \T1/ptm/m/n/10 oth-er-wise. That is,
[374] [375] [376] [377] [378] [379] [380] [381]
Underfull \hbox (badness 1038) in paragraph at lines 24645--24653
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1881) in paragraph at lines 24654--24657
[]\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 24673--24675
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[382]
Underfull \hbox (badness 10000) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 2142) in paragraph at lines 24756--24762
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 24769--24774
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[383] [384]
Underfull \vbox (badness 10000) has occurred while \output is active [385]
Underfull \hbox (badness 10000) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[386]
Underfull \hbox (badness 10000) in paragraph at lines 25047--25050
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 25071--25073
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 1629) in paragraph at lines 25109--25120
\T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi
4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an
d

Underfull \hbox (badness 7203) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[387]
Underfull \hbox (badness 4084) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN OS X build),

Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
\T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric
ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C
RAN

Underfull \hbox (badness 7397) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m
/n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1082) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[388] [389] [390] [391] [392]
Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n
/10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
\T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[393] [394] [395] [396] [397]
Underfull \hbox (badness 1735) in paragraph at lines 25809--25813
[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\
T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu
e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which
[398] [399] [400] [401] [402] [403] [404] [405] [406]
Underfull \hbox (badness 2726) in paragraph at lines 26369--26372
[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418]
[419]
Underfull \hbox (badness 1052) in paragraph at lines 27186--27191
[]\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1
0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide
d
[420] [421] [422] [423] [424]
Underfull \vbox (badness 10000) has occurred while \output is active [425]
[426] [427] [428] [429] [430] [431]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[432] [433] [434]
Underfull \hbox (badness 1163) in paragraph at lines 28157--28168
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446]
[447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 29676--29680
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 1221) in paragraph at lines 29676--29680
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[459] [460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 1655) in paragraph at lines 30246--30248
[]\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
[468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
[479] [480] [481]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 2980) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[482] [483] [484]
Underfull \hbox (badness 2261) in paragraph at lines 31310--31315
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[485]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
[486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497]
[498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509]
[510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521]
[522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
Underfull \hbox (badness 1072) in paragraph at lines 34333--34337
[]\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 34338--34342
[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 3343) in paragraph at lines 34379--34386
\T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment 
vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 34379--34386
\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 34379--34386
\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
[532] [533] [534] [535] [536]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1152) in paragraph at lines 34670--34676
\T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c
om-po-nent which is
[537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548]
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[561] [562] [563] [564] [565]
Underfull \hbox (badness 3333) in paragraph at lines 36500--36505
[]\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
[566] [567] [568] [569] [570] [571] [572] [573] [574] [575]
Underfull \hbox (badness 1472) in paragraph at lines 37120--37123
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586]
Underfull \hbox (badness 2671) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 10000) in paragraph at lines 38200--38203
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[593] [594]
Underfull \hbox (badness 10000) in paragraph at lines 38318--38322
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[595]
Underfull \hbox (badness 10000) in paragraph at lines 38380--38384
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607]
[608] [609] [610] [611] [612] [613] [614] [615]
Underfull \hbox (badness 1990) in paragraph at lines 39706--39714
[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 4846) in paragraph at lines 39706--39714
\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
[616] [617] [618] [619]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[620] [621] [622] [623]
Underfull \hbox (badness 1917) in paragraph at lines 40208--40215
[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
[624] [625] [626] [627] [628] [629] [630] [631] [632] [633]
Underfull \hbox (badness 3668) in paragraph at lines 40869--40871
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[634] [635]
Underfull \hbox (badness 2401) in paragraph at lines 40974--40978
[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
[636] [637]
Underfull \hbox (badness 2111) in paragraph at lines 41143--41148
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.
[638]
Underfull \hbox (badness 6542) in paragraph at lines 41159--41164
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[639] [640] [641] [642] [643] [644] [645]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/zi4/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
[646]
Underfull \hbox (badness 5417) in paragraph at lines 41696--41700
[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[647]
Underfull \hbox (badness 10000) in paragraph at lines 41757--41761
[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[648] [649]) (./compiler-pkg.tex [650]
Chapter 2.
[651] [652] [653] [654]) (./datasets-pkg.tex
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666]
[667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678]
[679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690]
[691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701]
Underfull \vbox (badness 1515) has occurred while \output is active [702]
[703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714]
[715] [716] [717] [718] [719] [720] [721]
Underfull \hbox (badness 6658) in paragraph at lines 3940--3942
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h
ttp : / / www . ltrr . arizona . edu / ~hallman /
[722]
Underfull \vbox (badness 10000) has occurred while \output is active [723]
[724] [725] [726]
Underfull \vbox (badness 10000) has occurred while \output is active [727]
Underfull \vbox (badness 10000) has occurred while \output is active [728]
[729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736]
Chapter 4.
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750] [751] [752] [753]
Underfull \hbox (badness 5175) in paragraph at lines 1071--1073
[]\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
[754] [755] [756] [757]
Underfull \hbox (badness 1852) in paragraph at lines 1268--1271
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[758] [759] [760]
Underfull \hbox (badness 1490) in paragraph at lines 1474--1479
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[761]
Underfull \hbox (badness 2698) in paragraph at lines 1528--1531
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[762]
Underfull \hbox (badness 10000) in paragraph at lines 1597--1601
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when
[763] [764] [765] [766]
Underfull \hbox (badness 1325) in paragraph at lines 1880--1890
\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[767] [768]
Underfull \hbox (badness 10000) in paragraph at lines 1985--1987
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[769] [770] [771]
Underfull \hbox (badness 6758) in paragraph at lines 2146--2149
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[772] [773] [774] [775] [776] [777] [778] [779] [780]
Underfull \hbox (badness 10000) in paragraph at lines 2712--2713

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Underfull \hbox (badness 1152) in paragraph at lines 3150--3152
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[788] [789] [790] [791] [792]
Underfull \hbox (badness 2856) in paragraph at lines 3470--3473
[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

Underfull \hbox (badness 2662) in paragraph at lines 3484--3486
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[793] [794]
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\
T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to 
\T1/zi4/m/n/10 width \T1/ptm/m/n/10 by
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\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
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[]\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[810]
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\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as

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\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

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\T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess
 to more char-ac-ters and

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\T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes
e eas-ier to re-mem-ber,

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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
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[]\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
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[]\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
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[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

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\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

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\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[816]
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[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

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\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
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[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
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[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
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[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[843] [844] [845]) (./graphics-pkg.tex [846]
Chapter 5.
[847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857]
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[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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\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
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
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[]\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
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
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\T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i
s ex-ited by the com-mand
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po
int
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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l.8735 \HeaderA{units}{Graphical Units}{units}
                                               [989] [990] [991] [992])
(./grid-pkg.tex
Chapter 6.

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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[]\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
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104]
Chapter 7.
[1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115]
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

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\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in
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\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
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[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

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[]\T1/ptm/m/n/10 The
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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[]\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

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\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
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\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

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\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and

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[]\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
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[]\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
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[]\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z
i4/m/n/10 initialize \T1/ptm/m/n/10 and
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\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
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l.6828 \aliasA{S4}{S3Part}{S4}
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                                                 [1205]
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[]\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
[1206] [1207] [1208]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219]
[1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230]
[1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241]
[1242]
Underfull \hbox (badness 1852) in paragraph at lines 9765--9769
[]\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.,
[1243] [1244] [1245] [1246]) (./parallel-pkg.tex
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 15--17
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]
[1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
Underfull \hbox (badness 3386) in paragraph at lines 1254--1257
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1267] [1268]) (./splines-pkg.tex
Chapter 9.

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279]
[1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284]
Chapter 10.
[1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295]
[1296] [1297]
Underfull \hbox (badness 1412) in paragraph at lines 846--848
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305]
Underfull \hbox (badness 2503) in paragraph at lines 1327--1330
[]\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 ,
[1306] [1307] [1308]
Underfull \hbox (badness 10000) in paragraph at lines 1506--1510
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]
Underfull \hbox (badness 3965) in paragraph at lines 2166--2168
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1320] [1321] [1322] [1323] [1324]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335]
[1336] [1337]
Underfull \hbox (badness 2503) in paragraph at lines 3325--3328
[]\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 ,
[1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348]
[1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
Underfull \hbox (badness 3989) in paragraph at lines 4553--4560
[]\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 =
[1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367]
Underfull \hbox (badness 2556) in paragraph at lines 5164--5167
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5181--5183
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1368] [1369] [1370] [1371]
Underfull \hbox (badness 1142) in paragraph at lines 5422--5434
\T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is
 un-usual but avail-able for the sake of com-plete-ness.
[1372] [1373]
Underfull \hbox (badness 2503) in paragraph at lines 5561--5565
[]\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 ,
[1374]
Underfull \hbox (badness 1168) in paragraph at lines 5622--5627
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1375] [1376] [1377] [1378] [1379] [1380] [1381]
Underfull \hbox (badness 8132) in paragraph at lines 6064--6069
\T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa
me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node,
[1382] [1383] [1384] [1385] [1386]
Underfull \hbox (badness 7081) in paragraph at lines 6342--6345
[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 10000) in paragraph at lines 6346--6348
[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
[1387] [1388] [1389] [1390] [1391]
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[1393] [1394] [1395] [1396] [1397] [1398] [1399]
Underfull \hbox (badness 10000) in paragraph at lines 7159--7162
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1400] [1401]
Underfull \hbox (badness 10000) in paragraph at lines 7296--7299
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht
tps : / / cran . r-[]project . org / web / views /
[1402] [1403] [1404] [1405]
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[1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417]
[1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426]
Underfull \hbox (badness 2626) in paragraph at lines 8794--8797
[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
[1427]
Underfull \hbox (badness 2503) in paragraph at lines 8894--8898
[]\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 ,
[1428] [1429] [1430] [1431] [1432]
Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443]
[1444] [1445] [1446] [1447]
Underfull \hbox (badness 4518) in paragraph at lines 10155--10160
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1448] [1449] [1450] [1451]
Underfull \hbox (badness 2142) in paragraph at lines 10497--10500
[]\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 ^^@
[1452]
Underfull \hbox (badness 1253) in paragraph at lines 10516--10519
[]\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,
[1453]
Underfull \hbox (badness 1708) in paragraph at lines 10578--10582
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1454] [1455] [1456] [1457] [1458] [1459]
Underfull \hbox (badness 1694) in paragraph at lines 10974--10977
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to

Underfull \hbox (badness 1867) in paragraph at lines 10993--11002
\T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th
e or-der-ing of the cor-re-
[1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 11300--11303
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1465] [1466] [1467]pdfTeX warning (ext4): destination with the same identifier
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<to be read again> 
                   \relax 
l.11454 \aliasA{hat}{influence.measures}{hat}
                                              [1468] [1469]
Underfull \hbox (badness 1484) in paragraph at lines 11577--11579
[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478]
Underfull \hbox (badness 4441) in paragraph at lines 12135--12137
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

Underfull \hbox (badness 10000) in paragraph at lines 12142--12144
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1479] [1480] [1481] [1482] [1483] [1484]
Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495]
[1496]
Underfull \hbox (badness 4518) in paragraph at lines 13171--13176
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505]
Underfull \hbox (badness 4518) in paragraph at lines 13818--13823
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1506] [1507] [1508]
Underfull \hbox (badness 10000) in paragraph at lines 13956--13960
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface =

Underfull \hbox (badness 1199) in paragraph at lines 13963--13965
[]\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
[1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519]
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 2503) in paragraph at lines 15025--15029
[]\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 ,
[1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534]
Underfull \hbox (badness 1418) in paragraph at lines 15534--15540
[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1
/ptm/m/n/10 and
[1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
[1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556]
[1557] [1558] [1559]
Underfull \hbox (badness 2359) in paragraph at lines 17158--17160
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1560] [1561]
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[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574]
[1575]
Underfull \hbox (badness 1377) in paragraph at lines 18069--18074
[]\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 18074--18077
[]\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 1184) in paragraph at lines 18087--18091
\T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18095--18099
[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
[1576] [1577] [1578]
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[1580] [1581] [1582] [1583] [1584] [1585]
Underfull \hbox (badness 1337) in paragraph at lines 18711--18714
[]\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
[1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596]
[1597] [1598]
Underfull \hbox (badness 5563) in paragraph at lines 19441--19443
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

