Build log for r-base (3.5.1-1) on armhf

r-base → 3.5.1-1 → armhf → 2018-07-07 09:27:18

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| r-base 3.5.1-1 (armhf)                       Sat, 07 Jul 2018 08:34:45 +0000 |
+==============================================================================+

Package: r-base
Version: 3.5.1-1
Source Version: 3.5.1-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-679c497f-0d88-488d-bcb2-92450f6ff5c7' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.9 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.6 MB]
Fetched 23.5 MB in 11s (2209 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'r-base' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/edd/r-base.git
Please use:
git clone https://salsa.debian.org/edd/r-base.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 29.9 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-base 3.5.1-1 (dsc) [3008 B]
Get:2 http://172.17.0.1/private buster-staging/main r-base 3.5.1-1 (tar) [29.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main r-base 3.5.1-1 (diff) [88.0 kB]
Fetched 29.9 MB in 11s (2676 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-base-73GQCG/r-base-3.5.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-base-73GQCG' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-DXUHIB/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-DXUHIB/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-DXUHIB/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (11.7 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
  libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
  systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 36 not upgraded.
Need to get 844 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [844 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 844 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15728 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk | openjdk-10-jdk, mpack, bash-completion
Filtered Build-Depends: gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev, 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-DXUHIB/apt_archive/sbuild-build-depends-r-base-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-r-base-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ Sources [805 B]
Get:5 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ Packages [831 B]
Fetched 2969 B in 0s (16.4 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install r-base build dependencies (apt-based resolver)
------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  e2fsprogs-l10n libnss-systemd libsasl2-modules
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  adwaita-icon-theme autoconf automake autopoint autotools-dev bash-completion
  bison bsdmainutils ca-certificates-java dconf-gsettings-backend
  dconf-service debhelper default-jdk default-jdk-headless default-jre
  default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file
  fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern gettext
  gettext-base gfortran gfortran-7 gir1.2-freedesktop gir1.2-glib-2.0
  gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 glib-networking glib-networking-common
  glib-networking-services groff-base gsettings-desktop-schemas
  gtk-update-icon-cache hicolor-icon-theme icu-devtools intltool-debian
  java-common libarchive-zip-perl libasound2 libasound2-data
  libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0
  libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data
  libavahi-common3 libbison-dev libblas-dev libblas3 libbsd0 libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcolord2 libcroco3 libcups2 libcupsimage2 libcurl4 libcurl4-openssl-dev
  libdatrie1 libdconf1 libdrm-amdgpu1 libdrm-etnaviv1 libdrm-freedreno1
  libdrm-nouveau2 libdrm-radeon1 libedit2 libelf1 libepoxy0 libexpat1-dev
  libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
  libfontenc1 libfreetype6 libfreetype6-dev libfribidi-dev libfribidi0
  libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-7-dev libgfortran4
  libgif7 libgirepository-1.0-1 libgl1 libgl1-mesa-dri libglapi-mesa
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev
  libglib2.0-dev-bin libglvnd0 libglx-mesa0 libglx0 libgraphite2-3
  libgraphite2-dev libgs9 libgs9-common libgssapi-krb5-2 libgtk-3-0
  libgtk-3-common libgtk2.0-0 libgtk2.0-common libharfbuzz-dev
  libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6
  libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libijs-0.35 libjbig-dev
  libjbig0 libjbig2dec0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
  libjson-glib-1.0-0 libjson-glib-1.0-common libk5crypto3 libkeyutils1
  libkpathsea6 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2
  libllvm6.0 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmime-charset-perl
  libmpdec2 libncurses-dev libncurses5-dev libnghttp2-14 libnspr4 libnss3
  libopenjp2-7 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0
  libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre16-3
  libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1
  libpixman-1-0 libpixman-1-dev libpng-dev libpotrace0 libproxy1v5 libpsl5
  libptexenc1 libpthread-stubs0-dev libpython-stdlib libpython2-stdlib
  libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
  libpython3.6-minimal libpython3.6-stdlib libreadline-dev librest-0.7-0
  librsvg2-2 librsvg2-common librtmp1 libsensors4 libsigsegv2 libsm-dev libsm6
  libsombok3 libsoup-gnome2.4-1 libsoup2.4-1 libssh2-1 libsynctex2 libtcl8.6
  libtexlua52 libtexlua53 libtexluajit2 libtext-unidecode-perl libthai-data
  libthai0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtk8.6 libtool
  libunicode-linebreak-perl 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-shape0 libxcb-shm0
  libxcb-shm0-dev libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev
  libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev
  libxext6 libxfixes3 libxfont2 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 libxv1 libxxf86dga1 libxxf86vm1 libzzip-0-13 m4
  man-db mime-support mpack openjdk-10-jdk openjdk-10-jdk-headless
  openjdk-10-jre openjdk-10-jre-headless pkg-config po-debconf poppler-data
  preview-latex-style python python-minimal python2 python2-minimal python2.7
  python2.7-minimal python3 python3-distutils python3-lib2to3 python3-minimal
  python3.6 python3.6-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 texlive-plain-generic tk8.6 tk8.6-dev ucf uuid-dev
  x11-common x11-utils x11-xkb-utils x11proto-core-dev x11proto-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 gettext-doc libasprintf-dev libgettextpo-dev
  gfortran-doc gfortran-7-doc libgfortran4-dbg libcoarrays-dev groff
  libasound2-plugins alsa-utils liblapack-doc libcairo2-doc colord cups-common
  libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
  libssl-dev libglib2.0-doc libgraphite2-utils krb5-doc krb5-user gvfs
  libice-doc icu-doc liblcms2-utils liblzma-doc libencode-hanextra-perl
  libpod2-base-perl ncurses-doc imagemagick libpango1.0-doc pcscd readline-doc
  librsvg2-bin lm-sensors libsm-doc libtool-doc gcj-jdk libxcb-doc libxext-doc
  libxt-doc m4-doc apparmor less www-browser mail-transport-agent inews
  openjdk-10-demo openjdk-10-source visualvm libnss-mdns fonts-dejavu-extra
  fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei
  | fonts-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-doc python2.7-doc binfmt-support python3-doc
  python3-tk python3-venv python3.6-venv python3.6-doc tcl-tclreadline
  tcl8.6-doc texinfo-doc-nonfree gv | postscript-viewer perl-tk xpdf-reader
  | pdf-viewer chktex dvidvi dvipng fragmaster lacheck latexdiff latexmk
  purifyeps xindy cm-super texlive-fonts-extra-doc
  texlive-fonts-recommended-doc texlive-latex-base-doc python-pygments
  icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl
  texlive-latex-extra-doc texlive-latex-recommended-doc texlive-pstricks
  dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex
  tk8.6-doc mesa-utils
Recommended packages:
  curl | wget | lynx at-spi2-core bzip2-doc libcupsfilters1
  libarchive-cpio-perl libgdk-pixbuf2.0-bin xdg-user-dirs fonts-droid-fallback
  libgtk-3-bin libgail-common libgtk2.0-bin krb5-locales libpng-tools
  publicsuffix libltdl-dev libx11-doc libwww-perl libxml-sax-expat-perl
  fonts-dejavu-extra libmail-sendmail-perl lmodern ghostscript
  libfile-homedir-perl libyaml-tiny-perl ruby | ruby-interpreter
  fonts-adf-accanthis fonts-adf-berenis fonts-adf-gillius
  fonts-adf-universalis fonts-cabin fonts-comfortaa fonts-croscore
  fonts-crosextra-caladea fonts-crosextra-carlito fonts-ebgaramond
  fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf
  fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-complutum fonts-gfs-didot
  fonts-gfs-neohellenic fonts-gfs-olga fonts-gfs-solomos fonts-go
  fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobstertwo
  fonts-noto-hinted fonts-noto-mono fonts-oflb-asana-math fonts-open-sans
  fonts-roboto-hinted fonts-sil-gentium fonts-sil-gentium-basic
  fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix
  texlive-fonts-extra-links tex-gyre tipa tk xterm | x-terminal-emulator
  libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
  x11-xserver-utils
The following NEW packages will be installed:
  adwaita-icon-theme autoconf automake autopoint autotools-dev bash-completion
  bison bsdmainutils ca-certificates-java dconf-gsettings-backend
  dconf-service debhelper default-jdk default-jdk-headless default-jre
  default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file
  fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern gettext
  gettext-base gfortran gfortran-7 gir1.2-freedesktop gir1.2-glib-2.0
  gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 glib-networking glib-networking-common
  glib-networking-services groff-base gsettings-desktop-schemas
  gtk-update-icon-cache hicolor-icon-theme icu-devtools intltool-debian
  java-common libarchive-zip-perl libasound2 libasound2-data
  libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0
  libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data
  libavahi-common3 libbison-dev libblas-dev libblas3 libbsd0 libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcolord2 libcroco3 libcups2 libcupsimage2 libcurl4 libcurl4-openssl-dev
  libdatrie1 libdconf1 libdrm-amdgpu1 libdrm-etnaviv1 libdrm-freedreno1
  libdrm-nouveau2 libdrm-radeon1 libedit2 libelf1 libepoxy0 libexpat1-dev
  libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
  libfontenc1 libfreetype6 libfreetype6-dev libfribidi-dev libfribidi0
  libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-7-dev libgfortran4
  libgif7 libgirepository-1.0-1 libgl1 libgl1-mesa-dri libglapi-mesa
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev
  libglib2.0-dev-bin libglvnd0 libglx-mesa0 libglx0 libgraphite2-3
  libgraphite2-dev libgs9 libgs9-common libgssapi-krb5-2 libgtk-3-0
  libgtk-3-common libgtk2.0-0 libgtk2.0-common libharfbuzz-dev
  libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6
  libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libijs-0.35 libjbig-dev
  libjbig0 libjbig2dec0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
  libjson-glib-1.0-0 libjson-glib-1.0-common libk5crypto3 libkeyutils1
  libkpathsea6 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2
  libllvm6.0 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmime-charset-perl
  libmpdec2 libncurses-dev libncurses5-dev libnghttp2-14 libnspr4 libnss3
  libopenjp2-7 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0
  libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre16-3
  libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1
  libpixman-1-0 libpixman-1-dev libpng-dev libpotrace0 libproxy1v5 libpsl5
  libptexenc1 libpthread-stubs0-dev libpython-stdlib libpython2-stdlib
  libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
  libpython3.6-minimal libpython3.6-stdlib libreadline-dev librest-0.7-0
  librsvg2-2 librsvg2-common librtmp1 libsensors4 libsigsegv2 libsm-dev libsm6
  libsombok3 libsoup-gnome2.4-1 libsoup2.4-1 libssh2-1 libsynctex2 libtcl8.6
  libtexlua52 libtexlua53 libtexluajit2 libtext-unidecode-perl libthai-data
  libthai0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtk8.6 libtool
  libunicode-linebreak-perl 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-shape0 libxcb-shm0
  libxcb-shm0-dev libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev
  libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev
  libxext6 libxfixes3 libxfont2 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 libxv1 libxxf86dga1 libxxf86vm1 libzzip-0-13 m4
  man-db mime-support mpack openjdk-10-jdk openjdk-10-jdk-headless
  openjdk-10-jre openjdk-10-jre-headless pkg-config po-debconf poppler-data
  preview-latex-style python python-minimal python2 python2-minimal python2.7
  python2.7-minimal python3 python3-distutils python3-lib2to3 python3-minimal
  python3.6 python3.6-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
  texlive-plain-generic tk8.6 tk8.6-dev ucf uuid-dev x11-common x11-utils
  x11-xkb-utils x11proto-core-dev x11proto-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, 329 newly installed, 0 to remove and 36 not upgraded.
Need to get 740 MB/762 MB of archives.
After this operation, 2264 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-DXUHIB/apt_archive ./ sbuild-build-depends-r-base-dummy 0.invalid.0 [1112 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.5-1 [292 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.5-1 [683 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libxxf86dga1 armhf 2:1.1.4-1 [22.4 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf poppler-data all 0.4.9-2 [1473 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-1 [393 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-1 [1077 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-1 [1841 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-1 [298 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.6-1 [565 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.6-1 [1383 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.5-3 [36.2 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.6-1 [1638 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.6-1 [234 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.5-3 [19.7 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.5-3 [24.1 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf tex-common all 6.09 [53.2 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf bash-completion all 1:2.8-1 [207 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20180525-1 [70.6 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-6 [225 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.1-1+rpi1 [828 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libgdk-pixbuf2.0-common all 2.36.11-2 [312 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libgdk-pixbuf2.0-0 armhf 2.36.11-2 [153 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf gtk-update-icon-cache armhf 3.22.29-3+rpi1 [77.9 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-5 [280 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.0-5 [325 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.15.10-3 [575 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.0-5 [403 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 0.19.7-3 [44.2 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.12-1 [35.8 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.1-2 [159 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.1-2 [54.6 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.1-2 [44.5 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf adwaita-icon-theme all 3.28.0-1 [11.7 MB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libbison-dev armhf 2:3.0.4.dfsg-1+b1 [433 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf bison armhf 2:3.0.4.dfsg-1+b1 [743 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf java-common all 0.67 [14.3 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libavahi-common-data armhf 0.7-4 [122 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libavahi-common3 armhf 0.7-4 [51.1 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libavahi-client3 armhf 0.7-4 [53.7 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libcups2 armhf 2.2.8-4 [285 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf liblcms2-2 armhf 2.9-2 [117 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libnspr4 armhf 2:4.19-3+rpi1 [90.0 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libnss3 armhf 2:3.38-1 [935 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libpcsclite1 armhf 1.8.23-3 [55.2 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf openjdk-10-jre-headless armhf 10.0.1+10-4 [35.5 MB]
Get:71 http://172.17.0.1/private buster-staging/main armhf default-jre-headless armhf 2:1.10-67 [10.7 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf ca-certificates-java all 20180516 [15.5 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libdconf1 armhf 0.28.0-2 [33.1 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf dconf-service armhf 0.28.0-2 [30.8 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf dconf-gsettings-backend armhf 0.28.0-2 [22.5 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libgtk-3-common all 3.22.29-3+rpi1 [3510 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libatk1.0-data all 2.28.1-1 [145 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libatk1.0-0 armhf 2.28.1-1 [42.2 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libatspi2.0-0 armhf 2.28.0-3 [53.8 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libatk-bridge2.0-0 armhf 2.26.2-1 [51.5 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libcairo-gobject2 armhf 1.15.10-3 [101 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libjson-glib-1.0-common all 1.4.2-4 [50.6 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libjson-glib-1.0-0 armhf 1.4.2-4 [52.2 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libproxy1v5 armhf 0.4.15-1 [48.4 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf glib-networking-common all 2.56.0-1 [55.4 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf glib-networking-services armhf 2.56.0-1 [12.3 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf gsettings-desktop-schemas all 3.28.0-1 [522 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf glib-networking armhf 2.56.0-1 [54.3 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libsoup2.4-1 armhf 2.62.2-2 [255 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libsoup-gnome2.4-1 armhf 2.62.2-2 [16.7 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libgtk-3-0 armhf 3.22.29-3+rpi1 [2070 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libglvnd0 armhf 1.0.0+git20180308-3 [53.1 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libglapi-mesa armhf 18.1.2-1 [69.9 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libx11-xcb1 armhf 2:1.6.5-1 [185 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:108 http://172.17.0.1/private buster-staging/main armhf libdrm-amdgpu1 armhf 2.4.92-1+rpi1 [27.0 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libdrm-etnaviv1 armhf 2.4.92-1+rpi1 [20.0 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libdrm-freedreno1 armhf 2.4.92-1+rpi1 [25.2 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libdrm-nouveau2 armhf 2.4.92-1+rpi1 [24.4 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libdrm-radeon1 armhf 2.4.92-1+rpi1 [28.8 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libllvm6.0 armhf 1:6.0-3+rpi1 [12.5 MB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libsensors4 armhf 1:3.4.0-4+b1 [50.4 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libgl1-mesa-dri armhf 18.1.2-1 [4515 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf libglx-mesa0 armhf 18.1.2-1 [158 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libglx0 armhf 1.0.0+git20180308-3 [24.6 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libgl1 armhf 1.0.0+git20180308-3 [104 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf libgtk2.0-common all 2.24.32-2 [2695 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf libgtk2.0-0 armhf 2.24.32-2 [1497 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libfontenc1 armhf 1:1.1.3-1 [22.2 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libxcb-shape0 armhf 1.13-1 [98.5 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libxv1 armhf 2:1.0.11-1 [23.2 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf x11-utils armhf 7.7+4 [176 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf libatk-wrapper-java all 0.33.3-21 [45.2 kB]
Get:130 http://172.17.0.1/private buster-staging/main armhf libatk-wrapper-java-jni armhf 0.33.3-21 [33.6 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf libasound2-data all 1.1.6-1 [171 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf libasound2 armhf 1.1.6-1 [424 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf libgif7 armhf 5.1.4-3 [41.0 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf openjdk-10-jre armhf 10.0.1+10-4 [45.8 kB]
Get:135 http://172.17.0.1/private buster-staging/main armhf default-jre armhf 2:1.10-67 [1040 B]
Get:136 http://172.17.0.1/private buster-staging/main armhf openjdk-10-jdk-headless armhf 10.0.1+10-4 [70.8 MB]
Get:137 http://172.17.0.1/private buster-staging/main armhf default-jdk-headless armhf 2:1.10-67 [1100 B]
Get:138 http://172.17.0.1/private buster-staging/main armhf openjdk-10-jdk armhf 10.0.1+10-4 [17.1 kB]
Get:139 http://172.17.0.1/private buster-staging/main armhf default-jdk armhf 2:1.10-67 [1052 B]
Get:140 http://172.17.0.1/private buster-staging/main armhf fonts-lmodern all 2.004.5-3 [4540 kB]
Get:141 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-19 [232 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-19 [5459 kB]
Get:144 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.3.0-3+rpi1 [1436 B]
Get:145 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:146 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:147 http://172.17.0.1/private buster-staging/main armhf gir1.2-freedesktop armhf 1.56.1-1 [19.8 kB]
Get:148 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.8.1-1+rpi1 [622 kB]
Get:149 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.8.1-1+rpi1 [629 kB]
Get:150 http://172.17.0.1/private buster-staging/main armhf libpangoxft-1.0-0 armhf 1.42.1-2 [39.8 kB]
Get:151 http://172.17.0.1/private buster-staging/main armhf gir1.2-pango-1.0 armhf 1.42.1-2 [48.9 kB]
Get:152 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:154 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:155 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:156 http://172.17.0.1/private buster-staging/main armhf liblzo2-2 armhf 2.10-0.1 [48.4 kB]
Get:157 http://172.17.0.1/private buster-staging/main armhf libcairo-script-interpreter2 armhf 1.15.10-3 [129 kB]
Get:158 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:159 http://172.17.0.1/private buster-staging/main armhf libfreetype6-dev armhf 2.8.1-2 [2594 kB]
Get:160 http://172.17.0.1/private buster-staging/main armhf uuid-dev armhf 2.32-0.1 [91.3 kB]
Get:161 http://172.17.0.1/private buster-staging/main armhf libfontconfig1-dev armhf 2.13.0-5 [922 kB]
Get:162 http://172.17.0.1/private buster-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:163 http://172.17.0.1/private buster-staging/main armhf x11proto-dev all 2018.4-4 [251 kB]
Get:164 http://172.17.0.1/private buster-staging/main armhf x11proto-core-dev all 2018.4-4 [3128 B]
Get:165 http://172.17.0.1/private buster-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:166 http://172.17.0.1/private buster-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:167 http://172.17.0.1/private buster-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:168 http://172.17.0.1/private buster-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:169 http://172.17.0.1/private buster-staging/main armhf libxcb1-dev armhf 1.13-1 [168 kB]
Get:170 http://172.17.0.1/private buster-staging/main armhf libx11-dev armhf 2:1.6.5-1 [754 kB]
Get:171 http://172.17.0.1/private buster-staging/main armhf libxrender-dev armhf 1:0.9.10-1 [37.7 kB]
Get:172 http://172.17.0.1/private buster-staging/main armhf x11proto-xext-dev all 2018.4-4 [3128 B]
Get:173 http://172.17.0.1/private buster-staging/main armhf libxext-dev armhf 2:1.3.3-1+b2 [102 kB]
Get:174 http://172.17.0.1/private buster-staging/main armhf libice-dev armhf 2:1.0.9-2 [58.8 kB]
Get:175 http://172.17.0.1/private buster-staging/main armhf libsm-dev armhf 2:1.2.2-1+b3 [33.4 kB]
Get:176 http://172.17.0.1/private buster-staging/main armhf libpixman-1-dev armhf 0.34.0-2 [469 kB]
Get:177 http://172.17.0.1/private buster-staging/main armhf libxcb-render0-dev armhf 1.13-1 [110 kB]
Get:178 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0-dev armhf 1.13-1 [99.5 kB]
Get:179 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:180 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.6-1 [79.1 kB]
Get:181 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.6-1 [144 kB]
Get:182 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:183 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-9 [234 kB]
Get:184 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-9 [226 kB]
Get:185 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-9 [150 kB]
Get:186 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-9 [561 kB]
Get:187 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:188 http://172.17.0.1/private buster-staging/main armhf libcairo2-dev armhf 1.15.10-3 [597 kB]
Get:189 http://172.17.0.1/private buster-staging/main armhf libcupsimage2 armhf 2.2.8-4 [129 kB]
Get:190 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:191 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-1 [52.5 kB]
Get:192 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:193 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.60.0-2 [281 kB]
Get:194 http://172.17.0.1/private buster-staging/main armhf libcurl4-openssl-dev armhf 7.60.0-2 [353 kB]
Get:195 http://172.17.0.1/private buster-staging/main armhf libfribidi-dev armhf 0.19.7-3 [64.5 kB]
Get:196 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.11-2 [22.2 kB]
Get:197 http://172.17.0.1/private buster-staging/main armhf libijs-0.35 armhf 0.35-13 [16.7 kB]
Get:198 http://172.17.0.1/private buster-staging/main armhf libjbig2dec0 armhf 0.14-1 [52.9 kB]
Get:199 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:200 http://172.17.0.1/private buster-staging/main armhf libgs9-common all 9.22~dfsg-2.1 [5241 kB]
Get:201 http://172.17.0.1/private buster-staging/main armhf libgs9 armhf 9.22~dfsg-2.1 [1809 kB]
Get:202 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.8.1-1+rpi1 [615 kB]
Get:203 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:204 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:205 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.8.1-1+rpi1 [2378 kB]
Get:206 http://172.17.0.1/private buster-staging/main armhf libkpathsea6 armhf 2018.20180416.47457-5 [156 kB]
Get:207 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:208 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:209 http://172.17.0.1/private buster-staging/main armhf libmime-charset-perl all 1.012.2-1 [35.4 kB]
Get:210 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-4 [278 kB]
Get:211 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-4 [936 B]
Get:212 http://172.17.0.1/private buster-staging/main armhf libxft-dev armhf 2.3.2-2 [60.3 kB]
Get:213 http://172.17.0.1/private buster-staging/main armhf libpango1.0-dev armhf 1.42.1-2 [280 kB]
Get:214 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:215 http://172.17.0.1/private buster-staging/main armhf libpotrace0 armhf 1.15-1 [23.9 kB]
Get:216 http://172.17.0.1/private buster-staging/main armhf libptexenc1 armhf 2018.20180416.47457-5 [57.1 kB]
Get:217 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:218 http://172.17.0.1/private buster-staging/main armhf libsombok3 armhf 2.4.0-1 [27.0 kB]
Get:219 http://172.17.0.1/private buster-staging/main armhf libsynctex2 armhf 2018.20180416.47457-5 [66.7 kB]
Get:220 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [863 kB]
Get:221 http://172.17.0.1/private buster-staging/main armhf libtexlua52 armhf 2018.20180416.47457-5 [86.7 kB]
Get:222 http://172.17.0.1/private buster-staging/main armhf libtexlua53 armhf 2018.20180416.47457-5 [97.2 kB]
Get:223 http://172.17.0.1/private buster-staging/main armhf libtexluajit2 armhf 2018.20180416.47457-5 [204 kB]
Get:224 http://172.17.0.1/private buster-staging/main armhf libtext-unidecode-perl all 1.30-1 [103 kB]
Get:225 http://172.17.0.1/private buster-staging/main armhf libtiffxx5 armhf 4.0.9-6 [100 kB]
Get:226 http://172.17.0.1/private buster-staging/main armhf libtiff5-dev armhf 4.0.9-6 [337 kB]
Get:227 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.8-4 [657 kB]
Get:228 http://172.17.0.1/private buster-staging/main armhf libunicode-linebreak-perl armhf 0.0.20170401-1 [98.6 kB]
Get:229 http://172.17.0.1/private buster-staging/main armhf libxfont2 armhf 1:2.0.3-1 [120 kB]
Get:230 http://172.17.0.1/private buster-staging/main armhf libxkbfile1 armhf 1:1.0.9-2 [65.4 kB]
Get:231 http://172.17.0.1/private buster-staging/main armhf libxml-namespacesupport-perl all 1.12-1 [14.8 kB]
Get:232 http://172.17.0.1/private buster-staging/main armhf libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:233 http://172.17.0.1/private buster-staging/main armhf libxml-sax-perl all 1.00+dfsg-1 [58.6 kB]
Get:234 http://172.17.0.1/private buster-staging/main armhf libxml-libxml-perl armhf 2.0132+dfsg-2 [321 kB]
Get:235 http://172.17.0.1/private buster-staging/main armhf x11proto-scrnsaver-dev all 2018.4-4 [3136 B]
Get:236 http://172.17.0.1/private buster-staging/main armhf libxss-dev armhf 1:1.2.2-1 [22.7 kB]
Get:237 http://172.17.0.1/private buster-staging/main armhf libxt-dev armhf 1:1.1.5-1 [390 kB]
Get:238 http://172.17.0.1/private buster-staging/main armhf libzzip-0-13 armhf 0.13.62-3.1 [51.5 kB]
Get:239 http://172.17.0.1/private buster-staging/main armhf mpack armhf 1.6-8.2 [31.2 kB]
Get:240 http://172.17.0.1/private buster-staging/main armhf preview-latex-style all 11.91-1 [201 kB]
Get:241 http://172.17.0.1/private buster-staging/main armhf t1utils armhf 1.41-2 [52.0 kB]
Get:242 http://172.17.0.1/private buster-staging/main armhf tcl8.6 armhf 8.6.8+dfsg-4 [123 kB]
Get:243 http://172.17.0.1/private buster-staging/main armhf tcl8.6-dev armhf 8.6.8+dfsg-4 [892 kB]
Get:244 http://172.17.0.1/private buster-staging/main armhf texinfo armhf 6.5.0.dfsg.1-3 [1331 kB]
Get:245 http://172.17.0.1/private buster-staging/main armhf texlive-binaries armhf 2018.20180416.47457-5 [8512 kB]
Get:246 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:247 http://172.17.0.1/private buster-staging/main armhf texlive-base all 2018.20180505-1 [18.9 MB]
Get:248 http://172.17.0.1/private buster-staging/main armhf texlive-latex-base all 2018.20180505-1 [983 kB]
Get:249 http://172.17.0.1/private buster-staging/main armhf texlive-extra-utils all 2018.20180505-1 [30.4 MB]
Get:250 http://172.17.0.1/private buster-staging/main armhf texlive-fonts-extra all 2018.20180505-1 [378 MB]
Get:251 http://172.17.0.1/private buster-staging/main armhf texlive-fonts-recommended all 2018.20180505-1 [5292 kB]
Get:252 http://172.17.0.1/private buster-staging/main armhf texlive-plain-generic all 2018.20180505-1 [23.9 MB]
Get:253 http://172.17.0.1/private buster-staging/main armhf texlive-generic-recommended all 2018.20180505-1 [31.4 kB]
Get:254 http://172.17.0.1/private buster-staging/main armhf texlive-latex-recommended all 2018.20180505-1 [15.3 MB]
Get:255 http://172.17.0.1/private buster-staging/main armhf texlive-pictures all 2018.20180505-1 [4112 kB]
Get:256 http://172.17.0.1/private buster-staging/main armhf texlive-latex-extra all 2018.20180505-1 [11.0 MB]
Get:257 http://172.17.0.1/private buster-staging/main armhf tk8.6 armhf 8.6.8-4 [71.8 kB]
Get:258 http://172.17.0.1/private buster-staging/main armhf tk8.6-dev armhf 8.6.8-4 [667 kB]
Get:259 http://172.17.0.1/private buster-staging/main armhf x11-xkb-utils armhf 7.7+4 [138 kB]
Get:260 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:261 http://172.17.0.1/private buster-staging/main armhf xfonts-encodings all 1:1.0.4-2 [574 kB]
Get:262 http://172.17.0.1/private buster-staging/main armhf xfonts-utils armhf 1:7.7+6 [82.5 kB]
Get:263 http://172.17.0.1/private buster-staging/main armhf xfonts-base all 1:1.0.4+nmu1 [5911 kB]
Get:264 http://172.17.0.1/private buster-staging/main armhf xkb-data all 2.23.1-1 [675 kB]
Get:265 http://172.17.0.1/private buster-staging/main armhf xserver-common all 2:1.19.6-1 [2085 kB]
Get:266 http://172.17.0.1/private buster-staging/main armhf xvfb armhf 2:1.19.6-1 [2692 kB]
debconf: delaying package configuration, since apt-utils is not installed
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find: '/etc/bash_completion.d/': No such file or directory
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
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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
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Creating config file /etc/papersize with new version
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update-language: texlive-base not installed and configured, doing nothing!
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Not building database; man-db/auto-update is not 'true'.
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
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Setting up libpython3-stdlib:armhf (3.6.5-3) ...
Setting up libxcb-present0:armhf (1.13-1) ...
Setting up libfontconfig1:armhf (2.13.0-5) ...
Setting up libxcb-dri2-0:armhf (1.13-1) ...
Setting up libsm6:armhf (2:1.2.2-1+b3) ...
Setting up libxcb-dri3-0:armhf (1.13-1) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up libxcb-glx0:armhf (1.13-1) ...
Setting up libxcb-xfixes0:armhf (1.13-1) ...
Setting up libxcb-render0:armhf (1.13-1) ...
Setting up gsettings-desktop-schemas (3.28.0-1) ...
Setting up python3 (3.6.5-3) ...
Setting up libgtk-3-common (3.22.29-3+rpi1) ...
Setting up libx11-6:armhf (2:1.6.5-1) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up python2 (2.7.15-3) ...
Setting up libxmuu1:armhf (2:1.1.2-2) ...
Setting up libxcb-sync1:armhf (1.13-1) ...
Setting up libpython-stdlib:armhf (2.7.15-3) ...
Setting up gir1.2-harfbuzz-0.0:armhf (1.8.1-1+rpi1) ...
Setting up libfreetype6-dev:armhf (2.8.1-2) ...
Setting up libice-dev:armhf (2:1.0.9-2) ...
Setting up glib-networking:armhf (2.56.0-1) ...
Setting up libunicode-linebreak-perl (0.0.20170401-1) ...
Setting up libxcomposite1:armhf (1:0.4.4-2) ...
Setting up libxcb-shm0:armhf (1.13-1) ...
Setting up libxpm4:armhf (1:3.5.12-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxcb-shape0:armhf (1.13-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libxcb1-dev:armhf (1.13-1) ...
Setting up libavahi-client3:armhf (0.7-4) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libx11-dev:armhf (2:1.6.5-1) ...
Setting up libxft2:armhf (2.3.2-2) ...
Setting up python3-lib2to3 (3.6.6-1) ...
Setting up python3-distutils (3.6.6-1) ...
Setting up python (2.7.15-3) ...
Setting up xfonts-base (1:1.0.4+nmu1) ...
Setting up fontconfig (2.13.0-5) ...
Regenerating fonts cache... done.
Setting up libxkbfile1:armhf (1:1.0.9-2) ...
Setting up libfontconfig1-dev:armhf (2.13.0-5) ...
Setting up libsm-dev:armhf (2:1.2.2-1+b3) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libxfixes3:armhf (1:5.0.3-1) ...
Setting up libglib2.0-dev-bin (2.56.1-2) ...
Setting up libatspi2.0-0:armhf (2.28.0-3) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libxcb-shm0-dev:armhf (1.13-1) ...
Setting up libxrender-dev:armhf (1:0.9.10-1) ...
Setting up libglib2.0-dev:armhf (2.56.1-2) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libxcb-render0-dev:armhf (1.13-1) ...
Setting up libxft-dev:armhf (2.3.2-2) ...
Setting up libxcursor1:armhf (1:1.1.15-1) ...
Setting up libxxf86dga1:armhf (2:1.1.4-1) ...
Setting up libxext-dev:armhf (2:1.3.3-1+b2) ...
Setting up libpango-1.0-0:armhf (1.42.1-2) ...
Setting up libatk-bridge2.0-0:armhf (2.26.2-1) ...
Setting up libxv1:armhf (2:1.0.11-1) ...
Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ...
Setting up libxrandr2:armhf (2:1.5.1-1) ...
Setting up libcups2:armhf (2.2.8-4) ...
Setting up libxi6:armhf (2:1.7.9-1) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up libcairo2:armhf (1.15.10-3) ...
Setting up libxinerama1:armhf (2:1.1.3-1+b3) ...
Setting up libxt-dev:armhf (1:1.1.5-1) ...
Setting up libxdamage1:armhf (1:1.1.4-3) ...
Setting up x11-xkb-utils (7.7+4) ...
Setting up libcairo-script-interpreter2:armhf (1.15.10-3) ...
Setting up libtk8.6:armhf (8.6.8-4) ...
Setting up libcairo-gobject2:armhf (1.15.10-3) ...
Setting up libcurl4:armhf (7.60.0-2) ...
Setting up libxss-dev:armhf (1:1.2.2-1) ...
Setting up libxtst6:armhf (2:1.2.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.42.1-2) ...
Setting up libcupsimage2:armhf (2.2.8-4) ...
Setting up libgs9:armhf (9.22~dfsg-2.1) ...
Setting up libcurl4-openssl-dev:armhf (7.60.0-2) ...
Setting up xserver-common (2:1.19.6-1) ...
Setting up tk8.6 (8.6.8-4) ...
Setting up libcairo2-dev:armhf (1.15.10-3) ...
Setting up gir1.2-freedesktop:armhf (1.56.1-1) ...
Setting up tk8.6-dev:armhf (8.6.8-4) ...
Setting up libpangoxft-1.0-0:armhf (1.42.1-2) ...
Setting up libpangocairo-1.0-0:armhf (1.42.1-2) ...
Setting up gir1.2-pango-1.0:armhf (1.42.1-2) ...
Setting up default-jre-headless (2:1.10-67) ...
Setting up openjdk-10-jre-headless:armhf (10.0.1+10-4) ...
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up ca-certificates-java (20180516) ...
head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory
Adding debian:ACCVRAIZ1.pem
Adding debian:ACEDICOM_Root.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:AddTrust_Low-Value_Services_Root.pem
Adding debian:AddTrust_Public_Services_Root.pem
Adding debian:AddTrust_Qualified_Certificates_Root.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R1.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:CNNIC_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem
Adding debian:Camerfirma_Global_Chambersign_Root.pem
Adding debian:Certigna.pem
Adding debian:Certinomis_-_Autorité_Racine.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:Certplus_Root_CA_G1.pem
Adding debian:Certplus_Root_CA_G2.pem
Adding debian:Certum_Root_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Comodo_Secure_Services_root.pem
Adding debian:Comodo_Trusted_Services_root.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DST_ACES_CA_X6.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:EC-ACC.pem
Adding debian:EE_Certification_Centre_Root_CA.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:GeoTrust_Global_CA_2.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OpenTrust_Root_CA_G1.pem
Adding debian:OpenTrust_Root_CA_G2.pem
Adding debian:OpenTrust_Root_CA_G3.pem
Adding debian:PSCProcert.pem
Adding debian:QuoVadis_Root_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_EV_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:Swisscom_Root_CA_1.pem
Adding debian:Swisscom_Root_CA_2.pem
Adding debian:Swisscom_Root_EV_CA_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:UTN_USERFirst_Hardware_Root_CA.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Visa_eCommerce_Root.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:LuxTrust_Global_Root_2.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
done.
Setting up dh-autoreconf (19) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up openjdk-10-jdk-headless:armhf (10.0.1+10-4) ...
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up default-jdk-headless (2:1.10-67) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libharfbuzz-icu0:armhf (1.8.1-1+rpi1) ...
Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up texlive-binaries (2018.20180416.47457-5) ...
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 libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up texlive-base (2018.20180505-1) ...
tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex
Setting up shared-mime-info (1.9-2) ...
Setting up icu-devtools (60.2-6) ...
Setting up libxml-libxml-perl (2.0132+dfsg-2) ...
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 texlive-fonts-recommended (2018.20180505-1) ...
Setting up texlive-plain-generic (2018.20180505-1) ...
Setting up texlive-generic-recommended (2018.20180505-1) ...
Setting up texlive-latex-base (2018.20180505-1) ...
Setting up texlive-latex-recommended (2018.20180505-1) ...
Setting up texlive-extra-utils (2018.20180505-1) ...
Setting up texlive-fonts-extra (2018.20180505-1) ...
Setting up libllvm6.0:armhf (1:6.0-3+rpi1) ...
Setting up gettext (0.19.8.1-6) ...
Setting up texlive-pictures (2018.20180505-1) ...
Setting up libgdk-pixbuf2.0-0:armhf (2.36.11-2) ...
Setting up libsoup2.4-1:armhf (2.62.2-2) ...
Setting up libgl1-mesa-dri:armhf (18.1.2-1) ...
Installing new version of config file /etc/drirc ...
Setting up libsoup-gnome2.4-1:armhf (2.62.2-2) ...
Setting up libicu-dev (60.2-6) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up gtk-update-icon-cache (3.22.29-3+rpi1) ...
Setting up librest-0.7-0:armhf (0.8.0-2) ...
Setting up texinfo (6.5.0.dfsg.1-3) ...
Running mktexlsr. This may take some time. ... done.
Setting up libharfbuzz-dev:armhf (1.8.1-1+rpi1) ...
Setting up libglx-mesa0:armhf (18.1.2-1) ...
Setting up librsvg2-2:armhf (2.40.20-2) ...
Setting up texlive-latex-extra (2018.20180505-1) ...
Setting up po-debconf (1.0.20) ...
Setting up librsvg2-common:armhf (2.40.20-2) ...
Setting up libpango1.0-dev (1.42.1-2) ...
Setting up libglx0:armhf (1.0.0+git20180308-3) ...
Setting up adwaita-icon-theme (3.28.0-1) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up debhelper (11.3.5) ...
Setting up libgtk2.0-0:armhf (2.24.32-2) ...
Setting up libgtk-3-0:armhf (3.22.29-3+rpi1) ...
Setting up libgl1:armhf (1.0.0+git20180308-3) ...
Setting up xvfb (2:1.19.6-1) ...
Setting up x11-utils (7.7+4) ...
Setting up libatk-wrapper-java (0.33.3-21) ...
Setting up libatk-wrapper-java-jni:armhf (0.33.3-21) ...
Setting up openjdk-10-jre:armhf (10.0.1+10-4) ...
Setting up openjdk-10-jdk:armhf (10.0.1+10-4) ...
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode
update-alternatives: using /usr/lib/jvm/java-10-openjdk-armhf/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up default-jre (2:1.10-67) ...
Setting up default-jdk (2:1.10-67) ...
Setting up sbuild-build-depends-r-base-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
Processing triggers for ca-certificates (20170717) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...

done.
done.
Processing triggers for tex-common (6.09) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.
Processing triggers for libgdk-pixbuf2.0-0:armhf (2.36.11-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.30-21+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 linux-libc-dev_4.16.12-1+rpi1
Package versions: adduser_3.117 adwaita-icon-theme_3.28.0-1 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3 bash-completion_1:2.8-1 binutils_2.30-21+rpi1 binutils-arm-linux-gnueabihf_2.30-21+rpi1 binutils-common_2.30-21+rpi1 bison_2:3.0.4.dfsg-1+b1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 ca-certificates-java_20180516 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dbus_1.12.8-3 dbus-user-session_1.12.8-3 dconf-gsettings-backend_0.28.0-2 dconf-service_0.28.0-2 debconf_1.5.67 debhelper_11.3.5 debianutils_4.8.6 default-jdk_2:1.10-67 default-jdk-headless_2:1.10-67 default-jre_2:1.10-67 default-jre-headless_2:1.10-67 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.8-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 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libzzip-0-13_0.13.62-3.1 linux-base_4.5 linux-libc-dev_4.16.12-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32-0.1 mpack_1.6-8.2 multiarch-support_2.27-3+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1+20180210-4 netbase_5.4 openjdk-10-jdk_10.0.1+10-4 openjdk-10-jdk-headless_10.0.1+10-4 openjdk-10-jre_10.0.1+10-4 openjdk-10-jre-headless_10.0.1+10-4 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 poppler-data_0.4.9-2 preview-latex-style_11.91-1 procps_2:3.3.15-2 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-1 python2.7-minimal_2.7.15-1 python3_3.6.5-3 python3-distutils_3.6.6-1 python3-lib2to3_3.6.6-1 python3-minimal_3.6.5-3 python3.6_3.6.6-1 python3.6-minimal_3.6.6-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-base-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 shared-mime-info_1.9-2 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 t1utils_1.41-2 tar_1.30+dfsg-2 tcl8.6_8.6.8+dfsg-4 tcl8.6-dev_8.6.8+dfsg-4 tex-common_6.09 texinfo_6.5.0.dfsg.1-3 texlive-base_2018.20180505-1 texlive-binaries_2018.20180416.47457-5 texlive-extra-utils_2018.20180505-1 texlive-fonts-extra_2018.20180505-1 texlive-fonts-recommended_2018.20180505-1 texlive-generic-recommended_2018.20180505-1 texlive-latex-base_2018.20180505-1 texlive-latex-extra_2018.20180505-1 texlive-latex-recommended_2018.20180505-1 texlive-pictures_2018.20180505-1 texlive-plain-generic_2018.20180505-1 tk8.6_8.6.8-4 tk8.6-dev_8.6.8-4 tzdata_2018e-1 ucf_3.0038 udev_238-4 util-linux_2.32-0.1 uuid-dev_2.32-0.1 x11-common_1:7.7+19 x11-utils_7.7+4 x11-xkb-utils_7.7+4 x11proto-core-dev_2018.4-4 x11proto-dev_2018.4-4 x11proto-scrnsaver-dev_2018.4-4 x11proto-xext-dev_2018.4-4 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 xfonts-base_1:1.0.4+nmu1 xfonts-encodings_1:1.0.4-2 xfonts-utils_1:7.7+6 xkb-data_2.23.1-1 xorg-sgml-doctools_1:1.11-1 xserver-common_2:1.19.6-1 xtrans-dev_1.3.5-1 xvfb_2:1.19.6-1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jul  2 10:17:09 2018 UTC
gpgv:                using RSA key A1489FE2AB99A21A
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-base_3.5.1-1.dsc
dpkg-source: info: extracting r-base in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-base_3.5.1.orig.tar.gz
dpkg-source: info: unpacking r-base_3.5.1-1.debian.tar.xz

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-679c497f-0d88-488d-bcb2-92450f6ff5c7
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package r-base
dpkg-buildpackage: info: source version 3.5.1-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build r-base-3.5.1
dpkg-buildpackage: info: host architecture armhf
 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"				\
CXXFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"				\
FFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong"				\
FCFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong"				\
CPPFLAGS=					\
LDFLAGS="-Wl,-z,relro"				\
FLIBS=						\
rsharedir=/usr/share/R/share			\
rincludedir=/usr/share/R/include		\
rdocdir=/usr/share/R/doc			\
./configure --prefix=/usr			\
	    --with-cairo			\
	    --with-jpeglib			\
	    --with-readline			\
	    --with-tcltk			\
	    --with-system-bzlib			\
	    --with-system-pcre			\
	    --with-system-zlib			\
	    --mandir=/usr/share/man		\
	    --infodir=/usr/share/info		\
	    --datadir=/usr/share/R/share	\
	    --includedir=/usr/share/R/include	\
	    --with-blas		\
	    --with-lapack		\
	    --enable-R-profiling		\
	    --enable-R-shlib			\
	    --enable-memory-profiling		\
	    --without-recommended-packages	\
	    --build arm-linux-gnueabihf
configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking whether ln -s works... yes
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for /usr/bin/pager... /usr/bin/pager
checking for 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 working aclocal... found
checking for working autoconf... found
checking for working autoheader... found
checking for bison... bison -y
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc -std=gnu99 needs -traditional... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... gcc -std=gnu99 -E
defining F77 to be gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g can compile C++ code... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc -std=gnu99 accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether g++ can compile ObjC++... no
checking whether  can compile ObjC++... no
no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf 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... mt
checking if mt 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_callback_sigcleanup exists and is declared... yes
checking whether rl_completion_matches exists and is declared... yes
checking whether rl_resize_terminal exists and is declared... yes
checking whether rl_sort_completion_matches exists and is declared... yes
checking for 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 for dlfcn.h... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.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 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/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 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 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 floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
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 sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.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... 8
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/arm-linux-gnueabihf/7 -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lgfortran -lm
checking how to get verbose linking output from gcc -std=gnu99... -v
checking for C libraries of gcc -std=gnu99...  -L/usr/lib/gcc/arm-linux-gnueabihf/7 -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -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
./configure: line 27483: ::: command not found
checking for xmkmf... no
checking whether g++  supports C++98 features with -std=gnu++98... yes
checking whether g++  supports C++11 features with -std=gnu++11... yes
checking whether g++  supports C++14 features with -std=gnu++14... yes
checking whether g++  supports C++17 features with -std=gnu++17... 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 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... no
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 select exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether setrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
checking whether gmtime_r exists and is declared... yes
checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking whether utimensat exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... yes
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... yes
checking for realpath... yes
checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
checking for dladdr... yes
checking for dlsym... yes
checking whether dladdr is declared... yes
checking whether dlsym is declared... yes
checking whether RTLD_DEFAULT is declared... yes
checking whether RTLD_NEXT is declared... yes
checking thread.h usability... no
checking thread.h presence... no
checking for thread.h... no
checking whether thr_stksegment exists and is declared... no
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
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 for working ctanh... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_... no
checking for ATL_xerbla in -latlas... no
checking for dgemm_ in -lblas... yes
checking for dgemm_ in -ldgemm... no
checking for dgemm_ in -lblas... (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 whether iconv accepts "CP1252"... yes
checking for iconvlist... no
checking for iconv... yes
checking for iconv declaration... 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking 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... yes
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 >= 8.20, < 10.0 and has UTF-8 support... yes
checking if PCRE version >= 8.32... yes
checking whether PCRE support suffices... yes
checking for pcre2-config... no
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 7.60.0
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 >= 7.22.0... 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

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

R is now configured for arm-unknown-linux-gnueabihf

  Source directory:          .
  Installation directory:    /usr

  C compiler:                gcc -std=gnu99  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  Fortran 77 compiler:       gfortran  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong

  Default C++ compiler:      g++   -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  C++98 compiler:            g++ -std=gnu++98 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  C++11 compiler:            g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  C++14 compiler:            g++ -std=gnu++14 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  C++17 compiler:            g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  Fortran 90/95 compiler:    gfortran -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"			\
		CXXFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"			\
		FFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong"			\
		FCFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong"			\
		CC="gcc -std=gnu99"				\
		CXX=g++			\
		F77=gfortran			\
		LDFLAGS="-Wl,-z,relro"			\
		PKG_BUILT_STAMP=""""	\
		R_GZIPCMD="/bin/gzip -n"		\
		R
make[1]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dchdc.f -o dchdc.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dpbfa.f -o dpbfa.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dpbsl.f -o dpbsl.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dpoco.f -o dpoco.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dpodi.f -o dpodi.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dpofa.f -o dpofa.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dposl.f -o dposl.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dqrdc.f -o dqrdc.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dqrls.f -o dqrls.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dqrsl.f -o dqrsl.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dqrutl.f -o dqrutl.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dsvdc.f -o dsvdc.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c dtrco.f -o dtrco.o
gfortran  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signrank.c -o signrank.o
ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[4]: Leaving directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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 altrep.d from altrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making radixsort.d from radixsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making g_alab_her.d from g_alab_her.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making g_her_glyph.d from g_her_glyph.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
make[4]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c altrep.c -o altrep.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c main.c -o main.o
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c xxxpr.f -o xxxpr.o
gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro  -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a    -lblas -lgfortran -lm   -lreadline  -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
make[5]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmain.c -o Rmain.o
gcc -std=gnu99 -Wl,--export-dynamic -fopenmp  -L"../../lib" -Wl,-z,relro -o R.bin Rmain.o  -lR 
make[5]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c sockconn.c -o sockconn.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR  
make[6]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Lapack.c -o Lapack.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o lapack.so  Lapack.o  -lR  -llapack -lblas -lgfortran -lm
make[6]: Entering directory '/<<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/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbitmap.c -o rbitmap.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt  -lR -lm 
gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dataentry.c -o dataentry.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt  -lR -lm 
make[5]: Leaving directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramRd.c -o gramRd.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR
make[7]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR
make[7]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devQuartz.c -o devQuartz.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[7]: Entering directory '/<<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/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../../../src/modules/X11  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cairoBM.c -o cairoBM.o
gcc -std=gnu99 -shared -L"../../../../../lib" -Wl,-z,relro -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm 
make[10]: Leaving directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stem.c -o stem.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[7]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c bsplvd.f -o bsplvd.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c bvalue.f -o bvalue.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c bvalus.f -o bvalus.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c loessf.f -o loessf.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c ppr.f -o ppr.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c qsbart.f -o qsbart.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c sgram.f -o sgram.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c sinerp.f -o sinerp.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c sslvrg.f -o sslvrg.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c stxwx.f -o stxwx.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c hclust.f -o hclust.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c kmns.f -o kmns.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c eureka.f -o eureka.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c stl.f -o stl.o
gfortran -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c portsrc.f -o portsrc.o
gfortran  -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -c lminfl.f -o lminfl.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lblas -lgfortran -lm -L../../../../lib -lR
make[7]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
make[7]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c viewport.c -o viewport.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[7]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR
make[7]: Entering directory '/<<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     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk.c -o tcltk.o
gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6     -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk_unix.c -o tcltk_unix.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -L/usr/lib/arm-linux-gnueabihf -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fork.c -o fork.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[7]: Entering directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"		\
		CXXFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"	\
		FFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.lo
gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro -o libRmath.so -Wl,-soname,libRmath.so.1 mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm
make[2]: Leaving directory '/<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.o
ar -cr libRmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o
ranlib libRmath.a
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gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-z,relro -DR_HOME='"/<<PKGBUILDDIR>>"' \
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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'
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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'.
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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'
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make[8]: Entering directory '/<<PKGBUILDDIR>>/src/library/grDevices/src/cairo'
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make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/library/grDevices'
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building package 'graphics'
make[5]: Entering directory '/<<PKGBUILDDIR>>/src/library/graphics'
all.R is unchanged
make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/library/graphics'
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make[6]: Entering directory '/<<PKGBUILDDIR>>/src/library/graphics/src'
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make[5]: Nothing to be done for 'mklazycomp'.
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make[4]: Entering directory '/<<PKGBUILDDIR>>/src/library/stats'
building package 'stats'
make[5]: Entering directory '/<<PKGBUILDDIR>>/src/library/stats'
all.R is unchanged
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make[6]: Entering directory '/<<PKGBUILDDIR>>/src/library/stats/src'
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make[5]: Nothing to be done for 'mklazycomp'.
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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'
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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'
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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
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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'
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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
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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 doc/NEWS
creating doc/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'
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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'
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make[2]: Entering directory '/<<PKGBUILDDIR>>/share'
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make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/scripts'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/scripts'
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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.
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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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -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'
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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/bin/java
Java version     : 10.0.1
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: 
Java archive tool: /usr/lib/jvm/default-java/bin/jar

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
make[3]: Entering directory '/tmp/Rjavareconf.BUXPvc'
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/<<PKGBUILDDIR>>/lib -lR
make[3]: Leaving directory '/tmp/Rjavareconf.BUXPvc'


JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -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'
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  base
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served strictly? Note that set-ting
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
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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/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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 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
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[][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls 
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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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 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(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
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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

Underfull \hbox (badness 1248) in paragraph at lines 6756--6762
\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 6756--6762
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
[105]
Underfull \hbox (badness 3568) in paragraph at lines 6818--6825
\T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z
i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
[106] [107]
Underfull \vbox (badness 10000) has occurred while \output is active [108]
[109] [110]
Underfull \hbox (badness 1077) in paragraph at lines 7135--7141
[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
1/ptm/m/n/10 . Con-di-tions of length greater