Underfull \hbox (badness 1194) in paragraph at lines 19444--19447
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1599] [1600] [1601] [1602] [1603] [1604]
Underfull \hbox (badness 2503) in paragraph at lines 19811--19814
[]\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 ,
[1605]
Underfull \hbox (badness 10000) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616]
[1617] [1618] [1619] [1620] [1621]
Underfull \hbox (badness 10000) in paragraph at lines 20863--20869
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632]
[1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643]
[1644]
Underfull \hbox (badness 1337) in paragraph at lines 22198--22204
[]\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
[1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655]
[1656] [1657]
Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666]
Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1667]
Underfull \hbox (badness 3690) in paragraph at lines 23619--23623
[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
[1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675]
Underfull \hbox (badness 3439) in paragraph at lines 24089--24095
[][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO
rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1
0 ,
[1676] [1677] [1678]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1679]
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\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
[1680] [1681] [1682] [1683] [1684] [1685] [1686]
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[]\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1703]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1705]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1706] [1707] [1708] [1709]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1711]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1712]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1713]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722]
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1733] [1734] [1735]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1736] [1737] [1738] [1739] [1740] [1741]
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[]\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
[1742] [1743]
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[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1744] [1745]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756]
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[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
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[1769] [1770]
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[]\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
[1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778]
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[]\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]
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
[1780] [1781] [1782] [1783] [1784] [1785]
Underfull \hbox (badness 10000) in paragraph at lines 30788--30793
[]\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or
[1786] [1787] [1788]) (./stats4-pkg.tex
Chapter 11.
[1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1795] [1796] [1797]
[1798]) (./tcltk-pkg.tex
Chapter 12.
[1799] [1800] [1801] [1802] [1803] [1804] [1805]
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Underfull \vbox (badness 10000) has occurred while \output is active [1807]
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[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818]
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[][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1819]) (./tools-pkg.tex [1820]
Chapter 13.
[1821]

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[1822]
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[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1823] [1824]
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[]\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

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\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

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\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

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\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1825] [1826]
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
[1838]
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1839]
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[]\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

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


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\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
[1840] [1841] [1842]
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1843] [1844] [1845]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

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[]\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
[1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1850]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from

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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
[1851] [1852] [1853] [1854] [1855] [1856]
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1857] [1858] [1859] [1860]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1861] [1862] [1863] [1864]

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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
[1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879]
[1880]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1881] [1882]
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1883] [1884] [1885] [1886]
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
[1887] [1888]
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR
UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10
 DependsList \T1/ptm/m/n/10 ob-ject

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\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
[1889] [1890]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and
[1891] [1892] [1893] [1894]) (./utils-pkg.tex
Chapter 14.
[1895]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1896] [1897]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de-

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[]\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the
 same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault
[1898] [1899] [1900] [1901] [1902] [1903]
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[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1904]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

Underfull \hbox (badness 4229) in paragraph at lines 657--663
\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1905]
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[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1916] [1917] [1918] [1919] [1920] [1921] [1922]
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[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1923] [1924]
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1925]
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1926] [1927] [1928] [1929]
Underfull \hbox (badness 1661) in paragraph at lines 2209--2216
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

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[]\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1930] [1931] [1932] [1933] [1934] [1935]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing
[1936]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944]
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[]\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/
10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1
0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the
[1945]
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(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] [3]
[4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]
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Chapter 1.

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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[1] [2]
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[]\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 .

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\T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1
/ptm/m/n/10 if

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\T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin
g \T1/ptm/m/n/10 is 0; oth-er-wise, it is

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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[3] [4] [5]
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[]\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]
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[]\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[7] [8]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ',
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[12] [13] [14] [15] [16] [17] [18]
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[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[19] [20] [21] [22]
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[]\T1/zi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/zi4/m/n/10 x mod y \T1/ptm/m
/n/10 and \T1/zi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I
t is guar-an-teed that
[23] [24] [25] [26] [27] [28] [29] [30]
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 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
[31] [32] [33]
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[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
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[49] [50] [51] [52] [53] [54] [55] [56]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71]
[72] [73] [74]
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[]\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
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[90] [91] [92]
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 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[93] [94] [95]
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[]\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca
n be spec-i-fied in sev-eral ways. The sim-plest is in
[96] [97] [98]
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[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : 
[99] [100]
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[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
[101] [102]
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-
move a

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\T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we
b-pages gen-er-ated by Mi-

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\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
[103]
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\T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z
i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
[104] [105]
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[107] [108] [109] [110] [111] [112] [113]
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\T1/zi4/m/n/10 status _ codes$[][] \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 .
[114]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h
igh-est, for
[115]
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 
getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed 
for

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[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[116] [117] [118] [119]
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[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[120] [121]
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[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),

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[][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods,
 [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i
t/10 Group \T1/ptm/m/n/10 meth-ods for
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[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[146] [147] [148] [149] [150]
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s
ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b
y \T1/zi4/m/n/10 R CMD check

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\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z
i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by
[151] [152]
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\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
zi4/m/n/10 https : / / en . wikipedia .
[153] [154] [155] [156] [157] [158]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse
[159]
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[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

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[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

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\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
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[]\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1
/ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a
l-lowed

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\T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e
r-a-tions are those of
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[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im-
ple-men-ta-tion as well as the ver-sion, for ex-am-ple
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[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[200]
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[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[201]
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[]\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
[202] [203]
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[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[204] [205]
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[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

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[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
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[]\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,
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[]\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
[222]
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[]\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides 
the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so

Underfull \hbox (badness 10000) in paragraph at lines 14436--14440
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[223]
Underfull \hbox (badness 10000) in paragraph at lines 14478--14482
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use

Underfull \hbox (badness 4156) in paragraph at lines 14478--14482
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[224]
Underfull \vbox (badness 3803) has occurred while \output is active [225]
[226] [227] [228] [229] [230] [231] [232]
Underfull \hbox (badness 2452) in paragraph at lines 15058--15062
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15058--15062
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
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Underfull \hbox (badness 1092) in paragraph at lines 15231--15236
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
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Underfull \hbox (badness 6741) in paragraph at lines 15479--15483
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
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Underfull \hbox (badness 1867) in paragraph at lines 15785--15792
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
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[249]
Underfull \hbox (badness 3679) in paragraph at lines 16166--16168
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[250] [251] [252] [253] [254] [255] [256] [257]
Underfull \hbox (badness 1478) in paragraph at lines 16711--16714
[]\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
[258] [259] [260] [261]
Underfull \hbox (badness 10000) in paragraph at lines 16964--16966
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1442) in paragraph at lines 17527--17529
[]\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
[271]
Underfull \hbox (badness 2452) in paragraph at lines 17619--17635
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[272] [273] [274] [275] [276] [277] [278]
Underfull \hbox (badness 1248) in paragraph at lines 18033--18036
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
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Underfull \hbox (badness 4739) in paragraph at lines 18291--18293
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
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[295] [296] [297] [298]
Underfull \hbox (badness 1360) in paragraph at lines 19249--19254
\T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS
SL used, but not all

Underfull \hbox (badness 10000) in paragraph at lines 19272--19278
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /

Underfull \hbox (badness 1127) in paragraph at lines 19272--19278
\T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S
SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv
/m/n/10 R
[299]
Underfull \hbox (badness 10000) in paragraph at lines 19345--19349
[]\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an
d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory

Underfull \hbox (badness 2460) in paragraph at lines 19345--19349
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[300] [301]
Underfull \hbox (badness 1509) in paragraph at lines 19480--19487
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1354) in paragraph at lines 19480--19487
\T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta
in just the names of all avail-able pack-ages, and

Underfull \hbox (badness 1014) in paragraph at lines 19496--19501
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313]
Underfull \hbox (badness 1264) in paragraph at lines 20227--20232
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
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Underfull \hbox (badness 10000) in paragraph at lines 20981--20983
[]\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
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[337] [338] [339] [340]
Underfull \hbox (badness 1077) in paragraph at lines 21979--21985
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
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Underfull \hbox (badness 1484) in paragraph at lines 22140--22148
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[344] [345] [346] [347]
Underfull \hbox (badness 2790) in paragraph at lines 22411--22414
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 22411--22414
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[348] [349] [350] [351]
Underfull \hbox (badness 1194) in paragraph at lines 22692--22695
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
[352] [353] [354] [355]
Underfull \hbox (badness 10000) in paragraph at lines 22898--22904
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 5862) in paragraph at lines 22898--22904
\T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE))
 \T1/ptm/m/n/10 which are also given by

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
[]\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute 
via the gen-eral rules:

Underfull \hbox (badness 10000) in paragraph at lines 22908--22911
\T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i
s eval-u-ated as
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[368] [369]
Underfull \hbox (badness 10000) in paragraph at lines 23839--23841
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[370] [371] [372] [373]
Underfull \hbox (badness 1199) in paragraph at lines 24066--24072
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/
10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode
[][][] \T1/zi4/m/n/10 "numeric"

Underfull \hbox (badness 2027) in paragraph at lines 24066--24072
\T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \
T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F
ALSE \T1/ptm/m/n/10 oth-er-wise. That is,
[374] [375] [376] [377] [378] [379] [380] [381]
Underfull \hbox (badness 1038) in paragraph at lines 24645--24653
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1881) in paragraph at lines 24654--24657
[]\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 24673--24675
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[382]
Underfull \hbox (badness 10000) in paragraph at lines 24745--24755
[]\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m
/n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 2142) in paragraph at lines 24756--24762
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 24769--24774
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 10000) in paragraph at lines 24779--24781
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[383] [384]
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Underfull \hbox (badness 10000) in paragraph at lines 25034--25040
[]\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 25034--25040
\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 25034--25040
\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
[386]
Underfull \hbox (badness 10000) in paragraph at lines 25047--25050
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 25071--25073
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 25103--25108
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 1629) in paragraph at lines 25109--25120
\T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi
4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an
d

Underfull \hbox (badness 7203) in paragraph at lines 25121--25124
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and
[387]
Underfull \hbox (badness 4084) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN OS X build),

Underfull \hbox (badness 10000) in paragraph at lines 25131--25143
\T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric
ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C
RAN

Underfull \hbox (badness 7397) in paragraph at lines 25131--25143
\T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m
/n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
[]\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda
te.packages[][][]\T1/ptm/m/n/10 . De-faults to

Underfull \hbox (badness 10000) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i
-ties to prompt for a

Underfull \hbox (badness 6380) in paragraph at lines 25145--25152
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1082) in paragraph at lines 25145--25152
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[388] [389] [390] [391] [392]
Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
[]\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n
/10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/
m/n/10 with di-men-sion

Underfull \hbox (badness 10000) in paragraph at lines 25491--25495
\T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 
A[c(arrayindex.x, arrayindex.y)]
[393] [394] [395] [396] [397]
Underfull \hbox (badness 1735) in paragraph at lines 25809--25813
[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\
T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu
e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which
[398] [399] [400] [401] [402] [403] [404] [405] [406]
Underfull \hbox (badness 2726) in paragraph at lines 26369--26372
[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418]
[419]
Underfull \hbox (badness 1052) in paragraph at lines 27186--27191
[]\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1
0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide
d
[420] [421] [422] [423] [424]
Underfull \vbox (badness 10000) has occurred while \output is active [425]
[426] [427] [428] [429] [430] [431]
Underfull \hbox (badness 1533) in paragraph at lines 27995--27998
[]\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
[432] [433] [434]
Underfull \hbox (badness 1163) in paragraph at lines 28157--28168
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446]
[447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 29676--29680
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 1221) in paragraph at lines 29676--29680
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 29698--29700
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[459] [460] [461] [462] [463] [464] [465] [466] [467]
Underfull \hbox (badness 1655) in paragraph at lines 30246--30248
[]\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
[468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478]
Underfull \hbox (badness 10000) in paragraph at lines 30914--30918
[]\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c
ur-rent workspace', i.e.,
[479] [480] [481]
Underfull \hbox (badness 2302) in paragraph at lines 31154--31161
[]\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d
e-fined as $[]$,