Underfull \hbox (badness 1231) in paragraph at lines 7135--7141
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[111] [112] [113] [114] [115] [116]
Underfull \hbox (badness 2096) in paragraph at lines 7476--7480
\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
 : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$
[][]\T1/ptm/m/n/10 .
[117]
Underfull \hbox (badness 3000) in paragraph at lines 7569--7571
[]\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
[118]
Underfull \hbox (badness 2351) in paragraph at lines 7594--7597
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[119] [120] [121] [122]
Underfull \hbox (badness 10000) in paragraph at lines 7849--7859
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[123]
Underfull \hbox (badness 4479) in paragraph at lines 7920--7930
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
[124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148] [149]
Underfull \hbox (badness 1394) in paragraph at lines 9676--9681
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[150] [151] [152] [153] [154]
Underfull \hbox (badness 1194) in paragraph at lines 10021--10026
[]\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 10021--10026
\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
[155] [156] [157]
Underfull \hbox (badness 1735) in paragraph at lines 10226--10230
\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 .
[158] [159] [160] [161] [162] [163] [164]
Underfull \hbox (badness 2150) in paragraph at lines 10649--10652
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 6396) in paragraph at lines 10663--10671
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
[165]
Underfull \hbox (badness 2735) in paragraph at lines 10692--10699
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177]
[178] [179] [180]
Underfull \hbox (badness 4569) in paragraph at lines 11772--11776
[]\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 11772--11776
\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
[181] [182] [183] [184] [185] [186] [187] [188] [189]
Underfull \hbox (badness 2698) in paragraph at lines 12349--12358
[]\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 12349--12358
\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
[190] [191] [192] [193] [194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 6236) in paragraph at lines 13008--13011
[]\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
[200] [201] [202] [203] [204] [205] [206]
Underfull \hbox (badness 2253) in paragraph at lines 13430--13432
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[207]
Underfull \hbox (badness 1565) in paragraph at lines 13501--13505
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[208]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13547
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[209] [210]
Underfull \hbox (badness 1466) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[211] [212]
Underfull \hbox (badness 10000) in paragraph at lines 13804--13808
[][][]\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 13815--13818
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[213] [214] [215] [216]
Underfull \hbox (badness 3965) in paragraph at lines 14097--14101
[]\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,
[217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228]
[229]
Underfull \hbox (badness 4429) in paragraph at lines 14859--14862
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
[230]
Underfull \hbox (badness 10000) in paragraph at lines 14959--14961
[]\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 14965--14969
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[231]
Underfull \hbox (badness 10000) in paragraph at lines 15004--15008
[]\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 15004--15008
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[232] [233] [234] [235] [236] [237] [238] [239] [240]
Underfull \hbox (badness 2452) in paragraph at lines 15596--15600
[]\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 15596--15600
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[241] [242] [243]
Underfull \hbox (badness 1092) in paragraph at lines 15769--15774
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[244] [245] [246]
Underfull \hbox (badness 6741) in paragraph at lines 16020--16024
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[247] [248] [249] [250] [251]
Underfull \hbox (badness 1867) in paragraph at lines 16326--16333
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[252] [253] [254] [255]
Underfull \vbox (badness 10000) has occurred while \output is active [256]
[257] [258]
Underfull \hbox (badness 3679) in paragraph at lines 16736--16738
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[259] [260] [261] [262] [263] [264] [265] [266]
Underfull \hbox (badness 1478) in paragraph at lines 17301--17304
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 17554--17556
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[270] [271] [272] [273] [274] [275] [276] [277] [278] [279]
Underfull \hbox (badness 1442) in paragraph at lines 18145--18147
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[280]
Underfull \hbox (badness 2452) in paragraph at lines 18237--18253
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1248) in paragraph at lines 18651--18654
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[288] [289] [290] [291]
Underfull \hbox (badness 4739) in paragraph at lines 18909--18911
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303]
[304] [305] [306] [307] [308]
Underfull \hbox (badness 2469) in paragraph at lines 19926--19931
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 19940--19947
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[309]
Underfull \hbox (badness 10000) in paragraph at lines 20014--20018
[]\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 20014--20018
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[310] [311]
Underfull \hbox (badness 1509) in paragraph at lines 20149--20156
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1552) in paragraph at lines 20149--20156
\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 20165--20170
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 1264) in paragraph at lines 20916--20921
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:

Underfull \hbox (badness 4441) in paragraph at lines 20945--20948
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 21679--21681
[]\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
[335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346]
[347] [348] [349] [350] [351]
Underfull \hbox (badness 1077) in paragraph at lines 22714--22720
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[352] [353] [354]
Underfull \hbox (badness 1484) in paragraph at lines 22877--22885
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[355] [356] [357] [358]
Underfull \hbox (badness 2790) in paragraph at lines 23162--23165
[]\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 23162--23165
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[359] [360] [361] [362]
Underfull \hbox (badness 1194) in paragraph at lines 23444--23447
[]\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
[363] [364] [365]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23656
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 7379) in paragraph at lines 23650--23656
\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 23660--23663
[]\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 23660--23663
\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
[366] [367] [368] [369] [370] [371]
Underfull \hbox (badness 10000) in paragraph at lines 24031--24034
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
[372] [373] [374] [375] [376] [377] [378] [379] [380]
Underfull \hbox (badness 10000) in paragraph at lines 24623--24625
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[381] [382] [383] [384]
Underfull \hbox (badness 1199) in paragraph at lines 24867--24873
[]\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 24867--24873
\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,
[385] [386] [387] [388] [389] [390] [391] [392] [393]
Underfull \hbox (badness 1038) in paragraph at lines 25459--25467
[]\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 25468--25471
[]\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 25487--25489
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[394]
Underfull \hbox (badness 10000) in paragraph at lines 25596--25606
[]\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 25607--25613
[]\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
[395]
Underfull \hbox (badness 1968) in paragraph at lines 25643--25648
[]\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 25653--25655
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[396] [397] [398]
Underfull \hbox (badness 10000) in paragraph at lines 25916--25922
[]\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 25916--25922
\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 25916--25922
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 25929--25932
[]\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 25953--25955
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[399]
Underfull \hbox (badness 10000) in paragraph at lines 25985--25990
[]\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 25991--26002
\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 26003--26006
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 3713) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN ma-cOS build),

Underfull \hbox (badness 7944) in paragraph at lines 26013--26025
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).

Underfull \hbox (badness 2351) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z
i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo
pard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26027--26034
[]\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 26027--26034
\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 26027--26034
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1874) in paragraph at lines 26027--26034
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[400] [401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 26371--26375
[]\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 26371--26375
\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)]
[405] [406] [407] [408] [409]
Underfull \hbox (badness 1735) in paragraph at lines 26690--26694
[]\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
[410] [411] [412] [413] [414] [415] [416] [417] [418] [419]
Underfull \hbox (badness 2726) in paragraph at lines 27265--27268
[]\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
[420] [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431]
[432]
Underfull \hbox (badness 1052) in paragraph at lines 28094--28099
[]\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
[433] [434] [435] [436] [437]
Underfull \vbox (badness 10000) has occurred while \output is active [438]
[439] [440] [441] [442] [443] [444] [445]
Underfull \hbox (badness 1533) in paragraph at lines 28926--28929
[]\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
[446] [447]
Underfull \hbox (badness 1163) in paragraph at lines 29089--29100
[]\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
[448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459]
[460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471]
Underfull \hbox (badness 10000) in paragraph at lines 30622--30626
[]\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 30622--30626
\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.
[472]
Underfull \hbox (badness 6188) in paragraph at lines 30644--30646
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 1655) in paragraph at lines 31187--31189
[]\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
[481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491]
Underfull \hbox (badness 10000) in paragraph at lines 31895--31899
[]\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.,
[492] [493] [494] [495]
Underfull \hbox (badness 2302) in paragraph at lines 32146--32153
[]\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 32146--32153
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3333) in paragraph at lines 32146--32153
\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 32146--32153
\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
[496] [497] [498]
Underfull \hbox (badness 2261) in paragraph at lines 32302--32307
[]\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 32329--32335
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[499]
Underfull \hbox (badness 10000) in paragraph at lines 32405--32410
[]\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
[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] [532] [533] [534] [535]
[536] [537] [538]
Underfull \vbox (badness 3803) has occurred while \output is active [539]
[540] [541] [542] [543] [544] [545] [546]
Underfull \hbox (badness 1072) in paragraph at lines 35447--35451
[]\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 35452--35456
[]\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 35480--35486
[]\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 35480--35486
\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 35480--35486
\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
[547]
Underfull \hbox (badness 3343) in paragraph at lines 35492--35499
\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 35492--35499
\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 35492--35499
\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
[548] [549] [550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 35833--35839
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1264) in paragraph at lines 35833--35839
\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
[553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564]
[565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576]
[577] [578] [579] [580] [581] [582]
Underfull \hbox (badness 3333) in paragraph at lines 37683--37688
[]\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
[583] [584] [585] [586] [587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 1472) in paragraph at lines 38315--38318
[]\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
[593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604]
[605] [606]
Underfull \hbox (badness 10000) in paragraph at lines 39221--39225
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e.,
[607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 39471--39474
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[611] [612]
Underfull \hbox (badness 10000) in paragraph at lines 39589--39593
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 10000) in paragraph at lines 39651--39655
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[614] [615] [616] [617] [618] [619] [620] [621] [622]
Underfull \hbox (badness 4013) in paragraph at lines 40264--40266
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / 
tz-[]link .
[623] [624] [625] [626] [627] [628]
Underfull \vbox (badness 10000) has occurred while \output is active [629]
[630] [631] [632] [633] [634] [635] [636]
Underfull \hbox (badness 3460) in paragraph at lines 41145--41148
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via

Underfull \hbox (badness 1990) in paragraph at lines 41152--41160
[]\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 41152--41160
\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
[637] [638] [639] [640]
Underfull \hbox (badness 10000) in paragraph at lines 41429--41432
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[641] [642] [643] [644]
Underfull \hbox (badness 1917) in paragraph at lines 41657--41664
[]\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
[645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655]
Underfull \hbox (badness 3668) in paragraph at lines 42378--42380
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[656] [657]
Underfull \hbox (badness 2401) in paragraph at lines 42506--42510
[]\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
[658] [659] [660]
Underfull \hbox (badness 2111) in paragraph at lines 42695--42700
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.

Underfull \hbox (badness 7362) in paragraph at lines 42711--42716
[]\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
[661] [662] [663] [664] [665] [666] [667] [668] [669]
Underfull \hbox (badness 5417) in paragraph at lines 43290--43294
[]\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
[670]
Underfull \hbox (badness 10000) in paragraph at lines 43351--43355
[]\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
[671] [672]) (./compiler-pkg.tex
Chapter 2.
[673] [674] [675] [676]) (./datasets-pkg.tex
Chapter 3.
[677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688]
[689] [690] [691] [692] [693]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705]
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
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[755] [756] [757]) (./grDevices-pkg.tex [758]
Chapter 4.
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[771] [772] [773] [774] [775]
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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
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[]\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
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\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
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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/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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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 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 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
[832]
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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
[833]
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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
[836]
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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 ,
[839]
Underfull \hbox (badness 10000) in paragraph at lines 5102--5109
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

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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 .
[840] [841] [842]
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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 ,
[843]
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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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Underfull \hbox (badness 10000) in paragraph at lines 5772--5775
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
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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
[866] [867] [868]) (./graphics-pkg.tex
Chapter 5.
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Underfull \hbox (badness 10000) in paragraph at lines 687--694
[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
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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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Underfull \hbox (badness 10000) in paragraph at lines 4785--4791
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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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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[948 </<<PKGBUILDDIR>>/library/graphics/help/figures/mai.pdf>]

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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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.pdf>] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986]
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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 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[1003] [1004] [1005] [1006] [1007] [1008] [1009]
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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
[1010]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8793 \HeaderA{units}{Graphical Units}{units}
                                               [1011] [1012] [1013] [1014])
(./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
[1088] [1089] [1090] [1091]
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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
[1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102]
[1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
Underfull \hbox (badness 10000) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
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Underfull \hbox (badness 7649) in paragraph at lines 6356--6359
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1122] [1123] [1124] [1125]) (./methods-pkg.tex [1126]
Chapter 7.
[1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134]
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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 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests
[1154]
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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

Underfull \hbox (badness 1038) in paragraph at lines 1981--1986
\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1155] [1156] [1157]
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1158] [1159] [1160] [1161] [1162]
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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
[1165]
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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
[1166] [1167] [1168] [1169] [1170] [1171] [1172]
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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
[1173] [1174] [1175] [1176] [1177]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
[1178]
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[]\T1/ptm/m/n/10 The
[1179]
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[] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))

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[1180]
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[]\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190]
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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
[1191]
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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 4531--4538
\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and
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[1202]
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[]\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1203]
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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
[1204]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1205] [1206] [1207] [1208]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216]
Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1217] [1218] [1219] [1220]
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                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
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l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
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l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
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l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1228]
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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
[1229] [1230] [1231]
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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
[1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242]
[1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253]
[1254] [1255] [1256] [1257] [1258]
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[1271] [1272] [1273]
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1274] [1275] [1276] [1277]) (./parallel-pkg.tex [1278]
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289]
[1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
Underfull \hbox (badness 3386) in paragraph at lines 1339--1342
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1300] [1301] [1302]) (./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
[1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313]
[1314] [1315] [1316] [1317]) (./stats-pkg.tex [1318]
Chapter 10.
[1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329]
[1330] [1331]
Underfull \hbox (badness 1412) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339]
Underfull \hbox (badness 2503) in paragraph at lines 1328--1331
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1340] [1341] [1342]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1343] [1344] [1345] [1346]
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[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via

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\T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-ing
[1347] [1348] [1349] [1350] [1351] [1352] [1353]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1354] [1355] [1356] [1357] [1358]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
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[1370]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1371] [1372]
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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 ,
[1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383]
[1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1393] [1394]
Underfull \hbox (badness 3612) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
[1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]
Underfull \hbox (badness 2556) in paragraph at lines 5270--5273
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5287--5289
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1403] [1404] [1405] [1406]
Underfull \hbox (badness 1142) in paragraph at lines 5528--5540
\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.
[1407] [1408] [1409]
Underfull \hbox (badness 2503) in paragraph at lines 5680--5684
[]\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 ,
[1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417]
Underfull \hbox (badness 8132) in paragraph at lines 6184--6189
\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,
[1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 7081) in paragraph at lines 6462--6465
[]\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
[1423] [1424] [1425] [1426] [1427]
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[1429] [1430] [1431] [1432] [1433] [1434] [1435]
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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
[1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446]
[1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457]
[1458] [1459] [1460] [1461] [1462]
Underfull \hbox (badness 2626) in paragraph at lines 8953--8956
[]\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
[1463]
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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 ,
[1464]
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[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-

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\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1465] [1466] [1467] [1468] [1469]
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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 . 
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480]
[1481] [1482] [1483] [1484]
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@

Underfull \hbox (badness 1253) in paragraph at lines 10729--10732
[]\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,
[1490]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\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 11208--11217
\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-
[1497] [1498] [1499] [1500] [1501]
Underfull \hbox (badness 10000) in paragraph at lines 11516--11519
[]\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.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1505] [1506]
Underfull \hbox (badness 1484) in paragraph at lines 11801--11803
[]\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
[1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516]
Underfull \hbox (badness 4441) in paragraph at lines 12387--12389
[]\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
[1517] [1518] [1519] [1520] [1521] [1522]
Underfull \hbox (badness 2894) in paragraph at lines 12730--12734
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533]
[1534]
Underfull \hbox (badness 4518) in paragraph at lines 13480--13485
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544]
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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
[1545] [1546]
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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
[1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557]
[1558] [1559] [1560] [1561] [1562] [1563]
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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 ,
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572]
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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
[1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583]
[1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594]
[1595] [1596] [1597] [1598]
Underfull \hbox (badness 2359) in paragraph at lines 17507--17509
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1599]
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[1613]
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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
[1614]
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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
[1615] [1616] [1617]
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 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

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 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

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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
[1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633]
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[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1634] [1635] [1636] [1637]
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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 ,
[1644]
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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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[1656] [1657] [1658] [1659] [1660] [1661] [1662]
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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 ,
[1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673]
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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
[1685] [1686] [1687] [1688] [1689] [1690] [1691] [1692]
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 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1693] [1694] [1695] [1696] [1697]
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706]
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[]\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
[1707]
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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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[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1717] [1718] [1719]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1720]
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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

Underfull \hbox (badness 10000) in paragraph at lines 24800--24804
\T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was

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\T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o
f un-de-ter-mined co-ef-fi-cients, e.g., for
[1721] [1722] [1723] [1724] [1725] [1726] [1727]
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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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[1739] [1740] [1741] [1742] [1743] [1744]
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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
[1745] [1746]
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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
[1747]
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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
[1748]
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 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1749]
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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
[1750] [1751] [1752] [1753]
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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
[1754]
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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
[1755]
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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
[1756] [1757]
Underfull \hbox (badness 3514) in paragraph at lines 27058--27063
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1758] [1759]
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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
[1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767]
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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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Underfull \hbox (badness 5431) in paragraph at lines 28286--28288
[]\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
[1778] [1779] [1780] [1781]
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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
[1782] [1783] [1784] [1785] [1786]
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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
[1787] [1788]
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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
[1789] [1790] [1791]
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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
[1811] [1812] [1813]
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[1815] [1816]
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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
[1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825]
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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
[1826]
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[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the

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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
[1827] [1828] [1829] [1830] [1831] [1832]
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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
[1833] [1834] [1835]) (./stats4-pkg.tex [1836]
Chapter 11.
[1837] [1838] [1839] [1840] [1841] [1842]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}
                                                   [1843] [1844] [1845]
[1846]) (./tcltk-pkg.tex
Chapter 12.
[1847] [1848] [1849] [1850] [1851] [1852] [1853]
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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 ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1867]) (./tools-pkg.tex [1868]
Chapter 13.
[1869]

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[1870]
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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
[1871] [1872]
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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
[1886]
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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-
[1887]
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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 ,
[1888] [1889] [1890]
Underfull \hbox (badness 10000) in paragraph at lines 1377--1379
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1891] [1892] [1893]
Underfull \hbox (badness 2293) in paragraph at lines 1551--1553
[]\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
[1894] [1895]
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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
[1896] [1897] [1898] [1899]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.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1900] [1901] [1902]
[1903] [1904]
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1905] [1906] [1907]
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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
[1908] [1909] [1910] [1911] [1912] [1913] [1914]

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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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[1930]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1931] [1932]
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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 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
[1935] [1936] [1937]
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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
[1938]
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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

Underfull \hbox (badness 7221) in paragraph at lines 4337--4342
\T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo
r in-stance if there was
[1939] [1940] [1941]
Underfull \hbox (badness 2197) in paragraph at lines 4486--4496
[]\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :

Underfull \hbox (badness 2229) in paragraph at lines 4486--4496
\T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T
1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if
[1942]
Underfull \hbox (badness 1571) in paragraph at lines 4549--4553
[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1943] [1944] [1945]) (./utils-pkg.tex [1946]
Chapter 14.
[1947]
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 ',
[1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955]
Underfull \hbox (badness 10000) in paragraph at lines 620--626
[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3343) in paragraph at lines 620--626
\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1956] [1957]
Underfull \hbox (badness 5847) in paragraph at lines 753--759
[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

Underfull \hbox (badness 4229) in paragraph at lines 753--759
\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1958]
Underfull \hbox (badness 3861) in paragraph at lines 821--826
[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
[1959] [1960] [1961]
Underfull \hbox (badness 1430) in paragraph at lines 992--999
\T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio
n to the for-

Underfull \hbox (badness 1931) in paragraph at lines 992--999
\T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo
re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 1038) in paragraph at lines 992--999
\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

Underfull \hbox (badness 1817) in paragraph at lines 992--999
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

Underfull \hbox (badness 10000) in paragraph at lines 1003--1005
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1962] [1963] [1964]
Underfull \vbox (badness 10000) has occurred while \output is active [1965]
[1966] [1967] [1968] [1969]
Underfull \hbox (badness 1371) in paragraph at lines 1482--1484
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1970] [1971] [1972] [1973] [1974] [1975] [1976]
Underfull \hbox (badness 2057) in paragraph at lines 1959--1961
[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1977] [1978]
Underfull \hbox (badness 10000) in paragraph at lines 2054--2056
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1979]
Underfull \hbox (badness 5189) in paragraph at lines 2156--2158
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1980] [1981] [1982] [1983]
Underfull \hbox (badness 1661) in paragraph at lines 2374--2381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

Underfull \hbox (badness 1748) in paragraph at lines 2390--2393
[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1984] [1985] [1986] [1987] [1988] [1989] [1990]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing

Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000]
Underfull \hbox (badness 1430) in paragraph at lines 3484--3492
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[2001]
Underfull \hbox (badness 1231) in paragraph at lines 3533--3539
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2002] [2003]
Underfull \hbox (badness 10000) in paragraph at lines 3686--3688
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]pdf
TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4373 ...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.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [2015] [2016] [2017]
[2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028]
[2029] [2030]
Underfull \hbox (badness 1371) in paragraph at lines 5370--5372
[]\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
[2031]
Underfull \hbox (badness 1502) in paragraph at lines 5459--5464
[]\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 5459--5464
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2032] [2033] [2034]
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2035]
Underfull \hbox (badness 2150) in paragraph at lines 5695--5698
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2036] [2037]
Underfull \hbox (badness 3118) in paragraph at lines 5832--5834
[]\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
[2038]
Underfull \hbox (badness 2409) in paragraph at lines 5865--5869
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[2039]
Underfull \hbox (badness 1325) in paragraph at lines 5973--5977
[]\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
[2040]
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
[]\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 6056--6059
\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.,
[2041]
Underfull \hbox (badness 3219) in paragraph at lines 6129--6136
[]\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 6129--6136
\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 6129--6136
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 6229--6234
[][][]\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 ,
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065]
[2066] [2067]
Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from

Underfull \hbox (badness 10000) in paragraph at lines 7676--7678
[]\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 7684--7689
[]\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,
[2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087]
[2088] [2089]
Underfull \hbox (badness 1097) in paragraph at lines 9111--9114
[]\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
[2090]
Underfull \hbox (badness 3000) in paragraph at lines 9247--9252
[][][]\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 ;
[2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099]
Underfull \hbox (badness 2134) in paragraph at lines 9830--9835
[][][]\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 ;
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
Underfull \hbox (badness 5077) in paragraph at lines 10255--10259
[]\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/
sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-

Underfull \hbox (badness 2269) in paragraph at lines 10255--10259
\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 10267--10271
[]\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 10267--10271
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2107] [2108] [2109] [2110] [2111]
Underfull \hbox (badness 4060) in paragraph at lines 10544--10547
[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

Overfull \hbox (18.77168pt too wide) in paragraph at lines 10567--10567
 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
[2112]
Underfull \hbox (badness 10000) in paragraph at lines 10630--10632
[]\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
[2113] [2114] [2115]
Underfull \hbox (badness 2150) in paragraph at lines 10806--10808
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2116] [2117] [2118] [2119]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2120] [2121]
Underfull \hbox (badness 2096) in paragraph at lines 11174--11177
[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether PNG fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1527) in paragraph at lines 11178--11181
[]\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
[2122]
Underfull \hbox (badness 1009) in paragraph at lines 11250--11261
[]\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
[2123] [2124] [2125] [2126] [2127]
Underfull \hbox (badness 3780) in paragraph at lines 11556--11560
[]\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 11572--11575
[]\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
[2128] [2129] [2130] [2131] [2132] [2133]
Underfull \hbox (badness 2818) in paragraph at lines 11941--11946
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), []
[]\T1/zi4/m/sl/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have

Underfull \hbox (badness 5970) in paragraph at lines 11950--11953
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2134] [2135] [2136] [2137] [2138]
Underfull \hbox (badness 10000) in paragraph at lines 12213--12215
[]\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
[2139] [2140]
Underfull \hbox (badness 1057) in paragraph at lines 12370--12377
[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
 then the avail-able syn-tax ob-jects are con-sulted in turn,
[2141] [2142] [2143] [2144]
Underfull \hbox (badness 6510) in paragraph at lines 12642--12646
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t
he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a
ble

Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 12649--12652
\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
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 10000) in paragraph at lines 13238--13243
[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

Underfull \hbox (badness 3861) in paragraph at lines 13238--13243
[][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i
gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n
/10 and

Underfull \hbox (badness 1052) in paragraph at lines 13244--13246
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2154]
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see

Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av
ailable = NULL \T1/ptm/m/n/10 make a call to

Underfull \hbox (badness 1297) in paragraph at lines 13274--13279
\T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T
1/ptm/m/n/10 and hence by

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Chapter 1.
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[]\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/
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[]\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob-
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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
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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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 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
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[][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls 
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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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 []\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
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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
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i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
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[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
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Underfull \hbox (badness 2096) in paragraph at lines 7476--7480
\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
 : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$
[][]\T1/ptm/m/n/10 .
[117]
Underfull \hbox (badness 3000) in paragraph at lines 7569--7571
[]\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
[118]
Underfull \hbox (badness 2351) in paragraph at lines 7594--7597
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[119] [120] [121] [122]
Underfull \hbox (badness 10000) in paragraph at lines 7849--7859
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[123]
Underfull \hbox (badness 4479) in paragraph at lines 7920--7930
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
[124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148] [149]
Underfull \hbox (badness 1394) in paragraph at lines 9676--9681
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[150] [151] [152] [153] [154]
Underfull \hbox (badness 1194) in paragraph at lines 10021--10026
[]\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 10021--10026
\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
[155] [156] [157]
Underfull \hbox (badness 1735) in paragraph at lines 10226--10230
\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 .
[158] [159] [160] [161] [162] [163] [164]
Underfull \hbox (badness 2150) in paragraph at lines 10649--10652
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 6396) in paragraph at lines 10663--10671
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
[165]
Underfull \hbox (badness 2735) in paragraph at lines 10692--10699
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177]
[178] [179] [180]
Underfull \hbox (badness 4569) in paragraph at lines 11772--11776
[]\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 11772--11776
\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
[181] [182] [183] [184] [185] [186] [187] [188] [189]
Underfull \hbox (badness 2698) in paragraph at lines 12349--12358
[]\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 12349--12358
\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
[190] [191] [192] [193] [194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 6236) in paragraph at lines 13008--13011
[]\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
[200] [201] [202] [203] [204] [205] [206]
Underfull \hbox (badness 2253) in paragraph at lines 13430--13432
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[207]
Underfull \hbox (badness 1565) in paragraph at lines 13501--13505
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[208]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13547
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[209] [210]
Underfull \hbox (badness 1466) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[211] [212]
Underfull \hbox (badness 10000) in paragraph at lines 13804--13808
[][][]\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 13815--13818
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[213] [214] [215] [216]
Underfull \hbox (badness 3965) in paragraph at lines 14097--14101
[]\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,
[217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228]
[229]
Underfull \hbox (badness 4429) in paragraph at lines 14859--14862
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
[230]
Underfull \hbox (badness 10000) in paragraph at lines 14959--14961
[]\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 14965--14969
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[231]
Underfull \hbox (badness 10000) in paragraph at lines 15004--15008
[]\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 15004--15008
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[232] [233] [234] [235] [236] [237] [238] [239] [240]
Underfull \hbox (badness 2452) in paragraph at lines 15596--15600
[]\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 15596--15600
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[241] [242] [243]
Underfull \hbox (badness 1092) in paragraph at lines 15769--15774
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[244] [245] [246]
Underfull \hbox (badness 6741) in paragraph at lines 16020--16024
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[247] [248] [249] [250] [251]
Underfull \hbox (badness 1867) in paragraph at lines 16326--16333
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[252] [253] [254] [255]
Underfull \vbox (badness 10000) has occurred while \output is active [256]
[257] [258]
Underfull \hbox (badness 3679) in paragraph at lines 16736--16738
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[259] [260] [261] [262] [263] [264] [265] [266]
Underfull \hbox (badness 1478) in paragraph at lines 17301--17304
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 17554--17556
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[270] [271] [272] [273] [274] [275] [276] [277] [278] [279]
Underfull \hbox (badness 1442) in paragraph at lines 18145--18147
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[280]
Underfull \hbox (badness 2452) in paragraph at lines 18237--18253
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1248) in paragraph at lines 18651--18654
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[288] [289] [290] [291]
Underfull \hbox (badness 4739) in paragraph at lines 18909--18911
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303]
[304] [305] [306] [307] [308]
Underfull \hbox (badness 2469) in paragraph at lines 19926--19931
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 19940--19947
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[309]
Underfull \hbox (badness 10000) in paragraph at lines 20014--20018
[]\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 20014--20018
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[310] [311]
Underfull \hbox (badness 1509) in paragraph at lines 20149--20156
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1552) in paragraph at lines 20149--20156
\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 20165--20170
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 1264) in paragraph at lines 20916--20921
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:

Underfull \hbox (badness 4441) in paragraph at lines 20945--20948
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 21679--21681
[]\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
[335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346]
[347] [348] [349] [350] [351]
Underfull \hbox (badness 1077) in paragraph at lines 22714--22720
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[352] [353] [354]
Underfull \hbox (badness 1484) in paragraph at lines 22877--22885
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[355] [356] [357] [358]
Underfull \hbox (badness 2790) in paragraph at lines 23162--23165
[]\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 23162--23165
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[359] [360] [361] [362]
Underfull \hbox (badness 1194) in paragraph at lines 23444--23447
[]\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
[363] [364] [365]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23656
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 7379) in paragraph at lines 23650--23656
\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 23660--23663
[]\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 23660--23663
\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
[366] [367] [368] [369] [370] [371]
Underfull \hbox (badness 10000) in paragraph at lines 24031--24034
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
[372] [373] [374] [375] [376] [377] [378] [379] [380]
Underfull \hbox (badness 10000) in paragraph at lines 24623--24625
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[381] [382] [383] [384]
Underfull \hbox (badness 1199) in paragraph at lines 24867--24873
[]\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 24867--24873
\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,
[385] [386] [387] [388] [389] [390] [391] [392] [393]
Underfull \hbox (badness 1038) in paragraph at lines 25459--25467
[]\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 25468--25471
[]\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 25487--25489
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[394]
Underfull \hbox (badness 10000) in paragraph at lines 25596--25606
[]\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 25607--25613
[]\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
[395]
Underfull \hbox (badness 1968) in paragraph at lines 25643--25648
[]\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 25653--25655
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[396] [397] [398]
Underfull \hbox (badness 10000) in paragraph at lines 25916--25922
[]\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 25916--25922
\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 25916--25922
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 25929--25932
[]\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 25953--25955
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[399]
Underfull \hbox (badness 10000) in paragraph at lines 25985--25990
[]\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 25991--26002
\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 26003--26006
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 3713) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN ma-cOS build),

Underfull \hbox (badness 7944) in paragraph at lines 26013--26025
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).