Underfull \hbox (badness 2837) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 2980) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 
, this is the same as the stan-dard de-vi-a-tion,

Underfull \hbox (badness 2181) in paragraph at lines 31154--31161
\T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti
ons with-out cen-ter-ing, use
[482] [483] [484]
Underfull \hbox (badness 2261) in paragraph at lines 31310--31315
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if

Underfull \hbox (badness 10000) in paragraph at lines 31337--31343
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[485]
Underfull \hbox (badness 10000) in paragraph at lines 31413--31418
[]\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r
a-tor and not a ter-mi-na-tor, read-ing a file by
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[498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509]
[510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521]
[522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
Underfull \hbox (badness 1072) in paragraph at lines 34333--34337
[]\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 34338--34342
[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

Underfull \hbox (badness 10000) in paragraph at lines 34366--34372
[]\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 34366--34372
\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 34366--34372
\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 3343) in paragraph at lines 34379--34386
\T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment 
vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 34379--34386
\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 34379--34386
\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
[532] [533] [534] [535] [536]
Underfull \hbox (badness 10000) in paragraph at lines 34670--34676
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1152) in paragraph at lines 34670--34676
\T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c
om-po-nent which is
[537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548]
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[561] [562] [563] [564] [565]
Underfull \hbox (badness 3333) in paragraph at lines 36500--36505
[]\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi
s may need to be matched ex-plic-itly: for ex-am-ple
[566] [567] [568] [569] [570] [571] [572] [573] [574] [575]
Underfull \hbox (badness 1472) in paragraph at lines 37120--37123
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586]
Underfull \hbox (badness 2671) in paragraph at lines 37785--37788
[]\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt
m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies
[587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 10000) in paragraph at lines 38200--38203
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[593] [594]
Underfull \hbox (badness 10000) in paragraph at lines 38318--38322
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[595]
Underfull \hbox (badness 10000) in paragraph at lines 38380--38384
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607]
[608] [609] [610] [611] [612] [613] [614] [615]
Underfull \hbox (badness 1990) in paragraph at lines 39706--39714
[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 4846) in paragraph at lines 39706--39714
\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
[616] [617] [618] [619]
Underfull \hbox (badness 1515) in paragraph at lines 39978--39983
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0
[620] [621] [622] [623]
Underfull \hbox (badness 1917) in paragraph at lines 40208--40215
[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
[624] [625] [626] [627] [628] [629] [630] [631] [632] [633]
Underfull \hbox (badness 3668) in paragraph at lines 40869--40871
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[634] [635]
Underfull \hbox (badness 2401) in paragraph at lines 40974--40978
[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
[636] [637]
Underfull \hbox (badness 2111) in paragraph at lines 41143--41148
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.
[638]
Underfull \hbox (badness 6542) in paragraph at lines 41159--41164
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[639] [640] [641] [642] [643] [644] [645]
Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
[]\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu
nc-tion than [][]\T1/zi4/m/n/10 rank[][][]

Underfull \hbox (badness 10000) in paragraph at lines 41604--41609
\T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim
-i-lar to
[646]
Underfull \hbox (badness 5417) in paragraph at lines 41696--41700
[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[647]
Underfull \hbox (badness 10000) in paragraph at lines 41757--41761
[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[648] [649]) (./compiler-pkg.tex [650]
Chapter 2.
[651] [652] [653] [654]) (./datasets-pkg.tex
Chapter 3.

Underfull \hbox (badness 10000) in paragraph at lines 12--14
[]\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple
te list, use
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666]
[667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678]
[679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690]
[691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701]
Underfull \vbox (badness 1515) has occurred while \output is active [702]
[703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714]
[715] [716] [717] [718] [719] [720] [721]
Underfull \hbox (badness 6658) in paragraph at lines 3940--3942
[]\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h
ttp : / / www . ltrr . arizona . edu / ~hallman /
[722]
Underfull \vbox (badness 10000) has occurred while \output is active [723]
[724] [725] [726]
Underfull \vbox (badness 10000) has occurred while \output is active [727]
Underfull \vbox (badness 10000) has occurred while \output is active [728]
[729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736]
Chapter 4.
[737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748]
[749] [750] [751] [752] [753]
Underfull \hbox (badness 5175) in paragraph at lines 1071--1073
[]\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
[754] [755] [756] [757]
Underfull \hbox (badness 1852) in paragraph at lines 1268--1271
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[758] [759] [760]
Underfull \hbox (badness 1490) in paragraph at lines 1474--1479
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[761]
Underfull \hbox (badness 2698) in paragraph at lines 1528--1531
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture,
 oth-er-wise a ma-trix of color names (for
[762]
Underfull \hbox (badness 10000) in paragraph at lines 1597--1601
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when
[763] [764] [765] [766]
Underfull \hbox (badness 1325) in paragraph at lines 1880--1890
\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[767] [768]
Underfull \hbox (badness 10000) in paragraph at lines 1985--1987
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[769] [770] [771]
Underfull \hbox (badness 6758) in paragraph at lines 2146--2149
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[772] [773] [774] [775] [776] [777] [778] [779] [780]
Underfull \hbox (badness 10000) in paragraph at lines 2712--2713

[781] [782] [783] [784] [785] [786] [787]
Underfull \hbox (badness 1152) in paragraph at lines 3150--3152
[]\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m
/n/10 giv-ing the num-ber of rows and columns, ful-fill-ing
[788] [789] [790] [791] [792]
Underfull \hbox (badness 2856) in paragraph at lines 3470--3473
[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as

Underfull \hbox (badness 2662) in paragraph at lines 3484--3486
[]\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/
n/10 ' field in the file. De-faults to
[793] [794]
Underfull \hbox (badness 1173) in paragraph at lines 3600--3610
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\
T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to 
\T1/zi4/m/n/10 width \T1/ptm/m/n/10 by
[795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805]
Underfull \hbox (badness 1067) in paragraph at lines 4307--4314
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[806] [807]
Underfull \hbox (badness 3364) in paragraph at lines 4468--4470
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
[808]
Underfull \hbox (badness 1789) in paragraph at lines 4545--4547
[]\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n
/10 com-ment in the file. De-faults to
[809]
Underfull \hbox (badness 1377) in paragraph at lines 4595--4600
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[810]
Underfull \hbox (badness 2671) in paragraph at lines 4622--4630
\T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/
m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as

Underfull \hbox (badness 1418) in paragraph at lines 4671--4678
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 2443) in paragraph at lines 4679--4688
\T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess
 to more char-ac-ters and

Underfull \hbox (badness 2653) in paragraph at lines 4679--4688
\T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes
e eas-ier to re-mem-ber,

Underfull \hbox (badness 1755) in paragraph at lines 4689--4691
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[811] [812]
Underfull \hbox (badness 1057) in paragraph at lines 4800--4805
[]\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
[813]
Underfull \hbox (badness 7344) in paragraph at lines 4860--4862
[]\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
[814] [815]
Underfull \hbox (badness 2035) in paragraph at lines 4984--4993
[]\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 4984--4993
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 4984--4993
\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[816]
Underfull \hbox (badness 10000) in paragraph at lines 5053--5060
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5053--5060
\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
[817] [818] [819]
Underfull \hbox (badness 1546) in paragraph at lines 5195--5203
[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
[820]
Underfull \hbox (badness 1648) in paragraph at lines 5272--5276
[]\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on
ly), de-fault
[821] [822] [823] [824] [825] [826] [827]
Underfull \hbox (badness 10000) in paragraph at lines 5724--5727
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[828] [829] [830] [831] [832] [833]
Underfull \hbox (badness 1189) in paragraph at lines 6121--6123
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[834] [835]
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[843] [844] [845]) (./graphics-pkg.tex [846]
Chapter 5.
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[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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\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
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[]\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol
s given by
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[]\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat
a con-tain
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[]\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
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
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[925]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
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\T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i
s ex-ited by the com-mand
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po
int
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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                                               [989] [990] [991] [992])
(./grid-pkg.tex
Chapter 6.

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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[]\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
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104]
Chapter 7.
[1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115]
[1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124]
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

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\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
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[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in
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\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
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[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

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[]\T1/ptm/m/n/10 The
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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[]\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

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\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
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\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

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\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and

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[]\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
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[]\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
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[]\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z
i4/m/n/10 initialize \T1/ptm/m/n/10 and
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\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
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[]\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
[1206] [1207] [1208]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219]
[1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230]
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[1242]
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[]\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.,
[1243] [1244] [1245] [1246]) (./parallel-pkg.tex
Chapter 8.

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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]
[1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266]
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[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1267] [1268]) (./splines-pkg.tex
Chapter 9.

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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279]
[1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284]
Chapter 10.
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[1296] [1297]
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
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[]\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 ,
[1306] [1307] [1308]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
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[1336] [1337]
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[]\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 ,
[1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348]
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[]\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 =
[1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367]
Underfull \hbox (badness 2556) in paragraph at lines 5164--5167
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5181--5183
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1368] [1369] [1370] [1371]
Underfull \hbox (badness 1142) in paragraph at lines 5422--5434
\T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is
 un-usual but avail-able for the sake of com-plete-ness.
[1372] [1373]
Underfull \hbox (badness 2503) in paragraph at lines 5561--5565
[]\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 ,
[1374]
Underfull \hbox (badness 1168) in paragraph at lines 5622--5627
[]\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith
m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and
[1375] [1376] [1377] [1378] [1379] [1380] [1381]
Underfull \hbox (badness 8132) in paragraph at lines 6064--6069
\T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa
me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node,
[1382] [1383] [1384] [1385] [1386]
Underfull \hbox (badness 7081) in paragraph at lines 6342--6345
[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 10000) in paragraph at lines 6346--6348
[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
[1387] [1388] [1389] [1390] [1391]
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[1393] [1394] [1395] [1396] [1397] [1398] [1399]
Underfull \hbox (badness 10000) in paragraph at lines 7159--7162
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1400] [1401]
Underfull \hbox (badness 10000) in paragraph at lines 7296--7299
[]\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht
tps : / / cran . r-[]project . org / web / views /
[1402] [1403] [1404] [1405]
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[1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417]
[1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426]
Underfull \hbox (badness 2626) in paragraph at lines 8794--8797
[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
[1427]
Underfull \hbox (badness 2503) in paragraph at lines 8894--8898
[]\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 ,
[1428] [1429] [1430] [1431] [1432]
Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of
 homogeneity of variances"\T1/ptm/m/n/10 . 
[1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443]
[1444] [1445] [1446] [1447]
Underfull \hbox (badness 4518) in paragraph at lines 10155--10160
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1448] [1449] [1450] [1451]
Underfull \hbox (badness 2142) in paragraph at lines 10497--10500
[]\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 ^^@
[1452]
Underfull \hbox (badness 1253) in paragraph at lines 10516--10519
[]\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,
[1453]
Underfull \hbox (badness 1708) in paragraph at lines 10578--10582
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1454] [1455] [1456] [1457] [1458] [1459]
Underfull \hbox (badness 1694) in paragraph at lines 10974--10977
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to

Underfull \hbox (badness 1867) in paragraph at lines 10993--11002
\T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th
e or-der-ing of the cor-re-
[1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 11300--11303
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1465] [1466] [1467]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11454 \aliasA{hat}{influence.measures}{hat}
                                              [1468] [1469]
Underfull \hbox (badness 1484) in paragraph at lines 11577--11579
[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478]
Underfull \hbox (badness 4441) in paragraph at lines 12135--12137
[]\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is
 fit-ted to

Underfull \hbox (badness 10000) in paragraph at lines 12142--12144
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when
[1479] [1480] [1481] [1482] [1483] [1484]
Underfull \hbox (badness 2894) in paragraph at lines 12476--12480
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495]
[1496]
Underfull \hbox (badness 4518) in paragraph at lines 13171--13176
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505]
Underfull \hbox (badness 4518) in paragraph at lines 13818--13823
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1506] [1507] [1508]
Underfull \hbox (badness 10000) in paragraph at lines 13956--13960
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface =

Underfull \hbox (badness 1199) in paragraph at lines 13963--13965
[]\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
[1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519]
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 2503) in paragraph at lines 15025--15029
[]\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 ,
[1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534]
Underfull \hbox (badness 1418) in paragraph at lines 15534--15540
[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1
/ptm/m/n/10 and
[1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
[1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556]
[1557] [1558] [1559]
Underfull \hbox (badness 2359) in paragraph at lines 17158--17160
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1560] [1561]
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Underfull \vbox (badness 10000) has occurred while \output is active [1563]
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574]
[1575]
Underfull \hbox (badness 1377) in paragraph at lines 18069--18074
[]\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 18074--18077
[]\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 1184) in paragraph at lines 18087--18091
\T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol
) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18095--18099
[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
[1576] [1577] [1578]
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[1580] [1581] [1582] [1583] [1584] [1585]
Underfull \hbox (badness 1337) in paragraph at lines 18711--18714
[]\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
[1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596]
[1597] [1598]
Underfull \hbox (badness 5563) in paragraph at lines 19441--19443
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read
y ex-ist-ing plot. Only valid for

Underfull \hbox (badness 1194) in paragraph at lines 19444--19447
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1599] [1600] [1601] [1602] [1603] [1604]
Underfull \hbox (badness 2503) in paragraph at lines 19811--19814
[]\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 ,
[1605]
Underfull \hbox (badness 10000) in paragraph at lines 19838--19840
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or
[1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616]
[1617] [1618] [1619] [1620] [1621]
Underfull \hbox (badness 10000) in paragraph at lines 20863--20869
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632]
[1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643]
[1644]
Underfull \hbox (badness 1337) in paragraph at lines 22198--22204
[]\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
[1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655]
[1656] [1657]
Underfull \hbox (badness 10000) in paragraph at lines 22991--22994
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666]
Underfull \hbox (badness 10000) in paragraph at lines 23568--23571
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x, k) \T1/ptm/m/n/10 sim-ply has
[1667]
Underfull \hbox (badness 3690) in paragraph at lines 23619--23623
[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
[1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675]
Underfull \hbox (badness 3439) in paragraph at lines 24089--24095
[][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO
rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1
0 ,
[1676] [1677] [1678]
Underfull \hbox (badness 1867) in paragraph at lines 24286--24288
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1679]
Underfull \hbox (badness 10000) in paragraph at lines 24299--24301
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback =
 use.fallback) \T1/ptm/m/n/10 and
[1680] [1681] [1682] [1683] [1684] [1685] [1686]
Underfull \hbox (badness 10000) in paragraph at lines 24757--24762
[]\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi
v-ing the num-ber of knots to use when
[1687] [1688] [1689]
Underfull \vbox (badness 3803) has occurred while \output is active [1690]
[1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701]
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Underfull \hbox (badness 3514) in paragraph at lines 25775--25780
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1703]
Underfull \hbox (badness 3514) in paragraph at lines 25837--25842
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1704]
Underfull \hbox (badness 3514) in paragraph at lines 25894--25899
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1705]
Underfull \hbox (badness 3514) in paragraph at lines 25955--25961
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1706] [1707] [1708] [1709]
Underfull \hbox (badness 3514) in paragraph at lines 26168--26173
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1710]
Underfull \hbox (badness 3514) in paragraph at lines 26224--26229
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1711]
Underfull \hbox (badness 3514) in paragraph at lines 26281--26286
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1712]
Underfull \hbox (badness 3514) in paragraph at lines 26336--26341
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1713]
Underfull \hbox (badness 6691) in paragraph at lines 26405--26410
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722]
Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-

Underfull \hbox (badness 10000) in paragraph at lines 26929--26932
\T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/
n/10 , the de-fault,
[1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732]
Underfull \hbox (badness 5431) in paragraph at lines 27535--27537
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1733] [1734] [1735]
Underfull \hbox (badness 5431) in paragraph at lines 27745--27748
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1736] [1737] [1738] [1739] [1740] [1741]
Underfull \hbox (badness 1337) in paragraph at lines 28057--28061
[]\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
[1742] [1743]
Underfull \hbox (badness 10000) in paragraph at lines 28174--28177
[]\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/
10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for
[1744] [1745]
Underfull \hbox (badness 1616) in paragraph at lines 28357--28360
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756]
[1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764]
Underfull \hbox (badness 10000) in paragraph at lines 29483--29487
[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect
[1765] [1766] [1767]
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[1769] [1770]
Underfull \hbox (badness 1337) in paragraph at lines 29847--29851
[]\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
[1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778]
Underfull \hbox (badness 1337) in paragraph at lines 30331--30335
[]\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
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[]\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if
 ar-gu-ment
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[]\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co
n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or
[1786] [1787] [1788]) (./stats4-pkg.tex
Chapter 11.
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                                                   [1795] [1796] [1797]
[1798]) (./tcltk-pkg.tex
Chapter 12.
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[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
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[][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh
ose
[1819]) (./tools-pkg.tex [1820]
Chapter 13.
[1821]

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[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
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[]\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

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\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

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\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

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\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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[]\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i
g-nored when
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
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[]\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

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


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\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
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[]\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
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                                                   [1850]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE
\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De
pendsList \T1/ptm/m/n/10 ob-ject

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r in-stance if there was
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR
UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10
 DependsList \T1/ptm/m/n/10 ob-ject

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r in-stance if there was
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and
[1891] [1892] [1893] [1894]) (./utils-pkg.tex
Chapter 14.
[1895]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1896] [1897]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive
, \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de-

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[]\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the
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[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1904]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

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\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1905]
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[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
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[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
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[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
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[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

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[]\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing
[1936]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/
10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1
0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the
[1945]
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[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the

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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
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                                                   [1960] [1961] [1962]
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[1974]
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1975]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-

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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[1979]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
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[]\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
[1982]
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[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[1983]
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[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able
[1984]
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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be passed

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\T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac
k-age in-stall. E.g.,
[1985]
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[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/
10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-

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\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages

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\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[1986]
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[][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/
10 ,
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[]\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut,
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[]\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
 given pack-age is found and can suc-cess-fully be read,
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[]\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
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[]\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b
e used on Win-dows, in which case
[2030]
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[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t
able[][][]\T1/ptm/m/n/10 ;
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[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
table[][][]\T1/ptm/m/n/10 ;
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[]\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/
sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-

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\T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s
ub-set-ting, co-er-cion, etc, see

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[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia
, The Free En-cy-clo-pe-dia.

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[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
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[]\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][]
[]\T1/ptm/m/n/10 s are nicely viewed via
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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
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[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n
ow taken from the en-vi-ron-ment vari-able

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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether PNG fig-ures should be gen-er-ated. Ig-nored if

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[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether JPEG fig-ures should be gen-er-ated. Ig-nored if
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
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[]\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1
/zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via

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[]\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp
e-cially: the value is taken from the cur-rent set-ting of
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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
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[]\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n
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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

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\T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9
2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX
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[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
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[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see

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[][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av
ailable = NULL \T1/ptm/m/n/10 make a call to

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[][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package
s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n
/10 ,
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[][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi
-gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](<basename>, package = "<pkg
>")
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
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[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_results 