Underfull \hbox (badness 2351) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z
i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo
pard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26027--26034
[]\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 26027--26034
\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 26027--26034
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1874) in paragraph at lines 26027--26034
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[400] [401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 26371--26375
[]\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 26371--26375
\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)]
[405] [406] [407] [408] [409]
Underfull \hbox (badness 1735) in paragraph at lines 26690--26694
[]\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
[410] [411] [412] [413] [414] [415] [416] [417] [418] [419]
Underfull \hbox (badness 2726) in paragraph at lines 27265--27268
[]\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
[420] [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431]
[432]
Underfull \hbox (badness 1052) in paragraph at lines 28094--28099
[]\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
[433] [434] [435] [436] [437]
Underfull \vbox (badness 10000) has occurred while \output is active [438]
[439] [440] [441] [442] [443] [444] [445]
Underfull \hbox (badness 1533) in paragraph at lines 28926--28929
[]\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
[446] [447]
Underfull \hbox (badness 1163) in paragraph at lines 29089--29100
[]\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
[448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459]
[460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471]
Underfull \hbox (badness 10000) in paragraph at lines 30622--30626
[]\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 30622--30626
\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.
[472]
Underfull \hbox (badness 6188) in paragraph at lines 30644--30646
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 1655) in paragraph at lines 31187--31189
[]\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
[481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491]
Underfull \hbox (badness 10000) in paragraph at lines 31895--31899
[]\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.,
[492] [493] [494] [495]
Underfull \hbox (badness 2302) in paragraph at lines 32146--32153
[]\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 32146--32153
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3333) in paragraph at lines 32146--32153
\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 32146--32153
\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
[496] [497] [498]
Underfull \hbox (badness 2261) in paragraph at lines 32302--32307
[]\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 32329--32335
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[499]
Underfull \hbox (badness 10000) in paragraph at lines 32405--32410
[]\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
[500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511]
[512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523]
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[536] [537] [538]
Underfull \vbox (badness 3803) has occurred while \output is active [539]
[540] [541] [542] [543] [544] [545] [546]
Underfull \hbox (badness 1072) in paragraph at lines 35447--35451
[]\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 35452--35456
[]\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 35480--35486
[]\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 35480--35486
\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 35480--35486
\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
[547]
Underfull \hbox (badness 3343) in paragraph at lines 35492--35499
\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 35492--35499
\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 35492--35499
\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
[548] [549] [550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 35833--35839
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1264) in paragraph at lines 35833--35839
\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
[553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564]
[565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576]
[577] [578] [579] [580] [581] [582]
Underfull \hbox (badness 3333) in paragraph at lines 37683--37688
[]\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
[583] [584] [585] [586] [587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 1472) in paragraph at lines 38315--38318
[]\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
[593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604]
[605] [606]
Underfull \hbox (badness 10000) in paragraph at lines 39221--39225
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e.,
[607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 39471--39474
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[611] [612]
Underfull \hbox (badness 10000) in paragraph at lines 39589--39593
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 10000) in paragraph at lines 39651--39655
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[614] [615] [616] [617] [618] [619] [620] [621] [622]
Underfull \hbox (badness 4013) in paragraph at lines 40264--40266
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / 
tz-[]link .
[623] [624] [625] [626] [627] [628]
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[630] [631] [632] [633] [634] [635] [636]
Underfull \hbox (badness 3460) in paragraph at lines 41145--41148
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via

Underfull \hbox (badness 1990) in paragraph at lines 41152--41160
[]\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 41152--41160
\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
[637] [638] [639] [640]
Underfull \hbox (badness 10000) in paragraph at lines 41429--41432
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[641] [642] [643] [644]
Underfull \hbox (badness 1917) in paragraph at lines 41657--41664
[]\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
[645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655]
Underfull \hbox (badness 3668) in paragraph at lines 42378--42380
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[656] [657]
Underfull \hbox (badness 2401) in paragraph at lines 42506--42510
[]\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
[658] [659] [660]
Underfull \hbox (badness 2111) in paragraph at lines 42695--42700
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.

Underfull \hbox (badness 7362) in paragraph at lines 42711--42716
[]\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
[661] [662] [663] [664] [665] [666] [667] [668] [669]
Underfull \hbox (badness 5417) in paragraph at lines 43290--43294
[]\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
[670]
Underfull \hbox (badness 10000) in paragraph at lines 43351--43355
[]\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
[671] [672]) (./compiler-pkg.tex
Chapter 2.
[673] [674] [675] [676]) (./datasets-pkg.tex
Chapter 3.
[677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688]
[689] [690] [691] [692] [693]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705]
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
[718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728]
Overfull \vbox (19.74611pt too high) has occurred while \output is active
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[741] [742] [743] [744]
Underfull \vbox (badness 10000) has occurred while \output is active [745]
[746] [747] [748]
Underfull \vbox (badness 10000) has occurred while \output is active [749]
[750] [751] [752] [753] [754]
Overfull \vbox (18.9959pt too high) has occurred while \output is active
[755] [756] [757]) (./grDevices-pkg.tex [758]
Chapter 4.
[759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770]
[771] [772] [773] [774] [775]
Underfull \hbox (badness 5175) in paragraph at lines 1082--1084
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[776] [777] [778] [779]
Underfull \hbox (badness 1852) in paragraph at lines 1279--1282
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[780] [781] [782]
Underfull \hbox (badness 1490) in paragraph at lines 1485--1490
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[783] [784]
Underfull \hbox (badness 10000) in paragraph at lines 1608--1612
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when
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Underfull \hbox (badness 1325) in paragraph at lines 1891--1901
\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[789] [790]
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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/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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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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[827] [828]
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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 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
[832]
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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
[833]
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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
[836]
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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
[837] [838]
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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 ,
[839]
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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 .
[840] [841] [842]
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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 ,
[843]
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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
[844] [845] [846] [847] [848] [849] [850]
Underfull \hbox (badness 10000) in paragraph at lines 5772--5775
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[851] [852] [853] [854] [855] [856]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[857] [858]
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[859] [860] [861] [862]
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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 ,
[863] [864] [865]
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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
[866] [867] [868]) (./graphics-pkg.tex
Chapter 5.
[869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879]
Underfull \hbox (badness 10000) in paragraph at lines 687--694
[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[880] [881] [882] [883] [884] [885] [886] [887] [888] [889]
Underfull \hbox (badness 4634) in paragraph at lines 1262--1265
[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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[902] [903] [904] [905] [906]
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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
[933] [934] [935] [936] [937] [938] [939] [940]
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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
[941] [942] [943] [944] [945]
Underfull \hbox (badness 10000) in paragraph at lines 4785--4791
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

Underfull \hbox (badness 5908) in paragraph at lines 4785--4791
\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
[946] [947]
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[948 </<<PKGBUILDDIR>>/library/graphics/help/figures/mai.pdf>]

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[950 </<<PKGBUILDDIR>>/library/graphics/help/figures/oma.pdf>]
[951]
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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
[952]
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Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639
[][] 
[975] [976 </<<PKGBUILDDIR>>/library/graphics/help/figures/pch
.pdf>] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986]
Underfull \hbox (badness 1048) in paragraph at lines 7347--7352
\T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i
s ex-ited by the com-mand
[987] [988]
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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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[1001] [1002]
Underfull \hbox (badness 1043) in paragraph at lines 8304--8308
[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[1003] [1004] [1005] [1006] [1007] [1008] [1009]
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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
[1010]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8793 \HeaderA{units}{Graphical Units}{units}
                                               [1011] [1012] [1013] [1014])
(./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
[1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030]
Underfull \hbox (badness 4279) in paragraph at lines 972--981
[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[1086] [1087]
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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
[1088] [1089] [1090] [1091]
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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
[1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102]
[1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
Underfull \hbox (badness 10000) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
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Underfull \hbox (badness 7649) in paragraph at lines 6356--6359
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1122] [1123] [1124] [1125]) (./methods-pkg.tex [1126]
Chapter 7.
[1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134]
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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 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests
[1154]
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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

Underfull \hbox (badness 1038) in paragraph at lines 1981--1986
\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1155] [1156] [1157]
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1158] [1159] [1160] [1161] [1162]
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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
[1165]
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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
[1166] [1167] [1168] [1169] [1170] [1171] [1172]
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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
[1173] [1174] [1175] [1176] [1177]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
[1178]
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[]\T1/ptm/m/n/10 The
[1179]
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[] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))

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[1180]
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[]\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
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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
[1191]
Underfull \hbox (badness 1092) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

Underfull \hbox (badness 1117) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and
[1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200]
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[1202]
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[]\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1203]
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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
[1204]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1205] [1206] [1207] [1208]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216]
Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1217] [1218] [1219] [1220]
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                   \relax 
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                                                 [1228]
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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
[1229] [1230] [1231]
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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
[1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242]
[1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253]
[1254] [1255] [1256] [1257] [1258]
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[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273]
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1274] [1275] [1276] [1277]) (./parallel-pkg.tex [1278]
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289]
[1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
Underfull \hbox (badness 3386) in paragraph at lines 1339--1342
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1300] [1301] [1302]) (./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
[1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313]
[1314] [1315] [1316] [1317]) (./stats-pkg.tex [1318]
Chapter 10.
[1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329]
[1330] [1331]
Underfull \hbox (badness 1412) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339]
Underfull \hbox (badness 2503) in paragraph at lines 1328--1331
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1340] [1341] [1342]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1343] [1344] [1345] [1346]
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[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via

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\T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-ing
[1347] [1348] [1349] [1350] [1351] [1352] [1353]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1354] [1355] [1356] [1357] [1358]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369]
[1370]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1371] [1372]
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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 ,
[1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383]
[1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1393] [1394]
Underfull \hbox (badness 3612) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
[1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]
Underfull \hbox (badness 2556) in paragraph at lines 5270--5273
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5287--5289
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1403] [1404] [1405] [1406]
Underfull \hbox (badness 1142) in paragraph at lines 5528--5540
\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.
[1407] [1408] [1409]
Underfull \hbox (badness 2503) in paragraph at lines 5680--5684
[]\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 ,
[1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417]
Underfull \hbox (badness 8132) in paragraph at lines 6184--6189
\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,
[1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 7081) in paragraph at lines 6462--6465
[]\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 6466--6468
[]\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
[1423] [1424] [1425] [1426] [1427]
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[1429] [1430] [1431] [1432] [1433] [1434] [1435]
Underfull \hbox (badness 10000) in paragraph at lines 7311--7314
[]\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
[1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446]
[1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457]
[1458] [1459] [1460] [1461] [1462]
Underfull \hbox (badness 2626) in paragraph at lines 8953--8956
[]\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
[1463]
Underfull \hbox (badness 2503) in paragraph at lines 9060--9064
[]\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 ,
[1464]
Underfull \hbox (badness 2564) in paragraph at lines 9112--9121
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-

Underfull \hbox (badness 1331) in paragraph at lines 9112--9121
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1465] [1466] [1467] [1468] [1469]
Overfull \hbox (3.53955pt too wide) in paragraph at lines 9434--9436
[]\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 . 
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480]
[1481] [1482] [1483] [1484]
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@

Underfull \hbox (badness 1253) in paragraph at lines 10729--10732
[]\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,
[1490]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\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 11208--11217
\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-
[1497] [1498] [1499] [1500] [1501]
Underfull \hbox (badness 10000) in paragraph at lines 11516--11519
[]\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.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1505] [1506]
Underfull \hbox (badness 1484) in paragraph at lines 11801--11803
[]\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
[1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516]
Underfull \hbox (badness 4441) in paragraph at lines 12387--12389
[]\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
[1517] [1518] [1519] [1520] [1521] [1522]
Underfull \hbox (badness 2894) in paragraph at lines 12730--12734
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533]
[1534]
Underfull \hbox (badness 4518) in paragraph at lines 13480--13485
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544]
Underfull \hbox (badness 4518) in paragraph at lines 14132--14137
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1545] [1546]
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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
[1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557]
[1558] [1559] [1560] [1561] [1562] [1563]
Underfull \hbox (badness 2503) in paragraph at lines 15345--15349
[]\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 ,
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572]
Underfull \hbox (badness 1584) in paragraph at lines 15857--15863
[]\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
[1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583]
[1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594]
[1595] [1596] [1597] [1598]
Underfull \hbox (badness 2359) in paragraph at lines 17507--17509
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1599]
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[1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612]
[1613]
Underfull \hbox (badness 1377) in paragraph at lines 18419--18424
[]\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
[1614]
Underfull \hbox (badness 1454) in paragraph at lines 18437--18441
\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 18445--18449
[]\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
[1615] [1616] [1617]
Overfull \hbox (15.73795pt too wide) in paragraph at lines 18669--18669
 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

Overfull \hbox (3.75941pt too wide) in paragraph at lines 18672--18672
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

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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 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
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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 ,
[1644]
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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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[]\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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[]\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/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\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
[1707]
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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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[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1717] [1718] [1719]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1720]
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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

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\T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was

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\T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o
f un-de-ter-mined co-ef-fi-cients, e.g., for
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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
[1745] [1746]
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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
[1747]
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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
[1748]
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 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1749]
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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
[1750] [1751] [1752] [1753]
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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
[1754]
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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
[1755]
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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
[1756] [1757]
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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
[1758] [1759]
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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
[1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767]
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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
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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
[1787] [1788]
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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
[1789] [1790] [1791]
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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
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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-
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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
[1826]
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[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the

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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
[1827] [1828] [1829] [1830] [1831] [1832]
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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
[1833] [1834] [1835]) (./stats4-pkg.tex [1836]
Chapter 11.
[1837] [1838] [1839] [1840] [1841] [1842]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}
                                                   [1843] [1844] [1845]
[1846]) (./tcltk-pkg.tex
Chapter 12.
[1847] [1848] [1849] [1850] [1851] [1852] [1853]
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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 ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1867]) (./tools-pkg.tex [1868]
Chapter 13.
[1869]

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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 ,
[1888] [1889] [1890]
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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/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
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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
[1896] [1897] [1898] [1899]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.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1900] [1901] [1902]
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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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[1930]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1931] [1932]
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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 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 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 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :

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\T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T
1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if
[1942]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1943] [1944] [1945]) (./utils-pkg.tex [1946]
Chapter 14.
[1947]
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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 ',
[1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955]
Underfull \hbox (badness 10000) in paragraph at lines 620--626
[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3343) in paragraph at lines 620--626
\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1956] [1957]
Underfull \hbox (badness 5847) in paragraph at lines 753--759
[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

Underfull \hbox (badness 4229) in paragraph at lines 753--759
\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1958]
Underfull \hbox (badness 3861) in paragraph at lines 821--826
[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
[1959] [1960] [1961]
Underfull \hbox (badness 1430) in paragraph at lines 992--999
\T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio
n to the for-

Underfull \hbox (badness 1931) in paragraph at lines 992--999
\T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo
re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 1038) in paragraph at lines 992--999
\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

Underfull \hbox (badness 1817) in paragraph at lines 992--999
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

Underfull \hbox (badness 10000) in paragraph at lines 1003--1005
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1962] [1963] [1964]
Underfull \vbox (badness 10000) has occurred while \output is active [1965]
[1966] [1967] [1968] [1969]
Underfull \hbox (badness 1371) in paragraph at lines 1482--1484
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1970] [1971] [1972] [1973] [1974] [1975] [1976]
Underfull \hbox (badness 2057) in paragraph at lines 1959--1961
[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1977] [1978]
Underfull \hbox (badness 10000) in paragraph at lines 2054--2056
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1979]
Underfull \hbox (badness 5189) in paragraph at lines 2156--2158
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1980] [1981] [1982] [1983]
Underfull \hbox (badness 1661) in paragraph at lines 2374--2381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

Underfull \hbox (badness 1748) in paragraph at lines 2390--2393
[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1984] [1985] [1986] [1987] [1988] [1989] [1990]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing

Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000]
Underfull \hbox (badness 1430) in paragraph at lines 3484--3492
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[2001]
Underfull \hbox (badness 1231) in paragraph at lines 3533--3539
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2002] [2003]
Underfull \hbox (badness 10000) in paragraph at lines 3686--3688
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]pdf
TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4373 ...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.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [2015] [2016] [2017]
[2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028]
[2029] [2030]
Underfull \hbox (badness 1371) in paragraph at lines 5370--5372
[]\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
[2031]
Underfull \hbox (badness 1502) in paragraph at lines 5459--5464
[]\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 5459--5464
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2032] [2033] [2034]
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2035]
Underfull \hbox (badness 2150) in paragraph at lines 5695--5698
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2036] [2037]
Underfull \hbox (badness 3118) in paragraph at lines 5832--5834
[]\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
[2038]
Underfull \hbox (badness 2409) in paragraph at lines 5865--5869
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[2039]
Underfull \hbox (badness 1325) in paragraph at lines 5973--5977
[]\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
[2040]
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
[]\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 6056--6059
\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.,
[2041]
Underfull \hbox (badness 3219) in paragraph at lines 6129--6136
[]\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 6129--6136
\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 6129--6136
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 6229--6234
[][][]\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 ,
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065]
[2066] [2067]
Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from

Underfull \hbox (badness 10000) in paragraph at lines 7676--7678
[]\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 7684--7689
[]\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,
[2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087]
[2088] [2089]
Underfull \hbox (badness 1097) in paragraph at lines 9111--9114
[]\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
[2090]
Underfull \hbox (badness 3000) in paragraph at lines 9247--9252
[][][]\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 ;
[2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099]
Underfull \hbox (badness 2134) in paragraph at lines 9830--9835
[][][]\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 ;
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
Underfull \hbox (badness 5077) in paragraph at lines 10255--10259
[]\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/
sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-

Underfull \hbox (badness 2269) in paragraph at lines 10255--10259
\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 10267--10271
[]\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 10267--10271
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2107] [2108] [2109] [2110] [2111]
Underfull \hbox (badness 4060) in paragraph at lines 10544--10547
[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

Overfull \hbox (18.77168pt too wide) in paragraph at lines 10567--10567
 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
[2112]
Underfull \hbox (badness 10000) in paragraph at lines 10630--10632
[]\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
[2113] [2114] [2115]
Underfull \hbox (badness 2150) in paragraph at lines 10806--10808
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2116] [2117] [2118] [2119]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2120] [2121]
Underfull \hbox (badness 2096) in paragraph at lines 11174--11177
[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether PNG fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1527) in paragraph at lines 11178--11181
[]\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
[2122]
Underfull \hbox (badness 1009) in paragraph at lines 11250--11261
[]\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
[2123] [2124] [2125] [2126] [2127]
Underfull \hbox (badness 3780) in paragraph at lines 11556--11560
[]\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 11572--11575
[]\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
[2128] [2129] [2130] [2131] [2132] [2133]
Underfull \hbox (badness 2818) in paragraph at lines 11941--11946
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), []
[]\T1/zi4/m/sl/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have

Underfull \hbox (badness 5970) in paragraph at lines 11950--11953
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2134] [2135] [2136] [2137] [2138]
Underfull \hbox (badness 10000) in paragraph at lines 12213--12215
[]\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
[2139] [2140]
Underfull \hbox (badness 1057) in paragraph at lines 12370--12377
[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
 then the avail-able syn-tax ob-jects are con-sulted in turn,
[2141] [2142] [2143] [2144]
Underfull \hbox (badness 6510) in paragraph at lines 12642--12646
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t
he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a
ble

Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 12649--12652
\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
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 10000) in paragraph at lines 13238--13243
[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

Underfull \hbox (badness 3861) in paragraph at lines 13238--13243
[][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i
gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n
/10 and

Underfull \hbox (badness 1052) in paragraph at lines 13244--13246
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2154]
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see

Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av
ailable = NULL \T1/ptm/m/n/10 make a call to

Underfull \hbox (badness 1297) in paragraph at lines 13274--13279
\T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T
1/ptm/m/n/10 and hence by

Underfull \hbox (badness 10000) in paragraph at lines 13303--13306
[][][]\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 ,
[2155] [2156] [2157] [2158]
Overfull \hbox (23.85939pt too wide) in paragraph at lines 13545--13548
[][][]\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
>")
[2159] [2160] [2161]
Underfull \hbox (badness 1454) in paragraph at lines 13696--13700
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[2162]
Underfull \hbox (badness 10000) in paragraph at lines 13766--13768
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
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Chapter 1.
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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
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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
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[]\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob-
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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/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
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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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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
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 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
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[][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls 
(but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m
/n/10 expression[][][]\T1/ptm/m/n/10 s where
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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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 []\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
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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
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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/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
1/ptm/m/n/10 . Con-di-tions of length greater

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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
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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 .
[117]
Underfull \hbox (badness 3000) in paragraph at lines 7569--7571
[]\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
[118]
Underfull \hbox (badness 2351) in paragraph at lines 7594--7597
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[119] [120] [121] [122]
Underfull \hbox (badness 10000) in paragraph at lines 7849--7859
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[123]
Underfull \hbox (badness 4479) in paragraph at lines 7920--7930
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
[124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148] [149]
Underfull \hbox (badness 1394) in paragraph at lines 9676--9681
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[150] [151] [152] [153] [154]
Underfull \hbox (badness 1194) in paragraph at lines 10021--10026
[]\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 10021--10026
\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
[155] [156] [157]
Underfull \hbox (badness 1735) in paragraph at lines 10226--10230
\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 .
[158] [159] [160] [161] [162] [163] [164]
Underfull \hbox (badness 2150) in paragraph at lines 10649--10652
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 6396) in paragraph at lines 10663--10671
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
[165]
Underfull \hbox (badness 2735) in paragraph at lines 10692--10699
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177]
[178] [179] [180]
Underfull \hbox (badness 4569) in paragraph at lines 11772--11776
[]\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 11772--11776
\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
[181] [182] [183] [184] [185] [186] [187] [188] [189]
Underfull \hbox (badness 2698) in paragraph at lines 12349--12358
[]\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 12349--12358
\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
[190] [191] [192] [193] [194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 6236) in paragraph at lines 13008--13011
[]\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
[200] [201] [202] [203] [204] [205] [206]
Underfull \hbox (badness 2253) in paragraph at lines 13430--13432
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[207]
Underfull \hbox (badness 1565) in paragraph at lines 13501--13505
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[208]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13547
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[209] [210]
Underfull \hbox (badness 1466) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[211] [212]
Underfull \hbox (badness 10000) in paragraph at lines 13804--13808
[][][]\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 13815--13818
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[213] [214] [215] [216]
Underfull \hbox (badness 3965) in paragraph at lines 14097--14101
[]\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,
[217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228]
[229]
Underfull \hbox (badness 4429) in paragraph at lines 14859--14862
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
[230]
Underfull \hbox (badness 10000) in paragraph at lines 14959--14961
[]\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 14965--14969
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[231]
Underfull \hbox (badness 10000) in paragraph at lines 15004--15008
[]\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 15004--15008
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[232] [233] [234] [235] [236] [237] [238] [239] [240]
Underfull \hbox (badness 2452) in paragraph at lines 15596--15600
[]\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 15596--15600
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[241] [242] [243]
Underfull \hbox (badness 1092) in paragraph at lines 15769--15774
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[244] [245] [246]
Underfull \hbox (badness 6741) in paragraph at lines 16020--16024
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[247] [248] [249] [250] [251]
Underfull \hbox (badness 1867) in paragraph at lines 16326--16333
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[252] [253] [254] [255]
Underfull \vbox (badness 10000) has occurred while \output is active [256]
[257] [258]
Underfull \hbox (badness 3679) in paragraph at lines 16736--16738
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[259] [260] [261] [262] [263] [264] [265] [266]
Underfull \hbox (badness 1478) in paragraph at lines 17301--17304
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 17554--17556
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[270] [271] [272] [273] [274] [275] [276] [277] [278] [279]
Underfull \hbox (badness 1442) in paragraph at lines 18145--18147
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[280]
Underfull \hbox (badness 2452) in paragraph at lines 18237--18253
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1248) in paragraph at lines 18651--18654
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[288] [289] [290] [291]
Underfull \hbox (badness 4739) in paragraph at lines 18909--18911
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303]
[304] [305] [306] [307] [308]
Underfull \hbox (badness 2469) in paragraph at lines 19926--19931
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 19940--19947
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[309]
Underfull \hbox (badness 10000) in paragraph at lines 20014--20018
[]\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 20014--20018
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[310] [311]
Underfull \hbox (badness 1509) in paragraph at lines 20149--20156
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1552) in paragraph at lines 20149--20156
\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 20165--20170
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 1264) in paragraph at lines 20916--20921
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:

Underfull \hbox (badness 4441) in paragraph at lines 20945--20948
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 21679--21681
[]\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
[335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346]
[347] [348] [349] [350] [351]
Underfull \hbox (badness 1077) in paragraph at lines 22714--22720
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[352] [353] [354]
Underfull \hbox (badness 1484) in paragraph at lines 22877--22885
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[355] [356] [357] [358]
Underfull \hbox (badness 2790) in paragraph at lines 23162--23165
[]\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 23162--23165
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[359] [360] [361] [362]
Underfull \hbox (badness 1194) in paragraph at lines 23444--23447
[]\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
[363] [364] [365]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23656
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 7379) in paragraph at lines 23650--23656
\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 23660--23663
[]\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 23660--23663
\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
[366] [367] [368] [369] [370] [371]
Underfull \hbox (badness 10000) in paragraph at lines 24031--24034
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
[372] [373] [374] [375] [376] [377] [378] [379] [380]
Underfull \hbox (badness 10000) in paragraph at lines 24623--24625
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[381] [382] [383] [384]
Underfull \hbox (badness 1199) in paragraph at lines 24867--24873
[]\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 24867--24873
\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,
[385] [386] [387] [388] [389] [390] [391] [392] [393]
Underfull \hbox (badness 1038) in paragraph at lines 25459--25467
[]\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 25468--25471
[]\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 25487--25489
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[394]
Underfull \hbox (badness 10000) in paragraph at lines 25596--25606
[]\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 25607--25613
[]\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
[395]
Underfull \hbox (badness 1968) in paragraph at lines 25643--25648
[]\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 25653--25655
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[396] [397] [398]
Underfull \hbox (badness 10000) in paragraph at lines 25916--25922
[]\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 25916--25922
\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 25916--25922
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 25929--25932
[]\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 25953--25955
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[399]
Underfull \hbox (badness 10000) in paragraph at lines 25985--25990
[]\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 25991--26002
\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 26003--26006
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 3713) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN ma-cOS build),

Underfull \hbox (badness 7944) in paragraph at lines 26013--26025
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).

Underfull \hbox (badness 2351) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z
i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo
pard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26027--26034
[]\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 26027--26034
\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 26027--26034
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1874) in paragraph at lines 26027--26034
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[400] [401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 26371--26375
[]\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 26371--26375
\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)]
[405] [406] [407] [408] [409]
Underfull \hbox (badness 1735) in paragraph at lines 26690--26694
[]\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
[410] [411] [412] [413] [414] [415] [416] [417] [418] [419]
Underfull \hbox (badness 2726) in paragraph at lines 27265--27268
[]\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
[420] [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431]
[432]
Underfull \hbox (badness 1052) in paragraph at lines 28094--28099
[]\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
[433] [434] [435] [436] [437]
Underfull \vbox (badness 10000) has occurred while \output is active [438]
[439] [440] [441] [442] [443] [444] [445]
Underfull \hbox (badness 1533) in paragraph at lines 28926--28929
[]\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
[446] [447]
Underfull \hbox (badness 1163) in paragraph at lines 29089--29100
[]\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
[448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459]
[460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471]
Underfull \hbox (badness 10000) in paragraph at lines 30622--30626
[]\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 30622--30626
\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.
[472]
Underfull \hbox (badness 6188) in paragraph at lines 30644--30646
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 1655) in paragraph at lines 31187--31189
[]\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
[481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491]
Underfull \hbox (badness 10000) in paragraph at lines 31895--31899
[]\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.,
[492] [493] [494] [495]
Underfull \hbox (badness 2302) in paragraph at lines 32146--32153
[]\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 32146--32153
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3333) in paragraph at lines 32146--32153
\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 32146--32153
\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
[496] [497] [498]
Underfull \hbox (badness 2261) in paragraph at lines 32302--32307
[]\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 32329--32335
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[499]
Underfull \hbox (badness 10000) in paragraph at lines 32405--32410
[]\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
[500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511]
[512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523]
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[536] [537] [538]
Underfull \vbox (badness 3803) has occurred while \output is active [539]
[540] [541] [542] [543] [544] [545] [546]
Underfull \hbox (badness 1072) in paragraph at lines 35447--35451
[]\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 35452--35456
[]\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 35480--35486
[]\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 35480--35486
\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 35480--35486
\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
[547]
Underfull \hbox (badness 3343) in paragraph at lines 35492--35499
\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 35492--35499
\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 35492--35499
\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
[548] [549] [550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 35833--35839
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1264) in paragraph at lines 35833--35839
\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
[553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564]
[565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576]
[577] [578] [579] [580] [581] [582]
Underfull \hbox (badness 3333) in paragraph at lines 37683--37688
[]\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
[583] [584] [585] [586] [587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 1472) in paragraph at lines 38315--38318
[]\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
[593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604]
[605] [606]
Underfull \hbox (badness 10000) in paragraph at lines 39221--39225
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e.,
[607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 39471--39474
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[611] [612]
Underfull \hbox (badness 10000) in paragraph at lines 39589--39593
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 10000) in paragraph at lines 39651--39655
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[614] [615] [616] [617] [618] [619] [620] [621] [622]
Underfull \hbox (badness 4013) in paragraph at lines 40264--40266
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / 
tz-[]link .
[623] [624] [625] [626] [627] [628]
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[630] [631] [632] [633] [634] [635] [636]
Underfull \hbox (badness 3460) in paragraph at lines 41145--41148
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via

Underfull \hbox (badness 1990) in paragraph at lines 41152--41160
[]\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 41152--41160
\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
[637] [638] [639] [640]
Underfull \hbox (badness 10000) in paragraph at lines 41429--41432
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
[641] [642] [643] [644]
Underfull \hbox (badness 1917) in paragraph at lines 41657--41664
[]\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
[645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [655]
Underfull \hbox (badness 3668) in paragraph at lines 42378--42380
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[656] [657]
Underfull \hbox (badness 2401) in paragraph at lines 42506--42510
[]\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
[658] [659] [660]
Underfull \hbox (badness 2111) in paragraph at lines 42695--42700
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.

Underfull \hbox (badness 7362) in paragraph at lines 42711--42716
[]\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
[661] [662] [663] [664] [665] [666] [667] [668] [669]
Underfull \hbox (badness 5417) in paragraph at lines 43290--43294
[]\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
[670]
Underfull \hbox (badness 10000) in paragraph at lines 43351--43355
[]\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
[671] [672]) (./compiler-pkg.tex
Chapter 2.
[673] [674] [675] [676]) (./datasets-pkg.tex
Chapter 3.
[677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688]
[689] [690] [691] [692] [693]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705]
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
[718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728]
Overfull \vbox (19.74611pt too high) has occurred while \output is active
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[741] [742] [743] [744]
Underfull \vbox (badness 10000) has occurred while \output is active [745]
[746] [747] [748]
Underfull \vbox (badness 10000) has occurred while \output is active [749]
[750] [751] [752] [753] [754]
Overfull \vbox (18.9959pt too high) has occurred while \output is active
[755] [756] [757]) (./grDevices-pkg.tex [758]
Chapter 4.
[759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770]
[771] [772] [773] [774] [775]
Underfull \hbox (badness 5175) in paragraph at lines 1082--1084
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[776] [777] [778] [779]
Underfull \hbox (badness 1852) in paragraph at lines 1279--1282
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[780] [781] [782]
Underfull \hbox (badness 1490) in paragraph at lines 1485--1490
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[783] [784]
Underfull \hbox (badness 10000) in paragraph at lines 1608--1612
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion 
also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when
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Underfull \hbox (badness 1325) in paragraph at lines 1891--1901
\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[789] [790]
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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/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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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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[827] [828]
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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 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
[832]
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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
[833]
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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
[836]
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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
[837] [838]
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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 ,
[839]
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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 .
[840] [841] [842]
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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 ,
[843]
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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
[844] [845] [846] [847] [848] [849] [850]
Underfull \hbox (badness 10000) in paragraph at lines 5772--5775
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[851] [852] [853] [854] [855] [856]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[857] [858]
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[859] [860] [861] [862]
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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 ,
[863] [864] [865]
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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
[866] [867] [868]) (./graphics-pkg.tex
Chapter 5.
[869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879]
Underfull \hbox (badness 10000) in paragraph at lines 687--694
[]\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p
tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt
m/m/n/10 in
[880] [881] [882] [883] [884] [885] [886] [887] [888] [889]
Underfull \hbox (badness 4634) in paragraph at lines 1262--1265
[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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[902] [903] [904] [905] [906]
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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
[933] [934] [935] [936] [937] [938] [939] [940]
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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
[941] [942] [943] [944] [945]
Underfull \hbox (badness 10000) in paragraph at lines 4785--4791
[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units.

Underfull \hbox (badness 5908) in paragraph at lines 4785--4791
\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
[946] [947]
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[948 </<<PKGBUILDDIR>>/library/graphics/help/figures/mai.pdf>]

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[950 </<<PKGBUILDDIR>>/library/graphics/help/figures/oma.pdf>]
[951]
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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
[952]
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Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639
[][] 
[975] [976 </<<PKGBUILDDIR>>/library/graphics/help/figures/pch
.pdf>] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986]
Underfull \hbox (badness 1048) in paragraph at lines 7347--7352
\T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i
s ex-ited by the com-mand
[987] [988]
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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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[1001] [1002]
Underfull \hbox (badness 1043) in paragraph at lines 8304--8308
[]\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[1003] [1004] [1005] [1006] [1007] [1008] [1009]
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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
[1010]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8793 \HeaderA{units}{Graphical Units}{units}
                                               [1011] [1012] [1013] [1014])
(./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
[1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030]
Underfull \hbox (badness 4279) in paragraph at lines 972--981
[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[1086] [1087]
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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
[1088] [1089] [1090] [1091]
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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
[1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102]
[1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
Underfull \hbox (badness 10000) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
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Underfull \hbox (badness 7649) in paragraph at lines 6356--6359
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1122] [1123] [1124] [1125]) (./methods-pkg.tex [1126]
Chapter 7.
[1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134]
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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 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests
[1154]
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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

Underfull \hbox (badness 1038) in paragraph at lines 1981--1986
\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1155] [1156] [1157]
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1158] [1159] [1160] [1161] [1162]
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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
[1165]
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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
[1166] [1167] [1168] [1169] [1170] [1171] [1172]
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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
[1173] [1174] [1175] [1176] [1177]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
[1178]
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[]\T1/ptm/m/n/10 The
[1179]
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[] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))

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[1180]
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[]\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
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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
[1191]
Underfull \hbox (badness 1092) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

Underfull \hbox (badness 1117) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and
[1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200]
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[1202]
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[]\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1203]
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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
[1204]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1205] [1206] [1207] [1208]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216]
Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1217] [1218] [1219] [1220]
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                   \relax 
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                                                 [1228]
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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
[1229] [1230] [1231]
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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
[1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242]
[1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253]
[1254] [1255] [1256] [1257] [1258]
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[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273]
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1274] [1275] [1276] [1277]) (./parallel-pkg.tex [1278]
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289]
[1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
Underfull \hbox (badness 3386) in paragraph at lines 1339--1342
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1300] [1301] [1302]) (./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
[1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313]
[1314] [1315] [1316] [1317]) (./stats-pkg.tex [1318]
Chapter 10.
[1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329]
[1330] [1331]
Underfull \hbox (badness 1412) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339]
Underfull \hbox (badness 2503) in paragraph at lines 1328--1331
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1340] [1341] [1342]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1343] [1344] [1345] [1346]
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[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via

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\T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-ing
[1347] [1348] [1349] [1350] [1351] [1352] [1353]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1354] [1355] [1356] [1357] [1358]
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[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369]
[1370]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1371] [1372]
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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 ,
[1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383]
[1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1393] [1394]
Underfull \hbox (badness 3612) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
[1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]
Underfull \hbox (badness 2556) in paragraph at lines 5270--5273
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5287--5289
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1403] [1404] [1405] [1406]
Underfull \hbox (badness 1142) in paragraph at lines 5528--5540
\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.
[1407] [1408] [1409]
Underfull \hbox (badness 2503) in paragraph at lines 5680--5684
[]\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 ,
[1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417]
Underfull \hbox (badness 8132) in paragraph at lines 6184--6189
\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,
[1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 7081) in paragraph at lines 6462--6465
[]\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 6466--6468
[]\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
[1423] [1424] [1425] [1426] [1427]
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[1429] [1430] [1431] [1432] [1433] [1434] [1435]
Underfull \hbox (badness 10000) in paragraph at lines 7311--7314
[]\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
[1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446]
[1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457]
[1458] [1459] [1460] [1461] [1462]
Underfull \hbox (badness 2626) in paragraph at lines 8953--8956
[]\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
[1463]
Underfull \hbox (badness 2503) in paragraph at lines 9060--9064
[]\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 ,
[1464]
Underfull \hbox (badness 2564) in paragraph at lines 9112--9121
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-

Underfull \hbox (badness 1331) in paragraph at lines 9112--9121
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1465] [1466] [1467] [1468] [1469]
Overfull \hbox (3.53955pt too wide) in paragraph at lines 9434--9436
[]\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 . 
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480]
[1481] [1482] [1483] [1484]
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@

Underfull \hbox (badness 1253) in paragraph at lines 10729--10732
[]\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,
[1490]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\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 11208--11217
\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-
[1497] [1498] [1499] [1500] [1501]
Underfull \hbox (badness 10000) in paragraph at lines 11516--11519
[]\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.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1505] [1506]
Underfull \hbox (badness 1484) in paragraph at lines 11801--11803
[]\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
[1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516]
Underfull \hbox (badness 4441) in paragraph at lines 12387--12389
[]\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
[1517] [1518] [1519] [1520] [1521] [1522]
Underfull \hbox (badness 2894) in paragraph at lines 12730--12734
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533]
[1534]
Underfull \hbox (badness 4518) in paragraph at lines 13480--13485
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544]
Underfull \hbox (badness 4518) in paragraph at lines 14132--14137
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1545] [1546]
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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
[1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557]
[1558] [1559] [1560] [1561] [1562] [1563]
Underfull \hbox (badness 2503) in paragraph at lines 15345--15349
[]\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 ,
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572]
Underfull \hbox (badness 1584) in paragraph at lines 15857--15863
[]\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
[1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583]
[1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594]
[1595] [1596] [1597] [1598]
Underfull \hbox (badness 2359) in paragraph at lines 17507--17509
[]\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For-
tran code used by
[1599]
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[1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612]
[1613]
Underfull \hbox (badness 1377) in paragraph at lines 18419--18424
[]\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
[1614]
Underfull \hbox (badness 1454) in paragraph at lines 18437--18441
\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 18445--18449
[]\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
[1615] [1616] [1617]
Overfull \hbox (15.73795pt too wide) in paragraph at lines 18669--18669
 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

Overfull \hbox (3.75941pt too wide) in paragraph at lines 18672--18672
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

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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 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
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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 ,
[1644]
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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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[]\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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[]\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/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\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
[1707]
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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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[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1717] [1718] [1719]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1720]
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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

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\T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was

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\T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o
f un-de-ter-mined co-ef-fi-cients, e.g., for
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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
[1745] [1746]
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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
[1747]
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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
[1748]
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 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1749]
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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
[1750] [1751] [1752] [1753]
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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
[1754]
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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
[1755]
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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
[1756] [1757]
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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
[1758] [1759]
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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
[1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767]
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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
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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
[1787] [1788]
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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
[1789] [1790] [1791]
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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
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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-
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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
[1826]
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[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the

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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
[1827] [1828] [1829] [1830] [1831] [1832]
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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
[1833] [1834] [1835]) (./stats4-pkg.tex [1836]
Chapter 11.
[1837] [1838] [1839] [1840] [1841] [1842]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}
                                                   [1843] [1844] [1845]
[1846]) (./tcltk-pkg.tex
Chapter 12.
[1847] [1848] [1849] [1850] [1851] [1852] [1853]
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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 ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1867]) (./tools-pkg.tex [1868]
Chapter 13.
[1869]

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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 ,
[1888] [1889] [1890]
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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/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
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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
[1896] [1897] [1898] [1899]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.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1900] [1901] [1902]
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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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[1930]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1931] [1932]
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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 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 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 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :

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\T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T
1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if
[1942]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1943] [1944] [1945]) (./utils-pkg.tex [1946]
Chapter 14.
[1947]
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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 ',
[1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955]
Underfull \hbox (badness 10000) in paragraph at lines 620--626
[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

Underfull \hbox (badness 3343) in paragraph at lines 620--626
\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1956] [1957]
Underfull \hbox (badness 5847) in paragraph at lines 753--759
[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

Underfull \hbox (badness 4229) in paragraph at lines 753--759
\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1958]
Underfull \hbox (badness 3861) in paragraph at lines 821--826
[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
[1959] [1960] [1961]
Underfull \hbox (badness 1430) in paragraph at lines 992--999
\T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio
n to the for-

Underfull \hbox (badness 1931) in paragraph at lines 992--999
\T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo
re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 1038) in paragraph at lines 992--999
\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

Underfull \hbox (badness 1817) in paragraph at lines 992--999
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

Underfull \hbox (badness 10000) in paragraph at lines 1003--1005
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1962] [1963] [1964]
Underfull \vbox (badness 10000) has occurred while \output is active [1965]
[1966] [1967] [1968] [1969]
Underfull \hbox (badness 1371) in paragraph at lines 1482--1484
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1970] [1971] [1972] [1973] [1974] [1975] [1976]
Underfull \hbox (badness 2057) in paragraph at lines 1959--1961
[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1977] [1978]
Underfull \hbox (badness 10000) in paragraph at lines 2054--2056
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1979]
Underfull \hbox (badness 5189) in paragraph at lines 2156--2158
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1980] [1981] [1982] [1983]
Underfull \hbox (badness 1661) in paragraph at lines 2374--2381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

Underfull \hbox (badness 1748) in paragraph at lines 2390--2393
[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1984] [1985] [1986] [1987] [1988] [1989] [1990]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing

Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 ,
[1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000]
Underfull \hbox (badness 1430) in paragraph at lines 3484--3492
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[2001]
Underfull \hbox (badness 1231) in paragraph at lines 3533--3539
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2002] [2003]
Underfull \hbox (badness 10000) in paragraph at lines 3686--3688
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]pdf
TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4373 ...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.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [2015] [2016] [2017]
[2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028]
[2029] [2030]
Underfull \hbox (badness 1371) in paragraph at lines 5370--5372
[]\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
[2031]
Underfull \hbox (badness 1502) in paragraph at lines 5459--5464
[]\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 5459--5464
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2032] [2033] [2034]
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2035]
Underfull \hbox (badness 2150) in paragraph at lines 5695--5698
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2036] [2037]
Underfull \hbox (badness 3118) in paragraph at lines 5832--5834
[]\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
[2038]
Underfull \hbox (badness 2409) in paragraph at lines 5865--5869
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[2039]
Underfull \hbox (badness 1325) in paragraph at lines 5973--5977
[]\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
[2040]
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
[]\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 6056--6059
\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.,
[2041]
Underfull \hbox (badness 3219) in paragraph at lines 6129--6136
[]\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 6129--6136
\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 6129--6136
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 6229--6234
[][][]\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 ,
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065]
[2066] [2067]
Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from

Underfull \hbox (badness 10000) in paragraph at lines 7676--7678
[]\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 7684--7689
[]\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,
[2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087]
[2088] [2089]
Underfull \hbox (badness 1097) in paragraph at lines 9111--9114
[]\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
[2090]
Underfull \hbox (badness 3000) in paragraph at lines 9247--9252
[][][]\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 ;
[2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099]
Underfull \hbox (badness 2134) in paragraph at lines 9830--9835
[][][]\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 ;
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
Underfull \hbox (badness 5077) in paragraph at lines 10255--10259
[]\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/
sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te-

Underfull \hbox (badness 2269) in paragraph at lines 10255--10259
\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 10267--10271
[]\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 10267--10271
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2107] [2108] [2109] [2110] [2111]
Underfull \hbox (badness 4060) in paragraph at lines 10544--10547
[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

Overfull \hbox (18.77168pt too wide) in paragraph at lines 10567--10567
 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
[2112]
Underfull \hbox (badness 10000) in paragraph at lines 10630--10632
[]\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
[2113] [2114] [2115]
Underfull \hbox (badness 2150) in paragraph at lines 10806--10808
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2116] [2117] [2118] [2119]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2120] [2121]
Underfull \hbox (badness 2096) in paragraph at lines 11174--11177
[]\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing 
whether PNG fig-ures should be gen-er-ated. Ig-nored if

Underfull \hbox (badness 1527) in paragraph at lines 11178--11181
[]\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
[2122]
Underfull \hbox (badness 1009) in paragraph at lines 11250--11261
[]\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
[2123] [2124] [2125] [2126] [2127]
Underfull \hbox (badness 3780) in paragraph at lines 11556--11560
[]\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 11572--11575
[]\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
[2128] [2129] [2130] [2131] [2132] [2133]
Underfull \hbox (badness 2818) in paragraph at lines 11941--11946
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), []
[]\T1/zi4/m/sl/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have

Underfull \hbox (badness 5970) in paragraph at lines 11950--11953
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2134] [2135] [2136] [2137] [2138]
Underfull \hbox (badness 10000) in paragraph at lines 12213--12215
[]\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
[2139] [2140]
Underfull \hbox (badness 1057) in paragraph at lines 12370--12377
[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
 then the avail-able syn-tax ob-jects are con-sulted in turn,
[2141] [2142] [2143] [2144]
Underfull \hbox (badness 6510) in paragraph at lines 12642--12646
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t
he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a
ble

Underfull \hbox (badness 10000) in paragraph at lines 12649--12652
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 12649--12652
\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
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 10000) in paragraph at lines 13238--13243
[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

Underfull \hbox (badness 3861) in paragraph at lines 13238--13243
[][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i
gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n
/10 and

Underfull \hbox (badness 1052) in paragraph at lines 13244--13246
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2154]
Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[]\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m
ined see

Underfull \hbox (badness 10000) in paragraph at lines 13274--13279
[][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av
ailable = NULL \T1/ptm/m/n/10 make a call to

Underfull \hbox (badness 1297) in paragraph at lines 13274--13279
\T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T
1/ptm/m/n/10 and hence by

Underfull \hbox (badness 10000) in paragraph at lines 13303--13306
[][][]\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 ,
[2155] [2156] [2157] [2158]
Overfull \hbox (23.85939pt too wide) in paragraph at lines 13545--13548
[][][]\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
>")
[2159] [2160] [2161]
Underfull \hbox (badness 1454) in paragraph at lines 13696--13700
[]\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For
 ex-am-ple,
[2162]
Underfull \hbox (badness 10000) in paragraph at lines 13766--13768
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion
[2163] [2164] [2165]) [2166] (./refman.ind [2167] [2168] [2169] [2170] [2171]
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TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi
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[1] Chapter 2 [2] Cross reference values unknown; you must run TeX again.
[3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[23] Chapter 5 [24] Chapter 6 [25]
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[28] [29] [30] [31] [32] [33]
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Appendix A [43] [44]
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[45] [46] [47] [48] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57]
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[]@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/
local/lib/amd64[] @textrm and
[76] [77] [78] Appendix D [79] [80] [81] [82] (Function and variable index)
[83]
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[86] )
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ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
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This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdfetex)
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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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[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3
[14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[23] Chapter 5 [24] Chapter 6 [25]
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 []@texttt [1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "met
hods"[] 
[26] [27]
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[]@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age
s. No ad-di-
[28] [29] [30] [31] [32] [33]
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 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text
tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] 
[34]
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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 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42]
Appendix A [43] [44]
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 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
disable-cpp[] 
[45] [46] [47] [48] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57]
[58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] [67] [68]
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[69]
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ig:/usr/lib/pkgconfig[] 

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[70] [71]
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s/Home[] 

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me/bin/javah[] 
[72] [73]
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olaris"[] 
[75]
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[]@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/
local/lib/amd64[] @textrm and
[76] [77] [78] Appendix D [79] [80] [81] [82] (Function and variable index)
[83] (Concept index) [84] (Environment variable index) [85] [86] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
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[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3
[14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
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[23] Chapter 5 [24] Chapter 6 [25]
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[28] [29] [30] [31] [32] [33]
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Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42]
Appendix A [43] [44]
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[45] [46] [47] [48] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57]
[58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] [67] [68]
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[76] [77] [78] Appendix D [79] [80] [81] [82] (Function and variable index)
[83] (Concept index) [84] (Environment variable index) [85] [86] )
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[1] [2] Chapter 1 [3]
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[17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7
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[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]
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[1] [2] Chapter 1 [3]
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[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]
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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] [24]
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LAGS)[] 
[25] [26] [27] [28]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[33] [34]
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[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
[51] [52] [53] [54] [55] [56] [57] [58] [59]
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version 52.0[] 
[60] [61] [62] [63]
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euro"[] 
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[71] [72] [73] Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83]
[84] [85] [86] [87]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[88] [89] [90] [91]
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[92] [93] Chapter 3 [94] [95] [96] [97] [98] [99] [100]
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[110] [111] [112]
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[113] [114]
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698f98,[] 
[119] [120] Chapter 5 [121] [122] [123] [124] [125] [126] [127] [128] [129]
[130] [131]
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[150]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[151] [152] [153] [154] [155] [156] [157]
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Chapter 6 [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176]
[177] [178]
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[182] [183] [184] [185] [186] Chapter 7 [187] [188] Chapter 8 [189] [190]
[191]
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[193] [194] [195] [196]
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[197] [198] [199] [200] [201]
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(Function and variable index) [202]
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[204] )
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page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
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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]
Writing index file R-exts.cp
[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] [24]
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 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF
LAGS)[] 
[25] [26] [27] [28]
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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 $(SOURCES:.cpp=.o)[] 
[29] [30]
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 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar
e defined.[]  
[31]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[32] [33]
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 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[34] [35]
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[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
[51] [52] [53] [54] [55] [56] [57] [58]
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 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 

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 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
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[59]
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 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 