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make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/src/modules/X11'
make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
/«PKGBUILDDIR»/modules/R_X11.so is unchanged
/«PKGBUILDDIR»/modules/R_de.so is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile'
building system startup profile
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations'
building package 'translations'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
building package 'base'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
building package 'tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src'
../../../../library/tools/libs/tools.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
building package 'compiler'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
building package 'utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
all.R is unchanged
make[5]: Nothing to be done for 'iconvlist'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src'
../../../../library/utils/libs/utils.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
building package 'grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src'
../../../../library/grDevices/libs/grDevices.so is unchanged
make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[10]: 'cairo.so' is up to date.
make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
building package 'graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src'
../../../../library/graphics/libs/graphics.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
building package 'stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src'
../../../../library/stats/libs/stats.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets'
building package 'datasets'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
building package 'methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src'
../../../../library/methods/libs/methods.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods'
make[5]: Nothing to be done for 'RfilesLazy'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
building package 'grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src'
../../../../library/grid/libs/grid.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
building package 'splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src'
../../../../library/splines/libs/splines.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
building package 'stats4'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
building package 'tcltk'
all.R is unchanged
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src'
../../../../library/tcltk/libs/tcltk.so is unchanged
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
building package 'parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
all.R is unchanged
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
make[6]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[7]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src'
../../../../library/parallel/libs/parallel.so is unchanged
make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src'
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel'
make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
make[2]: Entering directory '/«PKGBUILDDIR»/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tests'
make[2]: Entering directory '/«PKGBUILDDIR»/doc'
make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual'
make[4]: Entering directory '/«PKGBUILDDIR»/doc/html'
make[4]: Leaving directory '/«PKGBUILDDIR»/doc/html'
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
make[2]: Leaving directory '/«PKGBUILDDIR»/doc'
make[2]: Entering directory '/«PKGBUILDDIR»/src/library'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
installing parsed Rd
make[4]: Entering directory '/«PKGBUILDDIR»/src/library'
  base
  stats
  utils
  methods
  graphics
  grDevices
  datasets
  grid
  tools
  tcltk
  splines
  stats4
  compiler
  parallel
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
building/updating package metadata ...
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
writing package indices
make[4]: Entering directory '/«PKGBUILDDIR»/src/library'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[2]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[2]: Entering directory '/«PKGBUILDDIR»/src/library/Recommended'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/«PKGBUILDDIR»/src/library/Recommended'
make[2]: Entering directory '/«PKGBUILDDIR»/src/library'
building/updating vignettes for package 'grid' ...
processing 'grid.Rnw'
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
make[2]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[1]: Leaving directory '/«PKGBUILDDIR»'
touch make-indep-stamp
*** check ***
xvfb-run make check-all
make[1]: Entering directory '/«PKGBUILDDIR»'
make[2]: Entering directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
make[4]: Entering directory '/«PKGBUILDDIR»/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’ ...
files differ in number of lines:
12223a12224,12231
> Warning: namespace 'MASS' is not available and has been replaced
> by .GlobalEnv when processing object ''
> predict.glmmPQL :
> 	 function (object, newdata = NULL, type = c("link", "response"),      level = Q, na.action = na.pass, ...)  NULL 
> Warning: namespace 'MASS' is not available and has been replaced
> by .GlobalEnv when processing object ''
> predict.lda :
> 	 function (object, newdata, prior = object$prior, dimen, method = c("plug-in",      "predictive", "debiased"), ...)  NULL 
12227a12236,12243
> Warning: namespace 'MASS' is not available and has been replaced
> by .GlobalEnv when processing object ''
> predict.lqs :
> 	 function (object, newdata, na.action = na.pass, ...)  NULL 
> Warning: namespace 'MASS' is not available and has been replaced
> by .GlobalEnv when processing object ''
> predict.mca :
> 	 function (object, newdata, type = c("row", "factor"), ...)  NULL 
12239a12256,12259
> Warning: namespace 'MASS' is not available and has been replaced
> by .GlobalEnv when processing object ''
> predict.polr :
> 	 function (object, newdata, type = c("class", "probs"), ...)  NULL 
12251a12272,12279
> Warning: namespace 'MASS' is not available and has been replaced
> by .GlobalEnv when processing object ''
> predict.qda :
> 	 function (object, newdata, prior = object$prior, method = c("plug-in",      "predictive", "debiased", "looCV"), ...)  NULL 
> Warning: namespace 'MASS' is not available and has been replaced
> by .GlobalEnv when processing object ''
> predict.rlm :
> 	 function (object, newdata = NULL, scale = NULL, ...)  NULL 
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 '/«PKGBUILDDIR»/tests/Examples'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running strict specific tests
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
running code in 'eval-etc.R' ... OK
  comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
running code in 'simple-true.R' ... OK
  comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK
running code in 'arith-true.R' ... OK
  comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK
running code in 'arith.R' ... OK
  comparing 'arith.Rout' to './arith.Rout.save' ... OK
running code in 'lm-tests.R' ... OK
  comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
running code in 'ok-errors.R' ... OK
  comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
running code in 'method-dispatch.R' ... OK
  comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'any-all.R' ... OK
  comparing 'any-all.Rout' to './any-all.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ... OK
  comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
running sloppy specific tests
make[4]: Entering directory '/«PKGBUILDDIR»/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' ...405,409c405,409
< [1,] -0.4023  0.2877 -0.3638  0.5  0.6108
< [2,] -0.5338 -0.3474 -0.5742 -0.5 -0.1207
< [3,] -0.4177 -0.5380  0.6384  0.0  0.3585
< [4,] -0.4959  0.0733  0.1273  0.5 -0.6946
< [5,] -0.3644  0.7084  0.3378 -0.5  0.0369
---
> [1,] -0.4023  0.2877  0.3638  0.5  0.6108
> [2,] -0.5338 -0.3474  0.5742 -0.5 -0.1207
> [3,] -0.4177 -0.5380 -0.6384  0.0  0.3585
> [4,] -0.4959  0.0733 -0.1273  0.5 -0.6946
> [5,] -0.3644  0.7084 -0.3378 -0.5  0.0369
 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 '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running regression tests ...
make[4]: Entering directory '/«PKGBUILDDIR»/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-2.R' ... OK
  comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'p-qbeta-strict-tst.R' ... OK
running code in 'r-strict-tst.R' ... OK
running code in 'reg-IO.R' ... OK
  comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK
running code in 'reg-IO2.R' ... OK
  comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK
running code in 'reg-plot.R' ... OK
  comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK
running code in 'reg-S4.R' ... OK
  comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK
running code in 'reg-BLAS.R' ... OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[4]: Entering directory '/«PKGBUILDDIR»/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' ... OK
  comparing 'reg-plot-latin1.pdf' to './reg-plot-latin1.pdf.save' ... OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running tests of Internet functions
  expect some differences
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
running code in 'internet.R' ... OK
  comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247
< Warning message:
< In nsl("cran.r-project.org") :
<   nsl() was unable to resolve host 'cran.r-project.org'
---
> > 
> > # test do_download.
> > nrow(available.packages(contrib.url("http://cran.r-project.org")))
> [1] 8269
> > 
> > # test url connections on http
> > zz <- url("http://cran.r-project.org/")
> > readLines(zz)
>  [1] "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">"
>  [2] "<html>"                                                                                                   
>  [3] "<head>"                                                                                                   
>  [4] "<title>The Comprehensive R Archive Network</title>"                                                       
>  [5] "<META HTTP-EQUIV=\"content-type\" CONTENT=\"text/html; charset=utf-8\">"                                  
>  [6] "<link rel=\"icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                           
>  [7] "<link rel=\"shortcut icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                  
>  [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"                                               
>  [9] "</head>"                                                                                                  
> [10] ""                                                                                                         
> [11] "<FRAMESET cols=\"1*, 4*\" style=\"border: none;\">"                                                       
> [12] "<FRAMESET rows=\"120, 1*\">"                                                                              
> [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>"                                                    
> [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>"                                              
> [15] "</FRAMESET>"                                                                                              
> [16] "<FRAME src=\"banner.shtml\" name=\"banner\" frameborder=0>"                                               
> [17] "<noframes>"                                                                                               
> [18] "<h1>The Comprehensive R Archive Network</h1>"                                                             
> [19] ""                                                                                                         
> [20] "Your browser seems not to support frames,"                                                                
> [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN."                                           
> [22] "</noframes>"                                                                                              
> [23] "</FRAMESET>"                                                                                              
> > close(zz)
> > 
> > # and via read.table, test http and ftp.
> > 
> > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
>      V1  V2   V3    V4 V5
> 1     1 307  930 36.58  0
> 2     2 307  940 36.73  0
> 3     3 307  950 36.93  0
> 4     4 307 1000 37.15  0
> 5     5 307 1010 37.23  0
> 6     6 307 1020 37.24  0
> 7     7 307 1030 37.24  0
> 8     8 307 1040 36.90  0
> 9     9 307 1050 36.95  0
> 10   10 307 1100 36.89  0
> 11   11 307 1110 36.95  0
> 12   12 307 1120 37.00  0
> 13   13 307 1130 36.90  0
> 14   14 307 1140 36.99  0
> 15   15 307 1150 36.99  0
> 16   16 307 1200 37.01  0
> 17   17 307 1210 37.04  0
> 18   18 307 1220 37.04  0
> 19   19 307 1230 37.14  0
> 20   20 307 1240 37.07  0
> 21   21 307 1250 36.98  0
> 22   22 307 1300 37.01  0
> 23   23 307 1310 36.97  0
> 24   24 307 1320 36.97  0
> 25   25 307 1330 37.12  0
> 26   26 307 1340 37.13  0
> 27   27 307 1350 37.14  0
> 28   28 307 1400 37.15  0
> 29   29 307 1410 37.17  0
> 30   30 307 1420 37.12  0
> 31   31 307 1430 37.12  0
> 32   32 307 1440 37.17  0
> 33   33 307 1450 37.28  0
> 34   34 307 1500 37.28  0
> 35   35 307 1510 37.44  0
> 36   36 307 1520 37.51  0
> 37   37 307 1530 37.64  0
> 38   38 307 1540 37.51  0
> 39   39 307 1550 37.98  1
> 40   40 307 1600 38.02  1
> 41   41 307 1610 38.00  1
> 42   42 307 1620 38.24  1
> 43   43 307 1630 38.10  1
> 44   44 307 1640 38.24  1
> 45   45 307 1650 38.11  1
> 46   46 307 1700 38.02  1
> 47   47 307 1710 38.11  1
> 48   48 307 1720 38.01  1
> 49   49 307 1730 37.91  1
> 50   50 307 1740 37.96  1
> 51   51 307 1750 38.03  1
> 52   52 307 1800 38.17  1
> 53   53 307 1810 38.19  1
> 54   54 307 1820 38.18  1
> 55   55 307 1830 38.15  1
> 56   56 307 1840 38.04  1
> 57   57 307 1850 37.96  1
> 58   58 307 1900 37.84  1
> 59   59 307 1910 37.83  1
> 60   60 307 1920 37.84  1
> 61   61 307 1930 37.74  1
> 62   62 307 1940 37.76  1
> 63   63 307 1950 37.76  1
> 64   64 307 2000 37.64  1
> 65   65 307 2010 37.63  1
> 66   66 307 2020 38.06  1
> 67   67 307 2030 38.19  1
> 68   68 307 2040 38.35  1
> 69   69 307 2050 38.25  1
> 70   70 307 2100 37.86  1
> 71   71 307 2110 37.95  1
> 72   72 307 2120 37.95  1
> 73   73 307 2130 37.76  1
> 74   74 307 2140 37.60  1
> 75   75 307 2150 37.89  1
> 76   76 307 2200 37.86  1
> 77   77 307 2210 37.71  1
> 78   78 307 2220 37.78  1
> 79   79 307 2230 37.82  1
> 80   80 307 2240 37.76  1
> 81   81 307 2250 37.81  1
> 82   82 307 2300 37.84  1
> 83   83 307 2310 38.01  1
> 84   84 307 2320 38.10  1
> 85   85 307 2330 38.15  1
> 86   86 307 2340 37.92  1
> 87   87 307 2350 37.64  1
> 88   88 308    0 37.70  1
> 89   89 308   10 37.46  1
> 90   90 308   20 37.41  1
> 91   91 308   30 37.46  1
> 92   92 308   40 37.56  1
> 93   93 308   50 37.55  1
> 94   94 308  100 37.75  1
> 95   95 308  110 37.76  1
> 96   96 308  120 37.73  1
> 97   97 308  130 37.77  1
> 98   98 308  140 38.01  1
> 99   99 308  150 38.04  1
> 100 100 308  200 38.07  1
> > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
>      V1  V2   V3    V4 V5
> 1     1 307  930 36.58  0
> 2     2 307  940 36.73  0
> 3     3 307  950 36.93  0
> 4     4 307 1000 37.15  0
> 5     5 307 1010 37.23  0
> 6     6 307 1020 37.24  0
> 7     7 307 1030 37.24  0
> 8     8 307 1040 36.90  0
> 9     9 307 1050 36.95  0
> 10   10 307 1100 36.89  0
> 11   11 307 1110 36.95  0
> 12   12 307 1120 37.00  0
> 13   13 307 1130 36.90  0
> 14   14 307 1140 36.99  0
> 15   15 307 1150 36.99  0
> 16   16 307 1200 37.01  0
> 17   17 307 1210 37.04  0
> 18   18 307 1220 37.04  0
> 19   19 307 1230 37.14  0
> 20   20 307 1240 37.07  0
> 21   21 307 1250 36.98  0
> 22   22 307 1300 37.01  0
> 23   23 307 1310 36.97  0
> 24   24 307 1320 36.97  0
> 25   25 307 1330 37.12  0
> 26   26 307 1340 37.13  0
> 27   27 307 1350 37.14  0
> 28   28 307 1400 37.15  0
> 29   29 307 1410 37.17  0
> 30   30 307 1420 37.12  0
> 31   31 307 1430 37.12  0
> 32   32 307 1440 37.17  0
> 33   33 307 1450 37.28  0
> 34   34 307 1500 37.28  0
> 35   35 307 1510 37.44  0
> 36   36 307 1520 37.51  0
> 37   37 307 1530 37.64  0
> 38   38 307 1540 37.51  0
> 39   39 307 1550 37.98  1
> 40   40 307 1600 38.02  1
> 41   41 307 1610 38.00  1
> 42   42 307 1620 38.24  1
> 43   43 307 1630 38.10  1
> 44   44 307 1640 38.24  1
> 45   45 307 1650 38.11  1
> 46   46 307 1700 38.02  1
> 47   47 307 1710 38.11  1
> 48   48 307 1720 38.01  1
> 49   49 307 1730 37.91  1
> 50   50 307 1740 37.96  1
> 51   51 307 1750 38.03  1
> 52   52 307 1800 38.17  1
> 53   53 307 1810 38.19  1
> 54   54 307 1820 38.18  1
> 55   55 307 1830 38.15  1
> 56   56 307 1840 38.04  1
> 57   57 307 1850 37.96  1
> 58   58 307 1900 37.84  1
> 59   59 307 1910 37.83  1
> 60   60 307 1920 37.84  1
> 61   61 307 1930 37.74  1
> 62   62 307 1940 37.76  1
> 63   63 307 1950 37.76  1
> 64   64 307 2000 37.64  1
> 65   65 307 2010 37.63  1
> 66   66 307 2020 38.06  1
> 67   67 307 2030 38.19  1
> 68   68 307 2040 38.35  1
> 69   69 307 2050 38.25  1
> 70   70 307 2100 37.86  1
> 71   71 307 2110 37.95  1
> 72   72 307 2120 37.95  1
> 73   73 307 2130 37.76  1
> 74   74 307 2140 37.60  1
> 75   75 307 2150 37.89  1
> 76   76 307 2200 37.86  1
> 77   77 307 2210 37.71  1
> 78   78 307 2220 37.78  1
> 79   79 307 2230 37.82  1
> 80   80 307 2240 37.76  1
> 81   81 307 2250 37.81  1
> 82   82 307 2300 37.84  1
> 83   83 307 2310 38.01  1
> 84   84 307 2320 38.10  1
> 85   85 307 2330 38.15  1
> 86   86 307 2340 37.92  1
> 87   87 307 2350 37.64  1
> 88   88 308    0 37.70  1
> 89   89 308   10 37.46  1
> 90   90 308   20 37.41  1
> 91   91 308   30 37.46  1
> 92   92 308   40 37.56  1
> 93   93 308   50 37.55  1
> 94   94 308  100 37.75  1
> 95   95 308  110 37.76  1
> 96   96 308  120 37.73  1
> 97   97 308  130 37.77  1
> 98   98 308  140 38.01  1
> 99   99 308  150 38.04  1
> 100 100 308  200 38.07  1
> > 
 OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running tests of date-time printing
  expect platform-specific differences
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
running code in 'datetime2.R' ... OK
  comparing 'datetime2.Rout' to './datetime2.Rout.save' ...10,11c10,11
<  [1] "1890-01-10 13:00:00 CET" "1891-01-10 13:00:00 CET"
<  [3] "1892-01-10 13:00:00 CET" "1893-01-10 13:00:00 CET"
---
>  [1] "1890-01-10 12:49:56 RMT" "1891-01-10 12:49:56 RMT"
>  [3] "1892-01-10 12:49:56 RMT" "1893-01-10 12:49:56 RMT"
24c24
<  [1] "1890-01-10 12:09:21 PMT" "1891-01-10 12:09:21 PMT"
---
>  [1] "1890-01-10 12:09:21 LMT" "1891-01-10 12:09:21 LMT"
37c37
<  [1] "1890-01-10 12:09:21 PMT" "1891-01-10 12:09:21 PMT"
---
>  [1] "1890-01-10 12:09:21 LMT" "1891-01-10 12:09:21 LMT"
68c68
<  [1] "1890-01-10 12:09:21 PMT"  "1895-01-10 12:09:21 PMT" 
---
>  [1] "1890-01-10 12:09:21 LMT"  "1895-01-10 12:09:21 PMT" 
78c78
< [1] "1890-01-10 12:09:21 PMT"
---
> [1] "1890-01-10 12:09:21 LMT"
 OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running tests of documentation examples
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
running code in 'R-intro.R' ... OK
  comparing 'R-intro.Rout' to './R-intro.Rout.save' ... OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
gcc -std=gnu99 -I/«PKGBUILDDIR»/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R-exts.c -o R-exts.o
gcc -std=gnu99 -shared -L/«PKGBUILDDIR»/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R-exts.so R-exts.o -L/«PKGBUILDDIR»/lib -lR
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
running code in 'R-exts.R' ... OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running tests of consistency of as/is.*
make[4]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running tests of random deviate generation
make[4]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running demos from base and stats
make[4]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running tests of primitives
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
running code in 'primitives.R' ... OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running regexp regression tests
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running more Internet and socket tests
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
running code in 'internet2.R' ... OK
running code in 'libcurl.R' ... OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
running tests to possibly trigger segfaults
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
creating 'no-segfault.R'
running code in 'no-segfault.R' ... OK
make[4]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
testing building standalone Rmath
make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone'
check output can be found in src/nmath/standalone/check.log
make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
make[4]: Entering directory '/«PKGBUILDDIR»/tests'
checking package 'base'
* using log directory ‘/«PKGBUILDDIR»/tests/base.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... WARNING
Unknown packages ‘date’, ‘chron’, ‘nnet’, ‘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 examples ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/«PKGBUILDDIR»/tests/base.Rcheck/00check.log’
for details.