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version 52.0[] 
[60] [61] [62] [63]
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euro"[] 
[64] [65]
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mcpy[] 

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r[] 
[66] [67]
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 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr
unc[] 

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th C++17[] 
[68] [69] [70]
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 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String
)[] 
[71] [72] [73] Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83]
[84] [85] [86] [87]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[88] [89] [90] [91]
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[]@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file
[92] [93] Chapter 3 [94] [95] [96] [97] [98] [99] [100]
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 []                 @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1,
 28)))[] 
[101] [102] [103] Chapter 4 [104] [105] [106]
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ns=)?[] 
[107]
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e supply starting values[] 
[108]
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t, etastart = etastart,[] 
[109]
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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 .
[110] [111] [112]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[113] [114]
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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[]

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hift,[] 

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und,vptr[] 
[115]
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a de-fault part
[116]
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[117]
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assi,[] 

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cu)),[] 
[118]
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 []@texttt #5  0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9
698f98,[] 
[119] [120] Chapter 5 [121] [122] [123] [124] [125] [126] [127] [128] [129]
[130] [131]
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pha,[] 

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 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[132] [133] [134] [135] [136] [137] [138] [139]
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 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[140] [141] [142] [143] [144] [145] [146] [147] [148] [149]
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[150]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[151] [152] [153] [154] [155] [156] [157]
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orry"[] 
[158] [159]
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a)));[] 

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[160]
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[161]
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alue));[] 
[162] [163]
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xit);[] 
[164]
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[165]
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 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety
pe_t;[] 
Chapter 6 [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176]
[177] [178]
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[179] Warning: unbalanced parentheses in @def... [180] [181]
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 []                     @texttt void (*clean)(void *data, Rboolean jump), void 
*cdata,[] 
[182] [183] [184] [185] [186] Chapter 7 [187] [188] Chapter 8 [189] [190]
[191]
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tatic libR[] 
[192]
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 int);[] 

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nst char *);[] 
[193] [194] [195] [196]
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 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan
ohttp.c[] @textrm and @texttt src/
[197] [198] [199] [200] [201]
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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) [202] [203] [204] [205] (Concept index) [206]
[207] [208] )
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Output written on R-exts.pdf (215 pages, 962629 bytes).
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page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
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(/<<PKGBUILDDIR>>/doc/manual/R-exts.toc) (Acknowledgements)
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[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24]
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[25] [26] [27] [28]
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a07models.o $(SOURCES:.cpp=.o)[] 
[29] [30]
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[31]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
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[32] [33]
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[34] [35]
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[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
[51] [52] [53] [54] [55] [56] [57] [58]
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ersion")[] 

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[59]
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[60] [61] [62] [63]
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[64] [65]
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mcpy[] 

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r[] 
[66] [67]
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unc[] 

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)[] 
[71] [72] [73] Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83]
[84] [85] [86] [87]
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lename@texttt }[] @textrm and
[88] [89] [90] [91]
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[]@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file
[92] [93] Chapter 3 [94] [95] [96] [97] [98] [99] [100]
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[101] [102] [103] Chapter 4 [104] [105] [106]
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ns=)?[] 
[107]
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e supply starting values[] 
[108]
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[109]
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[110] [111] [112]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
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[113] [114]
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698f98,[] 
[119] [120] Chapter 5 [121] [122] [123] [124] [125] [126] [127] [128] [129]
[130] [131]
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[132] [133] [134] [135] [136] [137] [138] [139]
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[140] [141] [142] [143] [144] [145] [146] [147] [148] [149]
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[150]
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[151] [152] [153] [154] [155] [156] [157]
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[158] [159]
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[160]
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[162] [163]
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 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety
pe_t;[] 
Chapter 6 [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176]
[177] [178]
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[182] [183] [184] [185] [186] Chapter 7 [187] [188] Chapter 8 [189] [190]
[191]
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[192]
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[193] [194] [195] [196]
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 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan
ohttp.c[] @textrm and @texttt src/
[197] [198] [199] [200] [201]
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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) [202] [203] [204] [205] (Concept index) [206]
[207] [208] )
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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
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[17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6
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[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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[25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34]
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r-base-73GQCG/r-base-3.5.1/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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[]@textrm Users con-nected to the In-ter-net can use the @texttt install.packag
es()[] @textrm and
[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]
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Appendix E [102]
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Appendix F [103] [104] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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[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-73GQCG/r-base-3.5.1/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
ig11.pdf> [77] </<<PKGBUILDDIR>>/doc/manual/images/fig12.pdf>
[78] [79] [80] [81] Chapter 13 [82]
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es()[] @textrm and
[83] Chapter 14 [84] [85]
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extrm and
[86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95]
[96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E
[104] [105] Appendix F [106] [107] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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[-4] (/<<PKGBUILDDIR>>/doc/manual/R-intro.toc)
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[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-73GQCG/r-base-3.5.1/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
ig11.pdf> [77] </<<PKGBUILDDIR>>/doc/manual/images/fig12.pdf>
[78] [79] [80] [81] Chapter 13 [82]
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es()[] @textrm and
[83] Chapter 14 [84] [85]
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extrm and
[86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95]
[96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E
[104] [105] Appendix F [106] [107] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
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TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi
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[18]
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atrix 1.2-6[] 

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ics with methods[] 

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(group)generic[] 

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[19] [20] [21] [22] [23] [24] Chapter 2 [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
ib[]@textrm ,
[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] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11
[63] Chapter 12 [64] [65] (Function and variable index) [66] [67]
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(Concept index) [68]
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[69] )
(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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atrix 1.2-6[] 

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 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 

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 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 

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 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[] 
[19] [20] [21] [22] [23] [24] Chapter 2 [25]
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 []    @texttt if (!is.character(x)) x <- structure(as.character(x), names = na
mes(x))[] 
[26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34]
Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
Chapter 7 [48]
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sym-bolic link,

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@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl
ib[]@textrm ,
[49] Chapter 8 [50] [51] [52] [53] [54]
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sed for

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LE_

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 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa
tchArgs = FALSE[] @textrm and
[55] [56] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11
[63] Chapter 12 [64] [65] (Function and variable index) [66] [67] [68]
(Concept index) [69] [70] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
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 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
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[55] [56] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11
[63] Chapter 12 [64] [65] (Function and variable index) [66] [67] [68]
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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]
Underfull \hbox (badness 1178) in paragraph at lines 297--301
[]\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/
10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues
[6]
Underfull \hbox (badness 3977) in paragraph at lines 386--389
[]\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob-
served strictly? Note that set-ting
[7] [8]
Underfull \hbox (badness 2556) in paragraph at lines 534--540
[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ',
[9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
[12] [13] [14] [15] [16] [17] [18]
Underfull \hbox (badness 2671) in paragraph at lines 1147--1150
[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30]
Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922
 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
[31] [32] [33]
Underfull \hbox (badness 10000) in paragraph at lines 2120--2122
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]
[49] [50] [51] [52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3650--3652
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 3891--3891
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[61] [62]
Underfull \hbox (badness 1057) in paragraph at lines 3999--4002
[][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls 
(but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m
/n/10 expression[][][]\T1/ptm/m/n/10 s where
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76]
Underfull \hbox (badness 2521) in paragraph at lines 4882--4884
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91]
[92] [93] [94]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6035--6035
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[95] [96]
Underfull \hbox (badness 2096) in paragraph at lines 6223--6236
[]\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
[97] [98] [99] [100]
Overfull \hbox (56.34871pt too wide) in paragraph at lines 6432--6434
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : 
[101] [102]
Underfull \hbox (badness 10000) in paragraph at lines 6574--6577
[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
[103] [104]
Underfull \hbox (badness 1442) in paragraph at lines 6756--6762
[]\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 6756--6762
\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 6756--6762
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
[105]
Underfull \hbox (badness 3568) in paragraph at lines 6818--6825
\T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z
i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
[106] [107]
Underfull \vbox (badness 10000) has occurred while \output is active [108]
[109] [110]
Underfull \hbox (badness 1077) in paragraph at lines 7135--7141
[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
1/ptm/m/n/10 . Con-di-tions of length greater

Underfull \hbox (badness 1231) in paragraph at lines 7135--7141
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[111] [112] [113] [114] [115] [116]
Underfull \hbox (badness 2096) in paragraph at lines 7476--7480
\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
 : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$
[][]\T1/ptm/m/n/10 .
[117]
Underfull \hbox (badness 3000) in paragraph at lines 7569--7571
[]\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
[118]
Underfull \hbox (badness 2351) in paragraph at lines 7594--7597
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[119] [120] [121] [122]
Underfull \hbox (badness 10000) in paragraph at lines 7849--7859
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[123]
Underfull \hbox (badness 4479) in paragraph at lines 7920--7930
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
[124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148] [149]
Underfull \hbox (badness 1394) in paragraph at lines 9676--9681
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[150] [151] [152] [153] [154]
Underfull \hbox (badness 1194) in paragraph at lines 10021--10026
[]\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 10021--10026
\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
[155] [156] [157]
Underfull \hbox (badness 1735) in paragraph at lines 10226--10230
\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 .
[158] [159] [160] [161] [162] [163] [164]
Underfull \hbox (badness 2150) in paragraph at lines 10649--10652
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 6396) in paragraph at lines 10663--10671
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
[165]
Underfull \hbox (badness 2735) in paragraph at lines 10692--10699
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177]
[178] [179] [180]
Underfull \hbox (badness 4569) in paragraph at lines 11772--11776
[]\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 11772--11776
\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
[181] [182] [183] [184] [185] [186] [187] [188] [189]
Underfull \hbox (badness 2698) in paragraph at lines 12349--12358
[]\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 12349--12358
\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
[190] [191] [192] [193] [194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 6236) in paragraph at lines 13008--13011
[]\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
[200] [201] [202] [203] [204] [205] [206]
Underfull \hbox (badness 2253) in paragraph at lines 13430--13432
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[207]
Underfull \hbox (badness 1565) in paragraph at lines 13501--13505
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[208]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13547
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[209] [210]
Underfull \hbox (badness 1466) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[211] [212]
Underfull \hbox (badness 10000) in paragraph at lines 13804--13808
[][][]\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 13815--13818
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[213] [214] [215] [216]
Underfull \hbox (badness 3965) in paragraph at lines 14097--14101
[]\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,
[217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228]
[229]
Underfull \hbox (badness 4429) in paragraph at lines 14859--14862
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
[230]
Underfull \hbox (badness 10000) in paragraph at lines 14959--14961
[]\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 14965--14969
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[231]
Underfull \hbox (badness 10000) in paragraph at lines 15004--15008
[]\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 15004--15008
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[232] [233] [234] [235] [236] [237] [238] [239] [240]
Underfull \hbox (badness 2452) in paragraph at lines 15596--15600
[]\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 15596--15600
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[241] [242] [243]
Underfull \hbox (badness 1092) in paragraph at lines 15769--15774
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[244] [245] [246]
Underfull \hbox (badness 6741) in paragraph at lines 16020--16024
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[247] [248] [249] [250] [251]
Underfull \hbox (badness 1867) in paragraph at lines 16326--16333
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[252] [253] [254] [255]
Underfull \vbox (badness 10000) has occurred while \output is active [256]
[257] [258]
Underfull \hbox (badness 3679) in paragraph at lines 16736--16738
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[259] [260] [261] [262] [263] [264] [265] [266]
Underfull \hbox (badness 1478) in paragraph at lines 17301--17304
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 17554--17556
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[270] [271] [272] [273] [274] [275] [276] [277] [278] [279]
Underfull \hbox (badness 1442) in paragraph at lines 18145--18147
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[280]
Underfull \hbox (badness 2452) in paragraph at lines 18237--18253
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1248) in paragraph at lines 18651--18654
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[288] [289] [290] [291]
Underfull \hbox (badness 4739) in paragraph at lines 18909--18911
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303]
[304] [305] [306] [307] [308]
Underfull \hbox (badness 2469) in paragraph at lines 19926--19931
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 19940--19947
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[309]
Underfull \hbox (badness 10000) in paragraph at lines 20014--20018
[]\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 20014--20018
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[310] [311]
Underfull \hbox (badness 1509) in paragraph at lines 20149--20156
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1552) in paragraph at lines 20149--20156
\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 20165--20170
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 1264) in paragraph at lines 20916--20921
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:

Underfull \hbox (badness 4441) in paragraph at lines 20945--20948
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 21679--21681
[]\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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[347] [348] [349] [350] [351]
Underfull \hbox (badness 1077) in paragraph at lines 22714--22720
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[352] [353] [354]
Underfull \hbox (badness 1484) in paragraph at lines 22877--22885
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[355] [356] [357] [358]
Underfull \hbox (badness 2790) in paragraph at lines 23162--23165
[]\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 23162--23165
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[359] [360] [361] [362]
Underfull \hbox (badness 1194) in paragraph at lines 23444--23447
[]\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 23650--23656
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 7379) in paragraph at lines 23650--23656
\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 23660--23663
[]\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 23660--23663
\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
[366] [367] [368] [369] [370] [371]
Underfull \hbox (badness 10000) in paragraph at lines 24031--24034
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
[372] [373] [374] [375] [376] [377] [378] [379] [380]
Underfull \hbox (badness 10000) in paragraph at lines 24623--24625
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
[381] [382] [383] [384]
Underfull \hbox (badness 1199) in paragraph at lines 24867--24873
[]\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 24867--24873
\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,
[385] [386] [387] [388] [389] [390] [391] [392] [393]
Underfull \hbox (badness 1038) in paragraph at lines 25459--25467
[]\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 25468--25471
[]\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 25487--25489
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[394]
Underfull \hbox (badness 10000) in paragraph at lines 25596--25606
[]\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 25607--25613
[]\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
[395]
Underfull \hbox (badness 1968) in paragraph at lines 25643--25648
[]\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 25653--25655
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
[396] [397] [398]
Underfull \hbox (badness 10000) in paragraph at lines 25916--25922
[]\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 25916--25922
\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 25916--25922
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 25929--25932
[]\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 25953--25955
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[399]
Underfull \hbox (badness 10000) in paragraph at lines 25985--25990
[]\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 25991--26002
\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 26003--26006
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 3713) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN ma-cOS build),

Underfull \hbox (badness 7944) in paragraph at lines 26013--26025
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).

Underfull \hbox (badness 2351) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z
i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo
pard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26027--26034
[]\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 26027--26034
\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 26027--26034
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1874) in paragraph at lines 26027--26034
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[400] [401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 26371--26375
[]\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 26371--26375
\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)]
[405] [406] [407] [408] [409]
Underfull \hbox (badness 1735) in paragraph at lines 26690--26694
[]\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
[410] [411] [412] [413] [414] [415] [416] [417] [418] [419]
Underfull \hbox (badness 2726) in paragraph at lines 27265--27268
[]\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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[432]
Underfull \hbox (badness 1052) in paragraph at lines 28094--28099
[]\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
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Underfull \vbox (badness 10000) has occurred while \output is active [438]
[439] [440] [441] [442] [443] [444] [445]
Underfull \hbox (badness 1533) in paragraph at lines 28926--28929
[]\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
[446] [447]
Underfull \hbox (badness 1163) in paragraph at lines 29089--29100
[]\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
[448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459]
[460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471]
Underfull \hbox (badness 10000) in paragraph at lines 30622--30626
[]\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 30622--30626
\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.
[472]
Underfull \hbox (badness 6188) in paragraph at lines 30644--30646
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 1655) in paragraph at lines 31187--31189
[]\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
[481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491]
Underfull \hbox (badness 10000) in paragraph at lines 31895--31899
[]\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.,
[492] [493] [494] [495]
Underfull \hbox (badness 2302) in paragraph at lines 32146--32153
[]\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 32146--32153
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3333) in paragraph at lines 32146--32153
\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 32146--32153
\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
[496] [497] [498]
Underfull \hbox (badness 2261) in paragraph at lines 32302--32307
[]\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 32329--32335
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[499]
Underfull \hbox (badness 10000) in paragraph at lines 32405--32410
[]\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
[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] [532] [533] [534] [535]
[536] [537] [538]
Underfull \vbox (badness 3803) has occurred while \output is active [539]
[540] [541] [542] [543] [544] [545] [546]
Underfull \hbox (badness 1072) in paragraph at lines 35447--35451
[]\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 35452--35456
[]\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 35480--35486
[]\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 35480--35486
\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 35480--35486
\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
[547]
Underfull \hbox (badness 3343) in paragraph at lines 35492--35499
\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 35492--35499
\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 35492--35499
\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
[548] [549] [550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 35833--35839
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1264) in paragraph at lines 35833--35839
\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
[553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564]
[565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576]
[577] [578] [579] [580] [581] [582]
Underfull \hbox (badness 3333) in paragraph at lines 37683--37688
[]\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
[583] [584] [585] [586] [587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 1472) in paragraph at lines 38315--38318
[]\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
[593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604]
[605] [606]
Underfull \hbox (badness 10000) in paragraph at lines 39221--39225
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e.,
[607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 39471--39474
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[611] [612]
Underfull \hbox (badness 10000) in paragraph at lines 39589--39593
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 10000) in paragraph at lines 39651--39655
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
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Underfull \hbox (badness 4013) in paragraph at lines 40264--40266
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / 
tz-[]link .
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[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via

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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

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\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
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[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
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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
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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
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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
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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.

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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
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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
[670]
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[]\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
[671] [672]) (./compiler-pkg.tex
Chapter 2.
[673] [674] [675] [676]) (./datasets-pkg.tex
Chapter 3.
[677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688]
[689] [690] [691] [692] [693]
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[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
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[755] [756] [757]) (./grDevices-pkg.tex [758]
Chapter 4.
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[771] [772] [773] [774] [775]
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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
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[]\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
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\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
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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/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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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 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 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
[832]
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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
[833]
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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
[836]
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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 ,
[839]
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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 .
[840] [841] [842]
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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 ,
[843]
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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
[866] [867] [868]) (./graphics-pkg.tex
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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[]\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 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
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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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<to be read again> 
                   \relax 
l.8793 \HeaderA{units}{Graphical Units}{units}
                                               [1011] [1012] [1013] [1014])
(./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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[1086] [1087]
Underfull \hbox (badness 1067) in paragraph at lines 4355--4358
[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1088] [1089] [1090] [1091]
Underfull \hbox (badness 7256) in paragraph at lines 4600--4602
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102]
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Underfull \hbox (badness 10000) in paragraph at lines 5877--5883
\T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob-
jects (e.g.,
[1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121]
Underfull \hbox (badness 7649) in paragraph at lines 6356--6359
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like
[1122] [1123] [1124] [1125]) (./methods-pkg.tex [1126]
Chapter 7.
[1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134]
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Underfull \hbox (badness 2237) in paragraph at lines 1385--1387
[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
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Underfull \hbox (badness 1077) in paragraph at lines 1932--1939
[]\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests
[1154]
Underfull \hbox (badness 10000) in paragraph at lines 1981--1986
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

Underfull \hbox (badness 1038) in paragraph at lines 1981--1986
\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1155] [1156] [1157]
Underfull \hbox (badness 1242) in paragraph at lines 2214--2219
[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1158] [1159] [1160] [1161] [1162]
Underfull \hbox (badness 10000) in paragraph at lines 2574--2577
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1163] [1164]
Underfull \hbox (badness 1132) in paragraph at lines 2714--2718
[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in
[1165]
Underfull \hbox (badness 1033) in paragraph at lines 2746--2751
\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
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Underfull \hbox (badness 1102) in paragraph at lines 3303--3305
[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1173] [1174] [1175] [1176] [1177]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
[1178]
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[]\T1/ptm/m/n/10 The
[1179]
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[] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))

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[1180]
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[]\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190]
Underfull \hbox (badness 1436) in paragraph at lines 4443--4446
[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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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

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1191]
Underfull \hbox (badness 1092) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

Underfull \hbox (badness 1117) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and
[1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200]
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[1202]
Underfull \hbox (badness 10000) in paragraph at lines 5355--5356
[]\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1203]
Underfull \hbox (badness 4036) in paragraph at lines 5437--5440
[]\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10
 the method to use in re-sponse to a
[1204]
Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1205] [1206] [1207] [1208]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216]
Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1217] [1218] [1219] [1220]
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[1222] [1223] [1224]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
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nation with the same identifier (name{Rfn.Complex}) has been already used, dupl
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<to be read again> 
                   \relax 
l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate
 ignored
<to be read again> 
                   \relax 
l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
red
<to be read again> 
                   \relax 
l.7232 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored

<to be read again> 
                   \relax 
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1228]
Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1229] [1230] [1231]
Underfull \hbox (badness 1286) in paragraph at lines 7484--7486
[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242]
[1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253]
[1254] [1255] [1256] [1257] [1258]
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[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273]
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1274] [1275] [1276] [1277]) (./parallel-pkg.tex [1278]
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289]
[1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
Underfull \hbox (badness 3386) in paragraph at lines 1339--1342
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1300] [1301] [1302]) (./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
[1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313]
[1314] [1315] [1316] [1317]) (./stats-pkg.tex [1318]
Chapter 10.
[1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329]
[1330] [1331]
Underfull \hbox (badness 1412) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339]
Underfull \hbox (badness 2503) in paragraph at lines 1328--1331
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1340] [1341] [1342]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1343] [1344] [1345] [1346]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via

Underfull \hbox (badness 1546) in paragraph at lines 1773--1777
\T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-ing
[1347] [1348] [1349] [1350] [1351] [1352] [1353]
Underfull \hbox (badness 3965) in paragraph at lines 2183--2185
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1354] [1355] [1356] [1357] [1358]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369]
[1370]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1371] [1372]
Underfull \hbox (badness 2503) in paragraph at lines 3390--3393
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383]
[1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1393] [1394]
Underfull \hbox (badness 3612) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
[1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]
Underfull \hbox (badness 2556) in paragraph at lines 5270--5273
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5287--5289
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1403] [1404] [1405] [1406]
Underfull \hbox (badness 1142) in paragraph at lines 5528--5540
\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.
[1407] [1408] [1409]
Underfull \hbox (badness 2503) in paragraph at lines 5680--5684
[]\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 ,
[1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417]
Underfull \hbox (badness 8132) in paragraph at lines 6184--6189
\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,
[1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 7081) in paragraph at lines 6462--6465
[]\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 6466--6468
[]\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
[1423] [1424] [1425] [1426] [1427]
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[1429] [1430] [1431] [1432] [1433] [1434] [1435]
Underfull \hbox (badness 10000) in paragraph at lines 7311--7314
[]\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
[1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446]
[1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457]
[1458] [1459] [1460] [1461] [1462]
Underfull \hbox (badness 2626) in paragraph at lines 8953--8956
[]\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
[1463]
Underfull \hbox (badness 2503) in paragraph at lines 9060--9064
[]\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 ,
[1464]
Underfull \hbox (badness 2564) in paragraph at lines 9112--9121
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-

Underfull \hbox (badness 1331) in paragraph at lines 9112--9121
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1465] [1466] [1467] [1468] [1469]
Overfull \hbox (3.53955pt too wide) in paragraph at lines 9434--9436
[]\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 . 
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480]
[1481] [1482] [1483] [1484]
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@

Underfull \hbox (badness 1253) in paragraph at lines 10729--10732
[]\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,
[1490]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\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 11208--11217
\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-
[1497] [1498] [1499] [1500] [1501]
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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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<to be read again> 
                   \relax 
l.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1505] [1506]
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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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[]\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
[1517] [1518] [1519] [1520] [1521] [1522]
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[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533]
[1534]
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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
[1545] [1546]
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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
[1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557]
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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 ,
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572]
Underfull \hbox (badness 1584) in paragraph at lines 15857--15863
[]\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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[1595] [1596] [1597] [1598]
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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
[1599]
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[1613]
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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
[1614]
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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
[1615] [1616] [1617]
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 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

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 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

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[1619] [1620] [1621] [1622] [1623] [1624]
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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
[1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633]
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[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1634] [1635] [1636] [1637]
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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
[1638] [1639] [1640] [1641] [1642] [1643]
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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 ,
[1644]
Underfull \hbox (badness 10000) in paragraph at lines 20243--20245
[]\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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[1656] [1657] [1658] [1659] [1660] [1661] [1662]
Underfull \hbox (badness 10000) in paragraph at lines 21316--21322
[]\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 ,
[1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673]
[1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684]
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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
[1685] [1686] [1687] [1688] [1689] [1690] [1691] [1692]
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 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1693] [1694] [1695] [1696] [1697]
Underfull \hbox (badness 10000) in paragraph at lines 23466--23469
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706]
Underfull \hbox (badness 10000) in paragraph at lines 24051--24054
[]\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
[1707]
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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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[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1717] [1718] [1719]
Underfull \hbox (badness 1867) in paragraph at lines 24787--24789
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1720]
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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

Underfull \hbox (badness 10000) in paragraph at lines 24800--24804
\T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was

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\T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o
f un-de-ter-mined co-ef-fi-cients, e.g., for
[1721] [1722] [1723] [1724] [1725] [1726] [1727]
Underfull \hbox (badness 10000) in paragraph at lines 25272--25277
[]\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
[1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738]
[1739] [1740] [1741] [1742] [1743] [1744]
Underfull \hbox (badness 3514) in paragraph at lines 26328--26333
[]\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
[1745] [1746]
Underfull \hbox (badness 3514) in paragraph at lines 26424--26429
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1747]
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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
[1748]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26562--26562
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1749]
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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
[1750] [1751] [1752] [1753]
Underfull \hbox (badness 3514) in paragraph at lines 26812--26817
[]\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
[1754]
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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
[1755]
Underfull \hbox (badness 3514) in paragraph at lines 26964--26969
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1756] [1757]
Underfull \hbox (badness 3514) in paragraph at lines 27058--27063
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1758] [1759]
Underfull \hbox (badness 6691) in paragraph at lines 27150--27155
[]\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
[1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767]
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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,
[1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777]
Underfull \hbox (badness 5431) in paragraph at lines 28286--28288
[]\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
[1778] [1779] [1780] [1781]
Underfull \hbox (badness 5431) in paragraph at lines 28496--28499
[]\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
[1782] [1783] [1784] [1785] [1786]
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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
[1787] [1788]
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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
[1789] [1790] [1791]
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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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Underfull \hbox (badness 10000) in paragraph at lines 30240--30244
[]\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
[1811] [1812] [1813]
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[1815] [1816]
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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
[1817] [1818] [1819] [1820] [1821] [1822] [1823] [1824] [1825]
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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
[1826]
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[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the

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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
[1827] [1828] [1829] [1830] [1831] [1832]
Underfull \hbox (badness 10000) in paragraph at lines 31613--31618
[]\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
[1833] [1834] [1835]) (./stats4-pkg.tex [1836]
Chapter 11.
[1837] [1838] [1839] [1840] [1841] [1842]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}
                                                   [1843] [1844] [1845]
[1846]) (./tcltk-pkg.tex
Chapter 12.
[1847] [1848] [1849] [1850] [1851] [1852] [1853]
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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
[1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866]
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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 ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1867]) (./tools-pkg.tex [1868]
Chapter 13.
[1869]

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[1870]
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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
[1871] [1872]
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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
[1873] [1874]
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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
[1886]
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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-
[1887]
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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 ,
[1888] [1889] [1890]
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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
[1891] [1892] [1893]
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[]\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
[1894] [1895]
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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
[1896] [1897] [1898] [1899]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
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                   \relax 
l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1900] [1901] [1902]
[1903] [1904]
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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
[1908] [1909] [1910] [1911] [1912] [1913] [1914]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
(Font)              using `T1/zi4/m/n' instead on input line 2829.

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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
[1919] [1920] [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929]
[1930]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1931] [1932]
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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
[1933] [1934]
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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
[1935] [1936] [1937]
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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
[1938]
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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
[1939] [1940] [1941]
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[]\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :

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\T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T
1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if
[1942]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1943] [1944] [1945]) (./utils-pkg.tex [1946]
Chapter 14.
[1947]
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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 ',
[1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955]
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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
[1956] [1957]
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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
[1958]
Underfull \hbox (badness 3861) in paragraph at lines 821--826
[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
[1959] [1960] [1961]
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\T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio
n to the for-

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\T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo
re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

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\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

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\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
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[1966] [1967] [1968] [1969]
Underfull \hbox (badness 1371) in paragraph at lines 1482--1484
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1970] [1971] [1972] [1973] [1974] [1975] [1976]
Underfull \hbox (badness 2057) in paragraph at lines 1959--1961
[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1977] [1978]
Underfull \hbox (badness 10000) in paragraph at lines 2054--2056
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1979]
Underfull \hbox (badness 5189) in paragraph at lines 2156--2158
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1980] [1981] [1982] [1983]
Underfull \hbox (badness 1661) in paragraph at lines 2374--2381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

Underfull \hbox (badness 1748) in paragraph at lines 2390--2393
[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1984] [1985] [1986] [1987] [1988] [1989] [1990]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing

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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 ,
[1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000]
Underfull \hbox (badness 1430) in paragraph at lines 3484--3492
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[2001]
Underfull \hbox (badness 1231) in paragraph at lines 3533--3539
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2002] [2003]
Underfull \hbox (badness 10000) in paragraph at lines 3686--3688
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]pdf
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<to be read again> 
                   \relax 
l.4373 ...mat Unordered and Ordered Lists}{format}
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ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
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<to be read again> 
                   \relax 
l.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [2015] [2016] [2017]
[2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028]
[2029] [2030]
Underfull \hbox (badness 1371) in paragraph at lines 5370--5372
[]\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
[2031]
Underfull \hbox (badness 1502) in paragraph at lines 5459--5464
[]\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 5459--5464
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2032] [2033] [2034]
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2035]
Underfull \hbox (badness 2150) in paragraph at lines 5695--5698
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2036] [2037]
Underfull \hbox (badness 3118) in paragraph at lines 5832--5834
[]\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
[2038]
Underfull \hbox (badness 2409) in paragraph at lines 5865--5869
[]\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the
 sub-architecture used by
[2039]
Underfull \hbox (badness 1325) in paragraph at lines 5973--5977
[]\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
[2040]
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
[]\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.,
[2041]
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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
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 6229--6234
[][][]\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 ,
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065]
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Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from

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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 7684--7689
[]\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,
[2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087]
[2088] [2089]
Underfull \hbox (badness 1097) in paragraph at lines 9111--9114
[]\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
[2090]
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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 ;
[2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099]
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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 ;
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
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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 10267--10271
[]\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 10267--10271
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2107] [2108] [2109] [2110] [2111]
Underfull \hbox (badness 4060) in paragraph at lines 10544--10547
[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

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 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
[2112]
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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
[2113] [2114] [2115]
Underfull \hbox (badness 2150) in paragraph at lines 10806--10808
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2116] [2117] [2118] [2119]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2120] [2121]
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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 
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tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30]
Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922
 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
[31] [32] [33]
Underfull \hbox (badness 10000) in paragraph at lines 2120--2122
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]
[49] [50] [51] [52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3650--3652
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 3891--3891
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[61] [62]
Underfull \hbox (badness 1057) in paragraph at lines 3999--4002
[][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls 
(but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m
/n/10 expression[][][]\T1/ptm/m/n/10 s where
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76]
Underfull \hbox (badness 2521) in paragraph at lines 4882--4884
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91]
[92] [93] [94]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6035--6035
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[95] [96]
Underfull \hbox (badness 2096) in paragraph at lines 6223--6236
[]\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
[97] [98] [99] [100]
Overfull \hbox (56.34871pt too wide) in paragraph at lines 6432--6434
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : 
[101] [102]
Underfull \hbox (badness 10000) in paragraph at lines 6574--6577
[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
[103] [104]
Underfull \hbox (badness 1442) in paragraph at lines 6756--6762
[]\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 6756--6762
\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 6756--6762
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
[105]
Underfull \hbox (badness 3568) in paragraph at lines 6818--6825
\T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z
i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
[106] [107]
Underfull \vbox (badness 10000) has occurred while \output is active [108]
[109] [110]
Underfull \hbox (badness 1077) in paragraph at lines 7135--7141
[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
1/ptm/m/n/10 . Con-di-tions of length greater

Underfull \hbox (badness 1231) in paragraph at lines 7135--7141
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[111] [112] [113] [114] [115] [116]
Underfull \hbox (badness 2096) in paragraph at lines 7476--7480
\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
 : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$
[][]\T1/ptm/m/n/10 .
[117]
Underfull \hbox (badness 3000) in paragraph at lines 7569--7571
[]\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
[118]
Underfull \hbox (badness 2351) in paragraph at lines 7594--7597
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[119] [120] [121] [122]
Underfull \hbox (badness 10000) in paragraph at lines 7849--7859
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[123]
Underfull \hbox (badness 4479) in paragraph at lines 7920--7930
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
[124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148] [149]
Underfull \hbox (badness 1394) in paragraph at lines 9676--9681
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[150] [151] [152] [153] [154]
Underfull \hbox (badness 1194) in paragraph at lines 10021--10026
[]\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 10021--10026
\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
[155] [156] [157]
Underfull \hbox (badness 1735) in paragraph at lines 10226--10230
\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 .
[158] [159] [160] [161] [162] [163] [164]
Underfull \hbox (badness 2150) in paragraph at lines 10649--10652
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 6396) in paragraph at lines 10663--10671
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
[165]
Underfull \hbox (badness 2735) in paragraph at lines 10692--10699
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177]
[178] [179] [180]
Underfull \hbox (badness 4569) in paragraph at lines 11772--11776
[]\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 11772--11776
\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
[181] [182] [183] [184] [185] [186] [187] [188] [189]
Underfull \hbox (badness 2698) in paragraph at lines 12349--12358
[]\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 12349--12358
\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
[190] [191] [192] [193] [194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 6236) in paragraph at lines 13008--13011
[]\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
[200] [201] [202] [203] [204] [205] [206]
Underfull \hbox (badness 2253) in paragraph at lines 13430--13432
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[207]
Underfull \hbox (badness 1565) in paragraph at lines 13501--13505
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[208]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13547
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[209] [210]
Underfull \hbox (badness 1466) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[211] [212]
Underfull \hbox (badness 10000) in paragraph at lines 13804--13808
[][][]\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 13815--13818
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[213] [214] [215] [216]
Underfull \hbox (badness 3965) in paragraph at lines 14097--14101
[]\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,
[217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228]
[229]
Underfull \hbox (badness 4429) in paragraph at lines 14859--14862
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
[230]
Underfull \hbox (badness 10000) in paragraph at lines 14959--14961
[]\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 14965--14969
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[231]
Underfull \hbox (badness 10000) in paragraph at lines 15004--15008
[]\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 15004--15008
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[232] [233] [234] [235] [236] [237] [238] [239] [240]
Underfull \hbox (badness 2452) in paragraph at lines 15596--15600
[]\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 15596--15600
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[241] [242] [243]
Underfull \hbox (badness 1092) in paragraph at lines 15769--15774
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[244] [245] [246]
Underfull \hbox (badness 6741) in paragraph at lines 16020--16024
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[247] [248] [249] [250] [251]
Underfull \hbox (badness 1867) in paragraph at lines 16326--16333
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[252] [253] [254] [255]
Underfull \vbox (badness 10000) has occurred while \output is active [256]
[257] [258]
Underfull \hbox (badness 3679) in paragraph at lines 16736--16738
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[259] [260] [261] [262] [263] [264] [265] [266]
Underfull \hbox (badness 1478) in paragraph at lines 17301--17304
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 17554--17556
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[270] [271] [272] [273] [274] [275] [276] [277] [278] [279]
Underfull \hbox (badness 1442) in paragraph at lines 18145--18147
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[280]
Underfull \hbox (badness 2452) in paragraph at lines 18237--18253
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1248) in paragraph at lines 18651--18654
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[288] [289] [290] [291]
Underfull \hbox (badness 4739) in paragraph at lines 18909--18911
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303]
[304] [305] [306] [307] [308]
Underfull \hbox (badness 2469) in paragraph at lines 19926--19931
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 19940--19947
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[309]
Underfull \hbox (badness 10000) in paragraph at lines 20014--20018
[]\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 20014--20018
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[310] [311]
Underfull \hbox (badness 1509) in paragraph at lines 20149--20156
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1552) in paragraph at lines 20149--20156
\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 20165--20170
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 1264) in paragraph at lines 20916--20921
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:

Underfull \hbox (badness 4441) in paragraph at lines 20945--20948
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 21679--21681
[]\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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Underfull \hbox (badness 1077) in paragraph at lines 22714--22720
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[352] [353] [354]
Underfull \hbox (badness 1484) in paragraph at lines 22877--22885
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[355] [356] [357] [358]
Underfull \hbox (badness 2790) in paragraph at lines 23162--23165
[]\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 23162--23165
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
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Underfull \hbox (badness 1194) in paragraph at lines 23444--23447
[]\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 23650--23656
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 7379) in paragraph at lines 23650--23656
\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 23660--23663
[]\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 23660--23663
\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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Underfull \hbox (badness 10000) in paragraph at lines 24031--24034
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
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Underfull \hbox (badness 10000) in paragraph at lines 24623--24625
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
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Underfull \hbox (badness 1199) in paragraph at lines 24867--24873
[]\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 24867--24873
\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 25459--25467
[]\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 25468--25471
[]\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 25487--25489
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[394]
Underfull \hbox (badness 10000) in paragraph at lines 25596--25606
[]\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 25607--25613
[]\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
[395]
Underfull \hbox (badness 1968) in paragraph at lines 25643--25648
[]\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 25653--25655
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
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Underfull \hbox (badness 10000) in paragraph at lines 25916--25922
[]\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 25916--25922
\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 25916--25922
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 25929--25932
[]\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 25953--25955
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[399]
Underfull \hbox (badness 10000) in paragraph at lines 25985--25990
[]\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 25991--26002
\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 26003--26006
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 3713) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN ma-cOS build),

Underfull \hbox (badness 7944) in paragraph at lines 26013--26025
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).

Underfull \hbox (badness 2351) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z
i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo
pard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26027--26034
[]\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 26027--26034
\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 26027--26034
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1874) in paragraph at lines 26027--26034
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[400] [401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 26371--26375
[]\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 26371--26375
\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)]
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Underfull \hbox (badness 1735) in paragraph at lines 26690--26694
[]\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
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Underfull \hbox (badness 2726) in paragraph at lines 27265--27268
[]\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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[432]
Underfull \hbox (badness 1052) in paragraph at lines 28094--28099
[]\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
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Underfull \vbox (badness 10000) has occurred while \output is active [438]
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Underfull \hbox (badness 1533) in paragraph at lines 28926--28929
[]\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
[446] [447]
Underfull \hbox (badness 1163) in paragraph at lines 29089--29100
[]\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
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Underfull \hbox (badness 10000) in paragraph at lines 30622--30626
[]\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 30622--30626
\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.
[472]
Underfull \hbox (badness 6188) in paragraph at lines 30644--30646
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 1655) in paragraph at lines 31187--31189
[]\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
[481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491]
Underfull \hbox (badness 10000) in paragraph at lines 31895--31899
[]\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.,
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Underfull \hbox (badness 2302) in paragraph at lines 32146--32153
[]\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 32146--32153
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3333) in paragraph at lines 32146--32153
\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 32146--32153
\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
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Underfull \hbox (badness 2261) in paragraph at lines 32302--32307
[]\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 32329--32335
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[499]
Underfull \hbox (badness 10000) in paragraph at lines 32405--32410
[]\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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[512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523]
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Underfull \vbox (badness 3803) has occurred while \output is active [539]
[540] [541] [542] [543] [544] [545] [546]
Underfull \hbox (badness 1072) in paragraph at lines 35447--35451
[]\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 35452--35456
[]\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 35480--35486
[]\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 35480--35486
\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 35480--35486
\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
[547]
Underfull \hbox (badness 3343) in paragraph at lines 35492--35499
\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 35492--35499
\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 35492--35499
\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
[548] [549] [550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 35833--35839
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1264) in paragraph at lines 35833--35839
\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
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Underfull \hbox (badness 3333) in paragraph at lines 37683--37688
[]\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
[583] [584] [585] [586] [587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 1472) in paragraph at lines 38315--38318
[]\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
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[605] [606]
Underfull \hbox (badness 10000) in paragraph at lines 39221--39225
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e.,
[607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 39471--39474
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[611] [612]
Underfull \hbox (badness 10000) in paragraph at lines 39589--39593
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 10000) in paragraph at lines 39651--39655
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[614] [615] [616] [617] [618] [619] [620] [621] [622]
Underfull \hbox (badness 4013) in paragraph at lines 40264--40266
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / 
tz-[]link .
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[630] [631] [632] [633] [634] [635] [636]
Underfull \hbox (badness 3460) in paragraph at lines 41145--41148
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via

Underfull \hbox (badness 1990) in paragraph at lines 41152--41160
[]\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 41152--41160
\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
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Underfull \hbox (badness 10000) in paragraph at lines 41429--41432
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
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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
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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
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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
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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.

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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
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Underfull \hbox (badness 5417) in paragraph at lines 43290--43294
[]\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
[670]
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[]\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
[671] [672]) (./compiler-pkg.tex
Chapter 2.
[673] [674] [675] [676]) (./datasets-pkg.tex
Chapter 3.
[677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688]
[689] [690] [691] [692] [693]
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[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
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Overfull \vbox (18.9959pt too high) has occurred while \output is active
[755] [756] [757]) (./grDevices-pkg.tex [758]
Chapter 4.
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[771] [772] [773] [774] [775]
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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
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[]\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
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\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
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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/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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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 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 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
[832]
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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
[833]
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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
[836]
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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
[837] [838]
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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 ,
[839]
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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 .
[840] [841] [842]
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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 ,
[843]
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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
[844] [845] [846] [847] [848] [849] [850]
Underfull \hbox (badness 10000) in paragraph at lines 5772--5775
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[851] [852] [853] [854] [855] [856]
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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 ,
[863] [864] [865]
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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
[866] [867] [868]) (./graphics-pkg.tex
Chapter 5.
[869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879]
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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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[][] 
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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 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[1003] [1004] [1005] [1006] [1007] [1008] [1009]
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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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ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8793 \HeaderA{units}{Graphical Units}{units}
                                               [1011] [1012] [1013] [1014])
(./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
[1088] [1089] [1090] [1091]
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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
[1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102]
[1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
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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.,
[1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121]
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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
[1122] [1123] [1124] [1125]) (./methods-pkg.tex [1126]
Chapter 7.
[1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134]
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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
[1146] [1147] [1148] [1149] [1150] [1151] [1152] [1153]
Underfull \hbox (badness 1077) in paragraph at lines 1932--1939
[]\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests
[1154]
Underfull \hbox (badness 10000) in paragraph at lines 1981--1986
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

Underfull \hbox (badness 1038) in paragraph at lines 1981--1986
\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1155] [1156] [1157]
Underfull \hbox (badness 1242) in paragraph at lines 2214--2219
[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1158] [1159] [1160] [1161] [1162]
Underfull \hbox (badness 10000) in paragraph at lines 2574--2577
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1163] [1164]
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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
[1165]
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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
[1166] [1167] [1168] [1169] [1170] [1171] [1172]
Underfull \hbox (badness 1102) in paragraph at lines 3303--3305
[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1173] [1174] [1175] [1176] [1177]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
[1178]
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[]\T1/ptm/m/n/10 The
[1179]
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[] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))

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[1180]
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[]\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190]
Underfull \hbox (badness 1436) in paragraph at lines 4443--4446
[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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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

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1191]
Underfull \hbox (badness 1092) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

Underfull \hbox (badness 1117) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and
[1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200]
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[1202]
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[]\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1203]
Underfull \hbox (badness 4036) in paragraph at lines 5437--5440
[]\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10
 the method to use in re-sponse to a
[1204]
Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1205] [1206] [1207] [1208]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216]
Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1217] [1218] [1219] [1220]
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                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
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l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
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l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
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l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
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l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1228]
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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
[1229] [1230] [1231]
Underfull \hbox (badness 1286) in paragraph at lines 7484--7486
[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242]
[1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253]
[1254] [1255] [1256] [1257] [1258]
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[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273]
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1274] [1275] [1276] [1277]) (./parallel-pkg.tex [1278]
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289]
[1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
Underfull \hbox (badness 3386) in paragraph at lines 1339--1342
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1300] [1301] [1302]) (./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
[1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313]
[1314] [1315] [1316] [1317]) (./stats-pkg.tex [1318]
Chapter 10.
[1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329]
[1330] [1331]
Underfull \hbox (badness 1412) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339]
Underfull \hbox (badness 2503) in paragraph at lines 1328--1331
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1340] [1341] [1342]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1343] [1344] [1345] [1346]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via

Underfull \hbox (badness 1546) in paragraph at lines 1773--1777
\T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-ing
[1347] [1348] [1349] [1350] [1351] [1352] [1353]
Underfull \hbox (badness 3965) in paragraph at lines 2183--2185
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1354] [1355] [1356] [1357] [1358]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369]
[1370]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1371] [1372]
Underfull \hbox (badness 2503) in paragraph at lines 3390--3393
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383]
[1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1393] [1394]
Underfull \hbox (badness 3612) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
[1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]
Underfull \hbox (badness 2556) in paragraph at lines 5270--5273
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5287--5289
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1403] [1404] [1405] [1406]
Underfull \hbox (badness 1142) in paragraph at lines 5528--5540
\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.
[1407] [1408] [1409]
Underfull \hbox (badness 2503) in paragraph at lines 5680--5684
[]\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 ,
[1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417]
Underfull \hbox (badness 8132) in paragraph at lines 6184--6189
\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,
[1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 7081) in paragraph at lines 6462--6465
[]\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 6466--6468
[]\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
[1423] [1424] [1425] [1426] [1427]
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[1429] [1430] [1431] [1432] [1433] [1434] [1435]
Underfull \hbox (badness 10000) in paragraph at lines 7311--7314
[]\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
[1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446]
[1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457]
[1458] [1459] [1460] [1461] [1462]
Underfull \hbox (badness 2626) in paragraph at lines 8953--8956
[]\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
[1463]
Underfull \hbox (badness 2503) in paragraph at lines 9060--9064
[]\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 ,
[1464]
Underfull \hbox (badness 2564) in paragraph at lines 9112--9121
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-

Underfull \hbox (badness 1331) in paragraph at lines 9112--9121
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1465] [1466] [1467] [1468] [1469]
Overfull \hbox (3.53955pt too wide) in paragraph at lines 9434--9436
[]\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 . 
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480]
[1481] [1482] [1483] [1484]
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@

Underfull \hbox (badness 1253) in paragraph at lines 10729--10732
[]\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,
[1490]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\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 11208--11217
\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-
[1497] [1498] [1499] [1500] [1501]
Underfull \hbox (badness 10000) in paragraph at lines 11516--11519
[]\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.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1505] [1506]
Underfull \hbox (badness 1484) in paragraph at lines 11801--11803
[]\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
[1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516]
Underfull \hbox (badness 4441) in paragraph at lines 12387--12389
[]\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 12394--12396
[]\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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[]\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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[1534]
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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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[]\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/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

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 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

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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 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
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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 ,
[1644]
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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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[]\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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[]\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/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\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
[1707]
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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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[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1717] [1718] [1719]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1720]
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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

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\T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was

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\T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o
f un-de-ter-mined co-ef-fi-cients, e.g., for
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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
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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
[1747]
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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
[1748]
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 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1749]
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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
[1750] [1751] [1752] [1753]
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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
[1754]
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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
[1755]
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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
[1756] [1757]
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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
[1758] [1759]
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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
[1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767]
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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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Underfull \hbox (badness 5431) in paragraph at lines 28286--28288
[]\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
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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
[1787] [1788]
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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
[1789] [1790] [1791]
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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
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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
[1826]
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[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the

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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
[1833] [1834] [1835]) (./stats4-pkg.tex [1836]
Chapter 11.
[1837] [1838] [1839] [1840] [1841] [1842]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}
                                                   [1843] [1844] [1845]
[1846]) (./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 ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1867]) (./tools-pkg.tex [1868]
Chapter 13.
[1869]

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[1870]
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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-
[1887]
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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 ,
[1888] [1889] [1890]
Underfull \hbox (badness 10000) in paragraph at lines 1377--1379
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1891] [1892] [1893]
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[]\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
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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
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l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1900] [1901] [1902]
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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
[1908] [1909] [1910] [1911] [1912] [1913] [1914]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
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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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[1930]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1931] [1932]
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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
[1933] [1934]
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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
[1935] [1936] [1937]
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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
[1938]
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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 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :

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\T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T
1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if
[1942]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1943] [1944] [1945]) (./utils-pkg.tex [1946]
Chapter 14.
[1947]
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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 ',
[1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955]
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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
[1956] [1957]
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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
[1958]
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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 ,
[1959] [1960] [1961]
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\T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio
n to the for-

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\T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo
re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

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\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

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\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
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[1966] [1967] [1968] [1969]
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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
[1970] [1971] [1972] [1973] [1974] [1975] [1976]
Underfull \hbox (badness 2057) in paragraph at lines 1959--1961
[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1977] [1978]
Underfull \hbox (badness 10000) in paragraph at lines 2054--2056
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1979]
Underfull \hbox (badness 5189) in paragraph at lines 2156--2158
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1980] [1981] [1982] [1983]
Underfull \hbox (badness 1661) in paragraph at lines 2374--2381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

Underfull \hbox (badness 1748) in paragraph at lines 2390--2393
[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1984] [1985] [1986] [1987] [1988] [1989] [1990]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing

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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 ,
[1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000]
Underfull \hbox (badness 1430) in paragraph at lines 3484--3492
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[2001]
Underfull \hbox (badness 1231) in paragraph at lines 3533--3539
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2002] [2003]
Underfull \hbox (badness 10000) in paragraph at lines 3686--3688
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]pdf
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<to be read again> 
                   \relax 
l.4373 ...mat Unordered and Ordered Lists}{format}
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ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
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                   \relax 
l.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [2015] [2016] [2017]
[2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028]
[2029] [2030]
Underfull \hbox (badness 1371) in paragraph at lines 5370--5372
[]\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
[2031]
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[]\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 5459--5464
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2032] [2033] [2034]
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2035]
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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
[2036] [2037]
Underfull \hbox (badness 3118) in paragraph at lines 5832--5834
[]\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
[2038]
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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
[2039]
Underfull \hbox (badness 1325) in paragraph at lines 5973--5977
[]\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
[2040]
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
[]\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.,
[2041]
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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
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 6229--6234
[][][]\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 ,
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065]
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Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from

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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

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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,
[2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087]
[2088] [2089]
Underfull \hbox (badness 1097) in paragraph at lines 9111--9114
[]\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
[2090]
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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 ;
[2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099]
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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 ;
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
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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 10267--10271
[]\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 10267--10271
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2107] [2108] [2109] [2110] [2111]
Underfull \hbox (badness 4060) in paragraph at lines 10544--10547
[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

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 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
[2112]
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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
[2113] [2114] [2115]
Underfull \hbox (badness 2150) in paragraph at lines 10806--10808
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2116] [2117] [2118] [2119]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2120] [2121]
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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
[2122]
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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
[2123] [2124] [2125] [2126] [2127]
Underfull \hbox (badness 3780) in paragraph at lines 11556--11560
[]\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
[2128] [2129] [2130] [2131] [2132] [2133]
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tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
[19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30]
Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922
 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
[31] [32] [33]
Underfull \hbox (badness 10000) in paragraph at lines 2120--2122
[]\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by
[34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]
[49] [50] [51] [52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3650--3652
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 3891--3891
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[61] [62]
Underfull \hbox (badness 1057) in paragraph at lines 3999--4002
[][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls 
(but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m
/n/10 expression[][][]\T1/ptm/m/n/10 s where
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76]
Underfull \hbox (badness 2521) in paragraph at lines 4882--4884
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
[77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91]
[92] [93] [94]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6035--6035
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[95] [96]
Underfull \hbox (badness 2096) in paragraph at lines 6223--6236
[]\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
[97] [98] [99] [100]
Overfull \hbox (56.34871pt too wide) in paragraph at lines 6432--6434
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : 
[101] [102]
Underfull \hbox (badness 10000) in paragraph at lines 6574--6577
[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
[103] [104]
Underfull \hbox (badness 1442) in paragraph at lines 6756--6762
[]\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 6756--6762
\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 6756--6762
\T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o
m-mended) when writ-ing it
[105]
Underfull \hbox (badness 3568) in paragraph at lines 6818--6825
\T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z
i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as
[106] [107]
Underfull \vbox (badness 10000) has occurred while \output is active [108]
[109] [110]
Underfull \hbox (badness 1077) in paragraph at lines 7135--7141
[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
1/ptm/m/n/10 . Con-di-tions of length greater

Underfull \hbox (badness 1231) in paragraph at lines 7135--7141
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[111] [112] [113] [114] [115] [116]
Underfull \hbox (badness 2096) in paragraph at lines 7476--7480
\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
 : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$
[][]\T1/ptm/m/n/10 .
[117]
Underfull \hbox (badness 3000) in paragraph at lines 7569--7571
[]\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
[118]
Underfull \hbox (badness 2351) in paragraph at lines 7594--7597
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[119] [120] [121] [122]
Underfull \hbox (badness 10000) in paragraph at lines 7849--7859
[]\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to
 a data frame by call-ing
[123]
Underfull \hbox (badness 4479) in paragraph at lines 7920--7930
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
[124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135]
[136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]
[148] [149]
Underfull \hbox (badness 1394) in paragraph at lines 9676--9681
[]\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla
ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with
[150] [151] [152] [153] [154]
Underfull \hbox (badness 1194) in paragraph at lines 10021--10026
[]\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 10021--10026
\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
[155] [156] [157]
Underfull \hbox (badness 1735) in paragraph at lines 10226--10230
\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 .
[158] [159] [160] [161] [162] [163] [164]
Underfull \hbox (badness 2150) in paragraph at lines 10649--10652
[]\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered
 from the re-verse