checking package 'tools'
* using log directory ‘/«PKGBUILDDIR»/tests/tools.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... OK
* 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 ‘undoc.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: OK

checking package 'utils'
* using log directory ‘/«PKGBUILDDIR»/tests/utils.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... WARNING
Unknown package ‘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 ‘completion.R’
 OK
* 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 WARNING
See
  ‘/«PKGBUILDDIR»/tests/utils.Rcheck/00check.log’
for details.


checking package 'grDevices'
* using log directory ‘/«PKGBUILDDIR»/tests/grDevices.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... WARNING
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 ‘ps-tests.R’
  Comparing ‘ps-tests.Rout’ to ‘ps-tests.Rout.save’ ... OK
  Running ‘xfig-tests.R’
  Comparing ‘xfig-tests.Rout’ to ‘xfig-tests.Rout.save’ ... OK
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/«PKGBUILDDIR»/tests/grDevices.Rcheck/00check.log’
for details.


checking package 'graphics'
* using log directory ‘/«PKGBUILDDIR»/tests/graphics.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... WARNING
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 WARNING
See
  ‘/«PKGBUILDDIR»/tests/graphics.Rcheck/00check.log’
for details.


checking package 'stats'
* using log directory ‘/«PKGBUILDDIR»/tests/stats.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... WARNING
Unknown packages ‘coin’, ‘nlme’, ‘cluster’, ‘MASS’, ‘rpart’, ‘Matrix’, ‘pcaPP’, ‘Kendall’, ‘SuppDists’, ‘pspearman’, ‘survival’, ‘multcomp’ 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 ‘NLSstClosest.R’
  Running ‘arimaML.R’
  Running ‘cmdscale.R’
  Running ‘drop1-polr.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 ‘nls.R’
  Comparing ‘nls.Rout’ to ‘nls.Rout.save’ ...79a80,84
> Waiting for profiling to be done...
>      2.5%    97.5%
> a 1.00875 1.037847
> b 0.84138 0.914645
> c      NA 0.042807
141c146
<   2: 0.00060639084: 0.00517051 0.999153
---
>   2: 0.00060639084: 0.00517053 0.999153
150c155
< b  0.99915    0.00119  841.37   <2e-16 ***
---
> b  0.99915    0.00119  841.38   <2e-16 ***
331a337,345
> 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
360a375,377
> Waiting for profiling to be done...
>    2.5%   97.5% 
> 0.68704 0.70281 
368a386,388
> Waiting for profiling to be done...
>    2.5%   97.5% 
> 0.68704 0.70281 
374a395,398
> Waiting for profiling to be done...
>      2.5%   97.5%
> a 0.49494 0.50893
> b 0.70019 0.74767
382a407,410
> Waiting for profiling to be done...
>      2.5%   97.5%
> a 0.49494 0.50893
> b 0.70019 0.74767
388a417,421
> 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
396a430,434
> 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
403a442,446
>    2.5%   97.5% 
> 0.70019 0.74767 
>          2.5%   97.5%
> b     0.45105 0.91471
> logc -0.64625 0.40933
473a517,519
>   2.5% 97.5%
> a 0.96  5.20
> b   NA  1.07
524a571,574
> 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’ ...359,364c359,392
< > proc.time()
<    user  system elapsed 
<   0.346   0.029   0.362 
< Warning message:
< In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
<   there is no package called 'MASS'
---
> > 
> > ## 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 ‘ts-tests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/«PKGBUILDDIR»/tests/stats.Rcheck/00check.log’
for details.


checking package 'datasets'
* using log directory ‘/«PKGBUILDDIR»/tests/datasets.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ‘/«PKGBUILDDIR»/tests/methods.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.class1’ ‘.missingMethod’ ‘.selectDotsMethod’ ‘.setDummyField’
* 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 ... WARNING
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 ‘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 WARNING, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/methods.Rcheck/00check.log’
for details.


checking package 'grid'
* using log directory ‘/«PKGBUILDDIR»/tests/grid.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... WARNING
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 ‘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’ ... failed
   ‘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
 WARNING
Errors in running code in vignettes:
when running code in ‘grid.Rnw’
  ...

> leg(legLabels)

> popViewport(3)

> library(lattice)

  When sourcing ‘grid.R’:
Error: there is no package called ‘lattice’
Execution halted

* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/«PKGBUILDDIR»/tests/grid.Rcheck/00check.log’
for details.


checking package 'splines'
* using log directory ‘/«PKGBUILDDIR»/tests/splines.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ... WARNING
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 WARNING
See
  ‘/«PKGBUILDDIR»/tests/splines.Rcheck/00check.log’
for details.


checking package 'stats4'
* using log directory ‘/«PKGBUILDDIR»/tests/stats4.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ‘/«PKGBUILDDIR»/tests/tcltk.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ‘/«PKGBUILDDIR»/tests/compiler.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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 ‘envir.R’
  Running ‘jit.R’
  Running ‘loop.R’
  Running ‘switch.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: OK

checking package 'parallel'
* using log directory ‘/«PKGBUILDDIR»/tests/parallel.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* 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’
 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 '/«PKGBUILDDIR»/tests'
make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[3]: Entering directory '/«PKGBUILDDIR»/tests'
checking package 'MASS'
* using log directory ‘/«PKGBUILDDIR»/tests/MASS.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘MASS/DESCRIPTION’ ... OK
* this is package ‘MASS’ version ‘7.3-45’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 NOTE
Packages suggested but not available for checking:
  ‘lattice’ ‘nlme’ ‘nnet’ ‘survival’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'MASS' was found
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(MASS) : there is no package called ‘MASS’
Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/MASS.Rcheck/00check.log’
for details.


checking package 'lattice'
* using log directory ‘/«PKGBUILDDIR»/tests/lattice.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘lattice/DESCRIPTION’ ... OK
* this is package ‘lattice’ version ‘0.20-33’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 NOTE
Packages suggested but not available for checking: ‘KernSmooth’ ‘MASS’

Package which this enhances but not available for checking: ‘chron’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'lattice' was found
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(lattice) : there is no package called ‘lattice’
Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/lattice.Rcheck/00check.log’
for details.


checking package 'Matrix'
* using log directory ‘/«PKGBUILDDIR»/tests/Matrix.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘Matrix/DESCRIPTION’ ... OK
* this is package ‘Matrix’ version ‘1.2-6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 ERROR
Package required but not available: ‘lattice’

Packages suggested but not available for checking: ‘expm’ ‘MASS’

Packages which this enhances but not available for checking:
  ‘MatrixModels’ ‘graph’ ‘SparseM’ ‘sfsmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/«PKGBUILDDIR»/tests/Matrix.Rcheck/00check.log’
for details.


checking package 'nlme'
* using log directory ‘/«PKGBUILDDIR»/tests/nlme.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘nlme/DESCRIPTION’ ... OK
* this is package ‘nlme’ version ‘3.1-127’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 ERROR
Package required but not available: ‘lattice’

Packages suggested but not available for checking: ‘Hmisc’ ‘MASS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/«PKGBUILDDIR»/tests/nlme.Rcheck/00check.log’
for details.


checking package 'survival'
* using log directory ‘/«PKGBUILDDIR»/tests/survival.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘survival/DESCRIPTION’ ... OK
* this is package ‘survival’ version ‘2.39-2’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 ERROR
Package required but not available: ‘Matrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/«PKGBUILDDIR»/tests/survival.Rcheck/00check.log’
for details.


checking package 'boot'
* using log directory ‘/«PKGBUILDDIR»/tests/boot.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘boot/DESCRIPTION’ ... OK
* this is package ‘boot’ version ‘1.3-18’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 NOTE
Packages suggested but not available for checking: ‘MASS’ ‘survival’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'boot' was found
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(boot) : there is no package called ‘boot’
Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/boot.Rcheck/00check.log’
for details.


checking package 'cluster'
* using log directory ‘/«PKGBUILDDIR»/tests/cluster.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘cluster/DESCRIPTION’ ... OK
* this is package ‘cluster’ version ‘2.0.4’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 NOTE
Package suggested but not available for checking: ‘MASS’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'cluster' was found
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(cluster) : there is no package called ‘cluster’
Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/cluster.Rcheck/00check.log’
for details.


checking package 'codetools'
* using log directory ‘/«PKGBUILDDIR»/tests/codetools.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘codetools/DESCRIPTION’ ... OK
* this is package ‘codetools’ version ‘0.2-14’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(codetools) : there is no package called ‘codetools’
Execution halted
* DONE

Status: 1 ERROR
See
  ‘/«PKGBUILDDIR»/tests/codetools.Rcheck/00check.log’
for details.


checking package 'foreign'
* using log directory ‘/«PKGBUILDDIR»/tests/foreign.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘foreign/DESCRIPTION’ ... OK
* this is package ‘foreign’ version ‘0.8-66’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(foreign) : there is no package called ‘foreign’
Execution halted
* DONE

Status: 1 ERROR
See
  ‘/«PKGBUILDDIR»/tests/foreign.Rcheck/00check.log’
for details.


checking package 'KernSmooth'
* using log directory ‘/«PKGBUILDDIR»/tests/KernSmooth.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘KernSmooth/DESCRIPTION’ ... OK
* this is package ‘KernSmooth’ version ‘2.23-15’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 NOTE
Package suggested but not available for checking: ‘MASS’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(KernSmooth) : there is no package called ‘KernSmooth’
Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/KernSmooth.Rcheck/00check.log’
for details.


checking package 'rpart'
* using log directory ‘/«PKGBUILDDIR»/tests/rpart.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘rpart/DESCRIPTION’ ... OK
* this is package ‘rpart’ version ‘4.1-10’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 NOTE
Package suggested but not available for checking: ‘survival’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* skipping installation test
* checking package directory ... OK
* checking ‘build’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(rpart) : there is no package called ‘rpart’
Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/rpart.Rcheck/00check.log’
for details.


checking package 'class'
* using log directory ‘/«PKGBUILDDIR»/tests/class.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘class/DESCRIPTION’ ... OK
* this is package ‘class’ version ‘7.3-14’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 ERROR
Package required but not available: ‘MASS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/«PKGBUILDDIR»/tests/class.Rcheck/00check.log’
for details.


checking package 'nnet'
* using log directory ‘/«PKGBUILDDIR»/tests/nnet.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘nnet/DESCRIPTION’ ... OK
* this is package ‘nnet’ version ‘7.3-12’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 NOTE
Package suggested but not available for checking: ‘MASS’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'nnet' was found
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(nnet) : there is no package called ‘nnet’
Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/nnet.Rcheck/00check.log’
for details.


checking package 'spatial'
* using log directory ‘/«PKGBUILDDIR»/tests/spatial.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘spatial/DESCRIPTION’ ... OK
* this is package ‘spatial’ version ‘7.3-11’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 NOTE
Package suggested but not available for checking: ‘MASS’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'spatial' was found
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(spatial) : there is no package called ‘spatial’
Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/«PKGBUILDDIR»/tests/spatial.Rcheck/00check.log’
for details.


checking package 'mgcv'
* using log directory ‘/«PKGBUILDDIR»/tests/mgcv.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: i686-pc-linux-gnu (32-bit)
* using session charset: UTF-8
* checking for file ‘mgcv/DESCRIPTION’ ... OK
* this is package ‘mgcv’ version ‘1.8-12’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib:
  cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib:
  cannot download all files
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib:
  cannot download all files
 ERROR
Packages required but not available: ‘nlme’ ‘Matrix’

Packages suggested but not available for checking: ‘survival’ ‘MASS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/«PKGBUILDDIR»/tests/mgcv.Rcheck/00check.log’
for details.


make[3]: Leaving directory '/«PKGBUILDDIR»/tests'
make[2]: Leaving directory '/«PKGBUILDDIR»/tests'
make[1]: Leaving directory '/«PKGBUILDDIR»'
touch check-stamp
 fakeroot debian/rules binary-arch
*** install-arch ***
dh_testdir
dh_testroot
dh_prep -a
dh_installdirs -A
/«PKGBUILDDIR»/debian/r-base-core
/usr/bin/make DESTDIR=/«PKGBUILDDIR»/debian/r-base-core install
make[1]: Entering directory '/«PKGBUILDDIR»'
make[2]: Entering directory '/«PKGBUILDDIR»/m4'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/«PKGBUILDDIR»/m4'
make[2]: Entering directory '/«PKGBUILDDIR»/tools'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tools'
make[2]: Entering directory '/«PKGBUILDDIR»/doc'
installing doc ...
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/man/man1
make[3]: Entering directory '/«PKGBUILDDIR»/doc/html'
installing doc/html ...
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/html
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html'
make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual'
installing doc/manual ...
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/manual
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/manual/images
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
make[2]: Leaving directory '/«PKGBUILDDIR»/doc'
make[2]: Entering directory '/«PKGBUILDDIR»/etc'
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/etc
installing etc ...
make[2]: Leaving directory '/«PKGBUILDDIR»/etc'
make[2]: Entering directory '/«PKGBUILDDIR»/share'
installing share ...
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/R
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/dictionaries
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/encodings
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/java
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/licenses
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/make
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/Rd
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/Rd/macros
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/sh
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/texmf
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/texmf/tex/latex
make[2]: Leaving directory '/«PKGBUILDDIR»/share'
make[2]: Entering directory '/«PKGBUILDDIR»/src'
make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts'
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/bin
make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts'
make[3]: Entering directory '/«PKGBUILDDIR»/src/include'
make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext'
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/include/R_ext
make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/include'
make[3]: Entering directory '/«PKGBUILDDIR»/src/extra'
make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/blas'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/blas'
make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre'
make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/xdr'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/xdr'
make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/intl'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/intl'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra'
make[3]: Entering directory '/«PKGBUILDDIR»/src/appl'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl'
make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath'
make[3]: Entering directory '/«PKGBUILDDIR»/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \
  -o Rscript ./Rscript.c
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/pkgconfig
make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix'
make[3]: Entering directory '/«PKGBUILDDIR»/src/main'
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/bin/exec
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[4]: Entering directory '/«PKGBUILDDIR»/src/main'
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/lib
make[4]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/main'
make[3]: Entering directory '/«PKGBUILDDIR»/src/modules'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet'
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/modules
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack'
make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11'
make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules'
make[3]: Entering directory '/«PKGBUILDDIR»/src/library'
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/library
installing packages ...
  building HTML index ...
make[3]: Leaving directory '/«PKGBUILDDIR»/src/library'
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
make[2]: Entering directory '/«PKGBUILDDIR»/tests'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/«PKGBUILDDIR»/tests'
make[1]: Leaving directory '/«PKGBUILDDIR»'
(cd src/unix; 						\
	rm -vf Rscript /«PKGBUILDDIR»/debian/r-base-core/usr/bin/Rscript;	\
	/usr/bin/make	CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"		\
		CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"	\
		FFLAGS="-g -O2 -fstack-protector-strong -D_REENTRANT"	\
		CC="gcc -std=gnu99"				\
		CXX=g++			\
		F77=gfortran			\
		RHOME=/usr/lib/R			\
		DESTDIR=/«PKGBUILDDIR»/debian/r-base-core			\
		install-Rscript )
removed 'Rscript'
removed '/«PKGBUILDDIR»/debian/r-base-core/usr/bin/Rscript'
make[1]: Entering directory '/«PKGBUILDDIR»/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \
  -o Rscript ./Rscript.c
make[1]: Leaving directory '/«PKGBUILDDIR»/src/unix'
#ls -ltr /«PKGBUILDDIR»/debian/r-base-core/usr/bin/
#strings src/unix/Rscript					
cp -vax src/unix/Rscript /«PKGBUILDDIR»/debian/r-base-core/usr/bin/
'src/unix/Rscript' -> '/«PKGBUILDDIR»/debian/r-base-core/usr/bin/Rscript'
#ls -ltr /«PKGBUILDDIR»/debian/r-base-core/usr/bin/
#strings /«PKGBUILDDIR»/debian/r-base-core/usr/bin/Rscript
(cd src/nmath/standalone;				\
	/usr/bin/make DESTDIR=/«PKGBUILDDIR»/debian/r-base-core install )
make[1]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone'
make[2]: Entering directory '/«PKGBUILDDIR»/src/include'
make[2]: 'Rmath.h' is up to date.
make[2]: Leaving directory '/«PKGBUILDDIR»/src/include'
/«PKGBUILDDIR»/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged
make[1]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone'
chmod a+x	/«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/sh/echo.sh		
rm -v	/«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/COPYING  		
removed '/«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/COPYING'
(cd /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/; \
	ln -s ../../share/common-licenses/GPL-2 COPYING)
rm -v	/«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/COPYING  	
removed '/«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/COPYING'
(cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc; \
	ln -s ../../../share/common-licenses/GPL-2 COPYING)
# edd 03 Oct 2006  use link into /usr/share/, not /usr/lib/
(cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/texmf/tex/latex && 	\
    ln -s ../../../R/share/texmf R)
dh_movefiles	--sourcedir=debian/r-base-core -pr-doc-html
dh_movefiles	--sourcedir=debian/r-base-core -pr-base-html
dh_movefiles	--sourcedir=debian/r-base-core -pr-base-latex
make		prefix=/«PKGBUILDDIR»/debian/r-base-core/usr			\
		rdocdir=/«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc	\
		install-pdf
make[1]: Entering directory '/«PKGBUILDDIR»'
make[2]: Entering directory '/«PKGBUILDDIR»/doc/manual'
installing R manuals in PDF format ...
make[2]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
make[1]: Leaving directory '/«PKGBUILDDIR»'
make		prefix=/«PKGBUILDDIR»/debian/r-base-core/usr  \
		infodir=/«PKGBUILDDIR»/debian/r-base-core/usr/share/info	install-info
make[1]: Entering directory '/«PKGBUILDDIR»'
make[2]: Entering directory '/«PKGBUILDDIR»/doc/manual'
mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/info
/usr/bin/install -c -m 644 "./dir" "/«PKGBUILDDIR»/debian/r-base-core/usr/share/info"
installing R info pages ...
updating '/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir' ...
you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually
you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually
you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually
you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually
you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually
you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually
you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually
make[2]: Leaving directory '/«PKGBUILDDIR»/doc/manual'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_movefiles	--sourcedir=debian/r-base-core -pr-doc-pdf
dh_movefiles	--sourcedir=debian/r-base-core -pr-doc-html
touch install-indep-stamp
gunzip -9v /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/*.gz
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-FAQ.info.gz:	 67.1% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-FAQ.info
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-admin.info.gz:	 68.2% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-admin.info
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-data.info.gz:	 70.6% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-data.info
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info-1.gz:	 66.8% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info-1
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info-2.gz:	 70.8% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info-2
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info.gz:	 68.4% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-intro.info.gz:	 70.0% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-intro.info
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-ints.info.gz:	 67.8% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-ints.info
/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-lang.info.gz:	 71.7% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-lang.info
dh_movefiles	--sourcedir=debian/r-base-core -pr-doc-info
rm -vf	/«PKGBUILDDIR»/debian/r-doc-info/usr/share/info/dir		\
	/«PKGBUILDDIR»/debian/r-doc-info/usr/share/info/dir.old	
removed '/«PKGBUILDDIR»/debian/r-doc-info/usr/share/info/dir'
dh_installdirs -pr-mathlib usr/include usr/lib \
				usr/share/lintian/overrides \
				usr/lib/pkgconfig
dh_movefiles	--sourcedir=debian/r-base-core -pr-mathlib
(cd /«PKGBUILDDIR»/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 1732
-rw-rw-r-- 1 root root 1116894 May  3 23:46 libRmath.a
-rwxrwxr-x 1 root root  651084 May  3 23:46 libRmath.so
drwxr-xr-x 2 root root    4096 May  3 23:46 pkgconfig
'libRmath.so' -> 'libRmath.so.1.0.0'
'libRmath.so.1' -> 'libRmath.so.1.0.0'
'libRmath.so' -> 'libRmath.so.1'
install -m 0644 src/include/Rmath.h			\
		/«PKGBUILDDIR»/debian/r-mathlib/usr/include
install -m 0644 debian/Rprofile.site /«PKGBUILDDIR»/debian/r-base-core/etc/R
install -m 0644 debian/Renviron.site /«PKGBUILDDIR»/debian/r-base-core/etc/R
(cd /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/etc; \
	cat /«PKGBUILDDIR»/debian/Renviron-R_LIBS.patch | patch --verbose;	\
	mv Makeconf repositories ldpaths ../../../../etc/R/;	\
	mv Renviron Renviron.ucf;				\
	ln -s  /etc/R/Makeconf	.;				\
	ln -s  /etc/R/Renviron	.;				\
	ln -s  /etc/R/Renviron.site .;				\
	ln -s  /etc/R/Rprofile.site .;				\
	ln -s  /etc/R/ldpaths   .;                              \
	ln -s  /etc/R/repositories .				)
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|--- Renviron.orig	2003-04-04 06:52:22.000000000 -0500
|+++ Renviron	2003-04-04 06:49:05.000000000 -0500
--------------------------
patching file Renviron
Using Plan A...
Hunk #1 succeeded at 43 with fuzz 2 (offset 10 lines).
done
dh_bash-completion	
# edd 12 Jan 2016  new location
#install -m 0644 debian/R.bash-completion \
#	debian/r-base-core/usr/share/bash-completion/completions/R
(cd /«PKGBUILDDIR»/debian/r-base-core/usr/lib/; \
	ln -sv R/lib/libR.so . )
'./libR.so' -> 'R/lib/libR.so'
(cd debian/icon-class-patch && munpack rlogo_icon.png.mpack)
rlogo_icon.png (application/octet-stream)
install -m 0644 debian/icon-class-patch/rlogo_icon.png	\
	debian/r-base-core/usr/share/icons/hicolor/48x48/apps
install -m 0644 debian/icon-class-patch/R.desktop		\
	debian/r-base-core/usr/share/applications
rm debian/icon-class-patch/rlogo_icon.png
touch install-arch-stamp
*** binary-arch ***
dh_testdir -a
dh_testroot -a
dh_installdocs -pr-base-core doc/NEWS.* README \
				debian/README.Atlas \
				debian/README.mathlib
dh_installdocs -pr-mathlib  doc/NEWS.* README \
				debian/README.mathlib
dh_installdocs -pr-base-core-dbg				
dh_installexamples -pr-mathlib	src/nmath/standalone/test.c
#dh_installmenu -a
# (cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .)
(cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .)
(cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/library .)
install -p -m 0644  debian/r-base-core.lintian \
   /«PKGBUILDDIR»/debian/r-base-core/usr/share/lintian/overrides/r-base-core
install -p -m 0644  debian/r-recommended.lintian \
   /«PKGBUILDDIR»/debian/r-recommended/usr/share/lintian/overrides/r-recommended
install -p -m 0644  debian/r-mathlib.lintian \
   /«PKGBUILDDIR»/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib
dh_installchangelogs -a	-k doc/NEWS 
dh_strip	--sourcedir=/«PKGBUILDDIR»/debian/r-base-core --dbg-package=r-base-core-dbg
dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding
dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: r-base-core r-mathlib r-base-core-dbg 
dh_strip debug symbol extraction: not adding gnu debuglinks since --dbg-package is given
dh_strip debug symbol extraction: packages to act on: r-base-core r-mathlib r-base-core-dbg 
dh_strip debug symbol extraction: ignored packages: 
we have -dbg package(s), not installing anything into ddeb
find: ‘/«PKGBUILDDIR»/debian/r-base-core-dbgsym’: No such file or directory
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
/usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol
we have -dbg package(s), not installing anything into ddeb
find: ‘/«PKGBUILDDIR»/debian/r-mathlib-dbgsym’: No such file or directory
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
/usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol
Unknown option: sourcedir
dh_strip 	--sourcedir=/«PKGBUILDDIR»/debian/r-mathlib
dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding
dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: r-base-core r-mathlib r-base-core-dbg 
dh_strip debug symbol extraction: packages to act on: r-base-core r-mathlib r-base-core-dbg 
dh_strip debug symbol extraction: ignored packages: 
pkg_create_dbgsym: /«PKGBUILDDIR»/debian/r-base-core-dbgsym already exists, ignoring
pkg_create_dbgsym: /«PKGBUILDDIR»/debian/r-mathlib-dbgsym already exists, ignoring
Unknown option: sourcedir
dh_compress -a
dh_fixperms -a
dh_link -a
dh_makeshlibs -a
dh_installdeb -a
dh_perl -a
dh_shlibdeps -a -l /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/lib
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libtk8.6.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 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package r-base-core: unknown substitution variable ${perl:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform i386: r-base-core r-mathlib r-base-core-dbg 
dh_gencontrol debug symbol wrapper: packages to act on: r-base-core r-mathlib r-base-core-dbg 
dh_gencontrol debug symbol wrapper: ignored packages: 
dh_gencontrol debug symbol wrapper: processing package r-base-core (pkgdir debian/r-base-core, ddeb package dir debian/r-base-core-dbgsym)
dh_gencontrol debug symbol wrapper: building r-base-core-dbgsym_3.3.0-1_i386.ddeb
dpkg-deb: building package 'r-base-core-dbgsym' in '../r-base-core-dbgsym_3.3.0-1_i386.ddeb'.
dh_gencontrol debug symbol wrapper: dpkg-distaddfile r-base-core-dbgsym_3.3.0-1_i386.ddeb gnu-r extra
dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_gencontrol debug symbol wrapper: processing package r-mathlib (pkgdir debian/r-mathlib, ddeb package dir debian/r-mathlib-dbgsym)
dh_gencontrol debug symbol wrapper: building r-mathlib-dbgsym_3.3.0-1_i386.ddeb
dpkg-deb: building package 'r-mathlib-dbgsym' in '../r-mathlib-dbgsym_3.3.0-1_i386.ddeb'.
dh_gencontrol debug symbol wrapper: dpkg-distaddfile r-mathlib-dbgsym_3.3.0-1_i386.ddeb gnu-r extra
dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
INFO: pkgstriptranslations version 129
INFO: pkgstriptranslations version 129
INFO: pkgstriptranslations version 129
pkgstriptranslations: processing r-base-core-dbg (in debian/r-base-core-dbg); do_strip: , oemstrip: 
pkgstriptranslations: processing r-base-core (in debian/r-base-core); do_strip: , oemstrip: 
pkgstriptranslations: processing r-mathlib (in debian/r-mathlib); do_strip: , oemstrip: 
debian/r-base-core/usr/share/applications/R.desktop: does not have gettext domain, not stripping
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/r-base-core/DEBIAN/control, package r-base-core, directory debian/r-base-core
.. removing usr/share/doc/r-base-core/changelog.gz
pkgstripfiles: Truncating usr/share/doc/r-base-core/changelog.Debian.gz to topmost ten records
pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core ...
WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/pch.png, ignoring
WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/mai.png, ignoring
WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/oma.png, ignoring
..ooooopkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/r-base-core-dbg/DEBIAN/control, package r-base-core-dbg, directory debian/r-base-core-dbg
.. removing usr/share/doc/r-base-core-dbg/changelog.gz
INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
oINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
oINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
o
pkgstripfiles: PNG optimization (8/0) for package r-base-core took 7 s
dpkg-deb: building package 'r-base-core' in '../r-base-core_3.3.0-1_i386.deb'.
INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ...
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/r-mathlib/DEBIAN/control, package r-mathlib, directory debian/r-mathlib
.. removing usr/share/doc/r-mathlib/changelog.gz
pkgstripfiles: Truncating usr/share/doc/r-mathlib/changelog.Debian.gz to topmost ten records
pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-mathlib ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.3.0-1_i386.deb'.
Searching for duplicated docs in dependency r-base-core...
  symlinking changelog.Debian.gz in r-base-core-dbg to file in r-base-core
pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core-dbg ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'r-base-core-dbg' in '../r-base-core-dbg_3.3.0-1_i386.deb'.
 dpkg-genchanges -B -mLaunchpad Build Daemon <buildd@lgw01-48.buildd> >../r-base_3.3.0-1_i386.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build r-base-3.3.0
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20160503-2347

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot                                                            │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


r-base_3.3.0-1_i386.changes:
────────────────────────────

Format: 1.8
Date: Tue, 03 May 2016 06:05:36 -0500
Source: r-base
Binary: r-base r-base-core r-base-dev r-mathlib r-base-html r-doc-pdf r-doc-html r-doc-info r-recommended r-base-core-dbg
Architecture: i386
Version: 3.3.0-1
Distribution: yakkety-proposed
Urgency: medium
Maintainer: Launchpad Build Daemon <buildd@lgw01-48.buildd>
Changed-By: Dirk Eddelbuettel <edd@debian.org>
Description:
 r-base     - GNU R statistical computation and graphics system
 r-base-core - GNU R core of statistical computation and graphics system
 r-base-core-dbg - GNU R debug symbols for statistical comp. language and environmen
 r-base-dev - GNU R installation of auxiliary GNU R packages
 r-base-html - GNU R html docs for statistical computing system functions
 r-doc-html - GNU R html manuals for statistical computing system
 r-doc-info - GNU R info manuals statistical computing system
 r-doc-pdf  - GNU R pdf manuals for statistical computing system
 r-mathlib  - GNU R standalone mathematics library
 r-recommended - GNU R collection of recommended packages [metapackage]
Changes:
 r-base (3.3.0-1) unstable; urgency=medium
 .
   * New upstream version released this morning
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


r-base-core-dbg_3.3.0-1_i386.deb
────────────────────────────────

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 Package: r-base-core-dbg
 Source: r-base
 Version: 3.3.0-1
 Architecture: i386
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Dirk Eddelbuettel <edd@debian.org>
 Installed-Size: 8649
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 Priority: extra
 Homepage: http://www.r-project.org/
 Description: GNU R debug symbols for statistical comp. language and environment
  R is a system for statistical computation and graphics.  It consists
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  stored in script files.
  .
  The design of R has been heavily influenced by two existing languages:
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r-base-core_3.3.0-1_i386.deb
────────────────────────────

 new debian package, version 2.0.
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 Package: r-base-core
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 Version: 3.3.0-1
 Architecture: i386
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Dirk Eddelbuettel <edd@debian.org>
 Installed-Size: 33725
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r-mathlib_3.3.0-1_i386.deb
──────────────────────────

 new debian package, version 2.0.
 size 1436606 bytes: control archive=2034 bytes.
    1838 bytes,    40 lines      control              
    1148 bytes,    17 lines      md5sums              
     370 bytes,    27 lines   *  postinst             
      21 bytes,     1 lines      shlibs               
      60 bytes,     2 lines      triggers             
 Package: r-mathlib
 Source: r-base
 Version: 3.3.0-1
 Architecture: i386
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Dirk Eddelbuettel <edd@debian.org>
 Installed-Size: 1973
 Depends: libc6 (>= 2.23)
 Recommends: r-base-core (= 3.3.0-1), r-base-dev (= 3.3.0-1)
 Section: gnu-r
 Priority: optional
 Homepage: http://www.r-project.org/
 Description: GNU R standalone mathematics library
  R is a system for statistical computation and graphics.  It consists
  of a language plus a run-time environment with graphics, a debugger,
  access to certain system functions, and the ability to run programs
  stored in script files.
  .
  The design of R has been heavily influenced by two existing languages:
  Becker, Chambers & Wilks' S and Sussman's Scheme.  Whereas the
  resulting language is very similar in appearance to S, the underlying
  implementation and semantics are derived from Scheme.
  .
  The core of R is an interpreted computer language which allows
  branching and looping as well as modular programming using functions.
  Most of the user-visible functions in R are written in R.  It is
  possible for the user to interface to procedures written in the
  C, C++, or FORTRAN languages for efficiency, and many of R's core
  functions do so.  The R distribution contains functionality for a
  large number of statistical procedures and underlying applied math
  computations.  There is also a large set of functions which provide
  a flexible graphical environment for creating various kinds of data
  presentations.
  .
  Additionally, several thousand extension "packages" are available from
  CRAN, the Comprehensive R Archive Network, many also as Debian packages,
  named 'r-cran-<name>'.
  .
  This package provides the libRmath shared and static libraries which can
  be called from standalone C or C++ code.

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drwxr-xr-x root/root         0 2016-05-03 23:47 ./usr/share/doc/r-mathlib/
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-rw-r--r-- root/root      2107 2014-07-07 22:15 ./usr/share/doc/r-mathlib/README.gz
-rw-r--r-- root/root      3026 2016-05-03 23:26 ./usr/share/doc/r-mathlib/README.mathlib
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-rw-r--r-- root/root     20761 2016-05-03 23:26 ./usr/share/doc/r-mathlib/copyright
drwxr-xr-x root/root         0 2016-05-03 23:46 ./usr/share/doc/r-mathlib/examples/
-rw-r--r-- root/root      1371 2015-08-25 22:18 ./usr/share/doc/r-mathlib/examples/test.c
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-rw-r--r-- root/root       231 2016-05-03 23:26 ./usr/share/lintian/overrides/r-mathlib


┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Not removing build depends: as requested
Keeping session: 

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Build Architecture: i386
Build-Space: 365532
Build-Time: 1271
Distribution: yakkety-proposed
Host Architecture: i386
Install-Time: 195
Job: r-base_3.3.0-1.dsc
Machine Architecture: amd64
Package: r-base
Package-Time: 1469
Source-Version: 3.3.0-1
Space: 365532
Status: successful
Version: 3.3.0-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20160503-2347
Build needed 00:24:29, 365532k disc space
RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-9686715']
Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-9686715/chroot-autobuild...
RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-9686715']
Unmounting chroot for build PACKAGEBUILD-9686715...
RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-9686715']
Removing build PACKAGEBUILD-9686715