Underfull \hbox (badness 6396) in paragraph at lines 10663--10671
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for
[165]
Underfull \hbox (badness 2735) in paragraph at lines 10692--10699
[]\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \
T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to
[166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177]
[178] [179] [180]
Underfull \hbox (badness 4569) in paragraph at lines 11772--11776
[]\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 11772--11776
\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
[181] [182] [183] [184] [185] [186] [187] [188] [189]
Underfull \hbox (badness 2698) in paragraph at lines 12349--12358
[]\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 12349--12358
\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
[190] [191] [192] [193] [194] [195] [196] [197] [198] [199]
Underfull \hbox (badness 6236) in paragraph at lines 13008--13011
[]\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
[200] [201] [202] [203] [204] [205] [206]
Underfull \hbox (badness 2253) in paragraph at lines 13430--13432
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[207]
Underfull \hbox (badness 1565) in paragraph at lines 13501--13505
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and
[208]
Underfull \hbox (badness 10000) in paragraph at lines 13545--13547
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with
[209] [210]
Underfull \hbox (badness 1466) in paragraph at lines 13685--13688
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[211] [212]
Underfull \hbox (badness 10000) in paragraph at lines 13804--13808
[][][]\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 13815--13818
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[213] [214] [215] [216]
Underfull \hbox (badness 3965) in paragraph at lines 14097--14101
[]\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,
[217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228]
[229]
Underfull \hbox (badness 4429) in paragraph at lines 14859--14862
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
[230]
Underfull \hbox (badness 10000) in paragraph at lines 14959--14961
[]\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 14965--14969
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so
[231]
Underfull \hbox (badness 10000) in paragraph at lines 15004--15008
[]\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 15004--15008
\T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in
 pack-ages which might be used with ear-lier ver-sions: use
[232] [233] [234] [235] [236] [237] [238] [239] [240]
Underfull \hbox (badness 2452) in paragraph at lines 15596--15600
[]\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 15596--15600
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[241] [242] [243]
Underfull \hbox (badness 1092) in paragraph at lines 15769--15774
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[244] [245] [246]
Underfull \hbox (badness 6741) in paragraph at lines 16020--16024
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[247] [248] [249] [250] [251]
Underfull \hbox (badness 1867) in paragraph at lines 16326--16333
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[252] [253] [254] [255]
Underfull \vbox (badness 10000) has occurred while \output is active [256]
[257] [258]
Underfull \hbox (badness 3679) in paragraph at lines 16736--16738
[]\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http
 : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for
[259] [260] [261] [262] [263] [264] [265] [266]
Underfull \hbox (badness 1478) in paragraph at lines 17301--17304
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[267] [268] [269]
Underfull \hbox (badness 10000) in paragraph at lines 17554--17556
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[270] [271] [272] [273] [274] [275] [276] [277] [278] [279]
Underfull \hbox (badness 1442) in paragraph at lines 18145--18147
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[280]
Underfull \hbox (badness 2452) in paragraph at lines 18237--18253
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[281] [282] [283] [284] [285] [286] [287]
Underfull \hbox (badness 1248) in paragraph at lines 18651--18654
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[288] [289] [290] [291]
Underfull \hbox (badness 4739) in paragraph at lines 18909--18911
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303]
[304] [305] [306] [307] [308]
Underfull \hbox (badness 2469) in paragraph at lines 19926--19931
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 19940--19947
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[309]
Underfull \hbox (badness 10000) in paragraph at lines 20014--20018
[]\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 20014--20018
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[310] [311]
Underfull \hbox (badness 1509) in paragraph at lines 20149--20156
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1
/zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu-
ment, it lists all avail-able pack-ages

Underfull \hbox (badness 1552) in paragraph at lines 20149--20156
\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 20165--20170
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323]
Underfull \hbox (badness 1264) in paragraph at lines 20916--20921
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:

Underfull \hbox (badness 4441) in paragraph at lines 20945--20948
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334]
Underfull \hbox (badness 10000) in paragraph at lines 21679--21681
[]\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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Underfull \hbox (badness 1077) in paragraph at lines 22714--22720
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[352] [353] [354]
Underfull \hbox (badness 1484) in paragraph at lines 22877--22885
\T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / 
www . microsoft . com / whdc / system / platform /
[355] [356] [357] [358]
Underfull \hbox (badness 2790) in paragraph at lines 23162--23165
[]\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 23162--23165
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
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Underfull \hbox (badness 1194) in paragraph at lines 23444--23447
[]\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 23650--23656
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing

Underfull \hbox (badness 7379) in paragraph at lines 23650--23656
\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 23660--23663
[]\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 23660--23663
\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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Underfull \hbox (badness 10000) in paragraph at lines 24031--24034
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
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Underfull \hbox (badness 10000) in paragraph at lines 24623--24625
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than
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Underfull \hbox (badness 1199) in paragraph at lines 24867--24873
[]\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 24867--24873
\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 25459--25467
[]\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 25468--25471
[]\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 25487--25489
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[394]
Underfull \hbox (badness 10000) in paragraph at lines 25596--25606
[]\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 25607--25613
[]\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
[395]
Underfull \hbox (badness 1968) in paragraph at lines 25643--25648
[]\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 25653--25655
[]\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v
alue
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Underfull \hbox (badness 10000) in paragraph at lines 25916--25922
[]\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 25916--25922
\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 25916--25922
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 25929--25932
[]\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 25953--25955
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[399]
Underfull \hbox (badness 10000) in paragraph at lines 25985--25990
[]\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 25991--26002
\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 26003--26006
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 3713) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t
he de-fault ex-cept un-der a CRAN ma-cOS build),

Underfull \hbox (badness 7944) in paragraph at lines 26013--26025
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).

Underfull \hbox (badness 2351) in paragraph at lines 26013--26025
\T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z
i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo
pard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26027--26034
[]\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 26027--26034
\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 26027--26034
\T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi
ng like

Underfull \hbox (badness 1874) in paragraph at lines 26027--26034
\T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr
an";
[400] [401] [402] [403] [404]
Underfull \hbox (badness 10000) in paragraph at lines 26371--26375
[]\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 26371--26375
\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)]
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Underfull \hbox (badness 1735) in paragraph at lines 26690--26694
[]\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
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Underfull \hbox (badness 2726) in paragraph at lines 27265--27268
[]\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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[432]
Underfull \hbox (badness 1052) in paragraph at lines 28094--28099
[]\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
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Underfull \vbox (badness 10000) has occurred while \output is active [438]
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Underfull \hbox (badness 1533) in paragraph at lines 28926--28929
[]\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
[446] [447]
Underfull \hbox (badness 1163) in paragraph at lines 29089--29100
[]\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
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Underfull \hbox (badness 10000) in paragraph at lines 30622--30626
[]\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 30622--30626
\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.
[472]
Underfull \hbox (badness 6188) in paragraph at lines 30644--30646
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 1655) in paragraph at lines 31187--31189
[]\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
[481] [482] [483] [484] [485] [486] [487] [488] [489] [490] [491]
Underfull \hbox (badness 10000) in paragraph at lines 31895--31899
[]\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.,
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Underfull \hbox (badness 2302) in paragraph at lines 32146--32153
[]\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 32146--32153
\T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no
n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non
-missing

Underfull \hbox (badness 3333) in paragraph at lines 32146--32153
\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 32146--32153
\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
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Underfull \hbox (badness 2261) in paragraph at lines 32302--32307
[]\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 32329--32335
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters
[499]
Underfull \hbox (badness 10000) in paragraph at lines 32405--32410
[]\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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[512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523]
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Underfull \vbox (badness 3803) has occurred while \output is active [539]
[540] [541] [542] [543] [544] [545] [546]
Underfull \hbox (badness 1072) in paragraph at lines 35447--35451
[]\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 35452--35456
[]\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 35480--35486
[]\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 35480--35486
\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 35480--35486
\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
[547]
Underfull \hbox (badness 3343) in paragraph at lines 35492--35499
\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 35492--35499
\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 35492--35499
\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
[548] [549] [550] [551] [552]
Underfull \hbox (badness 10000) in paragraph at lines 35833--35839
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is

Underfull \hbox (badness 1264) in paragraph at lines 35833--35839
\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
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Underfull \hbox (badness 3333) in paragraph at lines 37683--37688
[]\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
[583] [584] [585] [586] [587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 1472) in paragraph at lines 38315--38318
[]\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
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[605] [606]
Underfull \hbox (badness 10000) in paragraph at lines 39221--39225
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e.,
[607] [608] [609] [610]
Underfull \hbox (badness 10000) in paragraph at lines 39471--39474
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[611] [612]
Underfull \hbox (badness 10000) in paragraph at lines 39589--39593
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames
[][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[613]
Underfull \hbox (badness 10000) in paragraph at lines 39651--39655
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[614] [615] [616] [617] [618] [619] [620] [621] [622]
Underfull \hbox (badness 4013) in paragraph at lines 40264--40266
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / 
tz-[]link .
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[630] [631] [632] [633] [634] [635] [636]
Underfull \hbox (badness 3460) in paragraph at lines 41145--41148
[]\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the 
file to print to (via

Underfull \hbox (badness 1990) in paragraph at lines 41152--41160
[]\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 41152--41160
\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
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Underfull \hbox (badness 10000) in paragraph at lines 41429--41432
[]\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an
d sock-ets.
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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
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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
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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
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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.

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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
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Underfull \hbox (badness 5417) in paragraph at lines 43290--43294
[]\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
[670]
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[]\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
[671] [672]) (./compiler-pkg.tex
Chapter 2.
[673] [674] [675] [676]) (./datasets-pkg.tex
Chapter 3.
[677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688]
[689] [690] [691] [692] [693]
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[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
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Overfull \vbox (18.9959pt too high) has occurred while \output is active
[755] [756] [757]) (./grDevices-pkg.tex [758]
Chapter 4.
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[771] [772] [773] [774] [775]
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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
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[]\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
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\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
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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/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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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 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 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
[832]
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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
[833]
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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
[836]
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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
[837] [838]
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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 ,
[839]
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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 .
[840] [841] [842]
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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 ,
[843]
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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
[844] [845] [846] [847] [848] [849] [850]
Underfull \hbox (badness 10000) in paragraph at lines 5772--5775
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[851] [852] [853] [854] [855] [856]
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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 ,
[863] [864] [865]
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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
[866] [867] [868]) (./graphics-pkg.tex
Chapter 5.
[869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879]
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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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[][] 
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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 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly 
en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn
. For
[1003] [1004] [1005] [1006] [1007] [1008] [1009]
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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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ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8793 \HeaderA{units}{Graphical Units}{units}
                                               [1011] [1012] [1013] [1014])
(./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
[1088] [1089] [1090] [1091]
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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
[1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102]
[1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
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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.,
[1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121]
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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
[1122] [1123] [1124] [1125]) (./methods-pkg.tex [1126]
Chapter 7.
[1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134]
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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
[1146] [1147] [1148] [1149] [1150] [1151] [1152] [1153]
Underfull \hbox (badness 1077) in paragraph at lines 1932--1939
[]\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests
[1154]
Underfull \hbox (badness 10000) in paragraph at lines 1981--1986
[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

Underfull \hbox (badness 1038) in paragraph at lines 1981--1986
\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1155] [1156] [1157]
Underfull \hbox (badness 1242) in paragraph at lines 2214--2219
[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1158] [1159] [1160] [1161] [1162]
Underfull \hbox (badness 10000) in paragraph at lines 2574--2577
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1163] [1164]
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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
[1165]
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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
[1166] [1167] [1168] [1169] [1170] [1171] [1172]
Underfull \hbox (badness 1102) in paragraph at lines 3303--3305
[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1173] [1174] [1175] [1176] [1177]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments
[1178]
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[]\T1/ptm/m/n/10 The
[1179]
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[] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric",       
     longitude = "numeric", altitude = "numeric"))

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[1180]
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[]\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character")
,  contains = "numeric") 
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190]
Underfull \hbox (badness 1436) in paragraph at lines 4443--4446
[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/
10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w
ith ar-gu-ment

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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

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1191]
Underfull \hbox (badness 1092) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments
. In the pre-vi-ous ex-am-ple,

Underfull \hbox (badness 1117) in paragraph at lines 4531--4538
\T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \
T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth
-ods list and
[1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200]
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[1202]
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[]\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...)
[1203]
Underfull \hbox (badness 4036) in paragraph at lines 5437--5440
[]\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10
 the method to use in re-sponse to a
[1204]
Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1205] [1206] [1207] [1208]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216]
Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1217] [1218] [1219] [1220]
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                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
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l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
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l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
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l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
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l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1228]
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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
[1229] [1230] [1231]
Underfull \hbox (badness 1286) in paragraph at lines 7484--7486
[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242]
[1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253]
[1254] [1255] [1256] [1257] [1258]
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[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273]
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1274] [1275] [1276] [1277]) (./parallel-pkg.tex [1278]
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289]
[1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
Underfull \hbox (badness 3386) in paragraph at lines 1339--1342
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1300] [1301] [1302]) (./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
[1303] [1304] [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313]
[1314] [1315] [1316] [1317]) (./stats-pkg.tex [1318]
Chapter 10.
[1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329]
[1330] [1331]
Underfull \hbox (badness 1412) in paragraph at lines 847--849
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339]
Underfull \hbox (badness 2503) in paragraph at lines 1328--1331
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1340] [1341] [1342]
Underfull \hbox (badness 10000) in paragraph at lines 1508--1512
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/
10 or for mul-ti-ple re-sponses of class
[1343] [1344] [1345] [1346]
Underfull \hbox (badness 10000) in paragraph at lines 1773--1777
[]\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently,
 via

Underfull \hbox (badness 1546) in paragraph at lines 1773--1777
\T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can 
han-dle miss-ing
[1347] [1348] [1349] [1350] [1351] [1352] [1353]
Underfull \hbox (badness 3965) in paragraph at lines 2183--2185
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1354] [1355] [1356] [1357] [1358]
Underfull \hbox (badness 3965) in paragraph at lines 2534--2536
[]\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val
id for
[1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369]
[1370]
Underfull \hbox (badness 2726) in paragraph at lines 3260--3276
\T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm
, and en-hanced for
[1371] [1372]
Underfull \hbox (badness 2503) in paragraph at lines 3390--3393
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383]
[1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392]
Underfull \hbox (badness 3989) in paragraph at lines 4634--4641
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1393] [1394]
Underfull \hbox (badness 3612) in paragraph at lines 4754--4756
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por
t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b
y de-fault where
[1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402]
Underfull \hbox (badness 2556) in paragraph at lines 5270--5273
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5287--5289
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1403] [1404] [1405] [1406]
Underfull \hbox (badness 1142) in paragraph at lines 5528--5540
\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.
[1407] [1408] [1409]
Underfull \hbox (badness 2503) in paragraph at lines 5680--5684
[]\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 ,
[1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417]
Underfull \hbox (badness 8132) in paragraph at lines 6184--6189
\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,
[1418] [1419] [1420] [1421] [1422]
Underfull \hbox (badness 7081) in paragraph at lines 6462--6465
[]\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 6466--6468
[]\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
[1423] [1424] [1425] [1426] [1427]
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[1429] [1430] [1431] [1432] [1433] [1434] [1435]
Underfull \hbox (badness 10000) in paragraph at lines 7311--7314
[]\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
[1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446]
[1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457]
[1458] [1459] [1460] [1461] [1462]
Underfull \hbox (badness 2626) in paragraph at lines 8953--8956
[]\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
[1463]
Underfull \hbox (badness 2503) in paragraph at lines 9060--9064
[]\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 ,
[1464]
Underfull \hbox (badness 2564) in paragraph at lines 9112--9121
[]\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c
mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/zi4/m/n/10 hybrid = TRUE\T1/ptm/m/n
/10 , asymp-totic chi-squared prob-a-bil-i-

Underfull \hbox (badness 1331) in paragraph at lines 9112--9121
\T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied 
ver-sion thereof) spec-i-fied by
[1465] [1466] [1467] [1468] [1469]
Overfull \hbox (3.53955pt too wide) in paragraph at lines 9434--9436
[]\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 . 
[1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480]
[1481] [1482] [1483] [1484]
Underfull \hbox (badness 4518) in paragraph at lines 10362--10367
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2142) in paragraph at lines 10710--10713
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p
tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1
0 dev \OMS/cmsy/m/n/10 ^^@

Underfull \hbox (badness 1253) in paragraph at lines 10729--10732
[]\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,
[1490]
Underfull \hbox (badness 1708) in paragraph at lines 10791--10795
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1491] [1492] [1493] [1494] [1495] [1496]
Underfull \hbox (badness 1694) in paragraph at lines 11189--11192
[]\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 11208--11217
\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-
[1497] [1498] [1499] [1500] [1501]
Underfull \hbox (badness 10000) in paragraph at lines 11516--11519
[]\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.11670 \aliasA{hat}{influence.measures}{hat}
                                              [1505] [1506]
Underfull \hbox (badness 1484) in paragraph at lines 11801--11803
[]\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
[1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516]
Underfull \hbox (badness 4441) in paragraph at lines 12387--12389
[]\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 12394--12396
[]\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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[]\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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[1534]
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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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[]\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/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

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 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

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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 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
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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 ,
[1644]
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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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[]\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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[]\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/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
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[]\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
[1707]
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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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[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1717] [1718] [1719]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to
[1720]
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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

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\T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher
e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was

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\T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o
f un-de-ter-mined co-ef-fi-cients, e.g., for
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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
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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
[1747]
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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
[1748]
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 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1749]
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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
[1750] [1751] [1752] [1753]
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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
[1754]
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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
[1755]
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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
[1756] [1757]
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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
[1758] [1759]
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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
[1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767]
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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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Underfull \hbox (badness 5431) in paragraph at lines 28286--28288
[]\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
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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
[1787] [1788]
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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
[1789] [1790] [1791]
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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
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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
[1826]
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[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1
/ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al
so in the

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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
[1833] [1834] [1835]) (./stats4-pkg.tex [1836]
Chapter 11.
[1837] [1838] [1839] [1840] [1841] [1842]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}
                                                   [1843] [1844] [1845]
[1846]) (./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 ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1867]) (./tools-pkg.tex [1868]
Chapter 13.
[1869]

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[1870]
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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-
[1887]
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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 ,
[1888] [1889] [1890]
Underfull \hbox (badness 10000) in paragraph at lines 1377--1379
[]\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S
up-port func-tion for
[1891] [1892] [1893]
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[]\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
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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
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l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1900] [1901] [1902]
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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
[1908] [1909] [1910] [1911] [1912] [1913] [1914]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
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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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[1930]
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1931] [1932]
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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
[1933] [1934]
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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
[1935] [1936] [1937]
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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
[1938]
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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 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :

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\T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T
1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if
[1942]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1943] [1944] [1945]) (./utils-pkg.tex [1946]
Chapter 14.
[1947]
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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 ',
[1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955]
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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
[1956] [1957]
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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
[1958]
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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 ,
[1959] [1960] [1961]
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\T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio
n to the for-

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\T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo
re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

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\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

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\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
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[1966] [1967] [1968] [1969]
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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
[1970] [1971] [1972] [1973] [1974] [1975] [1976]
Underfull \hbox (badness 2057) in paragraph at lines 1959--1961
[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1977] [1978]
Underfull \hbox (badness 10000) in paragraph at lines 2054--2056
[]\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the 
`\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via
[1979]
Underfull \hbox (badness 5189) in paragraph at lines 2156--2158
[]\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w
hen
[1980] [1981] [1982] [1983]
Underfull \hbox (badness 1661) in paragraph at lines 2374--2381
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to
 an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i-

Underfull \hbox (badness 1748) in paragraph at lines 2390--2393
[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1984] [1985] [1986] [1987] [1988] [1989] [1990]
Underfull \hbox (badness 10000) in paragraph at lines 2800--2804
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing

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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 ,
[1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000]
Underfull \hbox (badness 1430) in paragraph at lines 3484--3492
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[2001]
Underfull \hbox (badness 1231) in paragraph at lines 3533--3539
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2002] [2003]
Underfull \hbox (badness 10000) in paragraph at lines 3686--3688
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]pdf
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<to be read again> 
                   \relax 
l.4373 ...mat Unordered and Ordered Lists}{format}
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ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
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                   \relax 
l.4373 ...mat Unordered and Ordered Lists}{format}
                                                   [2015] [2016] [2017]
[2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028]
[2029] [2030]
Underfull \hbox (badness 1371) in paragraph at lines 5370--5372
[]\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
[2031]
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[]\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 5459--5464
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2032] [2033] [2034]
Underfull \hbox (badness 10000) in paragraph at lines 5632--5641
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2035]
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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
[2036] [2037]
Underfull \hbox (badness 3118) in paragraph at lines 5832--5834
[]\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
[2038]
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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
[2039]
Underfull \hbox (badness 1325) in paragraph at lines 5973--5977
[]\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
[2040]
Underfull \hbox (badness 10000) in paragraph at lines 6056--6059
[]\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.,
[2041]
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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
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 6229--6234
[][][]\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 ,
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065]
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Underfull \hbox (badness 10000) in paragraph at lines 7662--7664
[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from

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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

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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,
[2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075] [2076]
Underfull \hbox (badness 1789) in paragraph at lines 8278--8280
[]\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
[2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087]
[2088] [2089]
Underfull \hbox (badness 1097) in paragraph at lines 9111--9114
[]\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
[2090]
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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 ;
[2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099]
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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 ;
[2100] [2101] [2102] [2103] [2104] [2105] [2106]
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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 10267--10271
[]\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 10267--10271
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2107] [2108] [2109] [2110] [2111]
Underfull \hbox (badness 4060) in paragraph at lines 10544--10547
[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

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 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
[2112]
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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
[2113] [2114] [2115]
Underfull \hbox (badness 2150) in paragraph at lines 10806--10808
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2116] [2117] [2118] [2119]
Underfull \hbox (badness 10000) in paragraph at lines 11025--11029
[]\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 11056--11062
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2120] [2121]
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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
[2122]
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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
[2123] [2124] [2125] [2126] [2127]
Underfull \hbox (badness 3780) in paragraph at lines 11556--11560
[]\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
[2128] [2129] [2130] [2131] [2132] [2133]
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[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), []
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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 ***
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/tzone'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/extra/tzone'
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \
  -o Rscript ./Rscript.c
mkdir -p -- /<<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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"		\
		CXXFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"	\
		FFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \
  -o Rscript ./Rscript.c
make[1]: Leaving directory '/<<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)
(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
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:	 67.0% -- 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:	 68.1% -- 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:	 66.6% -- 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:	 69.9% -- 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-3.gz:	 83.3% -- replaced with /<<PKGBUILDDIR>>/debian/r-base-core/usr/share/info/R-exts.info-3
/<<PKGBUILDDIR>>/debian/r-base-core/usr/share/info/R-exts.info.gz:	 69.5% -- 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:	 67.9% -- 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:	 71.6% -- 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 1968
-rw-rw-r-- 1 root root 1233166 Jul  7 09:26 libRmath.a
-rwxrwxr-x 1 root root  770800 Jul  7 09:26 libRmath.so
drwxr-xr-x 2 root root    4096 Jul  7 09:26 pkgconfig
renamed 'libRmath.so' -> 'libRmath.so.1.0.0'
'libRmath.so.1' -> 'libRmath.so.1.0.0'
'libRmath.so' -> 'libRmath.so.1'
install -m 0644 src/include/Rmath.h			\
		/<<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 --dbg-package=r-base-core-dbg
dh_compress -a
dh_fixperms -a
dh_link -a
dh_makeshlibs -a
dh_installdeb -a
dh_perl -a
dh_shlibdeps -a -l /<<PKGBUILDDIR>>/debian/r-base-core/usr/lib/R/lib
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-mathlib/usr/lib/libRmath.so.1.0.0 was not linked against libgomp.so.1 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libtcl8.6.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libtk8.6.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_de.so debian/r-base-core/usr/lib/R/modules/R_X11.so were not linked against libSM.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/library/tcltk/libs/tcltk.so was not linked against libXss.so.1 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_de.so debian/r-base-core/usr/lib/R/modules/R_X11.so were not linked against libICE.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/library/stats/libs/stats.so debian/r-base-core/usr/lib/R/lib/libR.so debian/r-base-core/usr/lib/R/modules/lapack.so were not linked against libgfortran.so.4 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_de.so debian/r-base-core/usr/lib/R/modules/R_X11.so debian/r-base-core/usr/lib/R/library/grDevices/libs/cairo.so were not linked against libglib-2.0.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_de.so debian/r-base-core/usr/lib/R/modules/R_X11.so debian/r-base-core/usr/lib/R/library/tcltk/libs/tcltk.so were not linked against libXext.so.6 (they use none of the library's symbols)
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package r-base-core: unknown substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'r-base-core' in '../r-base-core_3.5.1-1_armhf.deb'.
dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.5.1-1_armhf.deb'.
dpkg-deb: building package 'r-base-core-dbg' in '../r-base-core-dbg_3.5.1-1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../r-base_3.5.1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build r-base-3.5.1
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-07-07T09:27:09Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


r-base_3.5.1-1_armhf.changes:
-----------------------------

Format: 1.8
Date: Mon, 02 Jul 2018 05:08:37 -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: armhf
Version: 3.5.1-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
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 (3.5.1-1) unstable; urgency=medium
 .
   * New upstream version released this morning
 .
   * debian/Renviron.site: Added comment for R_LIBS_USER and %p and %v
Checksums-Sha1:
 a8e42d2a93ca4f480d443edc95584a691f9ce26f 4921816 r-base-core-dbg_3.5.1-1_armhf.deb
 b96e49e72cea424f3bc56aa8f17baaec77ad3767 23575560 r-base-core_3.5.1-1_armhf.deb
 1e2533ed281e630bd97d1b33b1548f86b85b78ef 15213 r-base_3.5.1-1_armhf.buildinfo
 f7c6e0cfd5739e1605eb9a6ebac9296d5ce8b8fc 1798712 r-mathlib_3.5.1-1_armhf.deb
Checksums-Sha256:
 687f30b37d4d64827f23daaf30296e1f619c5b38946383a0007110877f701511 4921816 r-base-core-dbg_3.5.1-1_armhf.deb
 40b50855df253b3b2c808a0a4646fd3f9079c6bc0c98f8201cbade1f581355c7 23575560 r-base-core_3.5.1-1_armhf.deb
 388e9f29cee766f2863fa9350c6259b4ae321d49d13175db368e7b0aaa6f219f 15213 r-base_3.5.1-1_armhf.buildinfo
 72812c958f356e6875870b893d0a8ab947f5a182a80ebf918dbdab9257066f48 1798712 r-mathlib_3.5.1-1_armhf.deb
Files:
 c9a251afd141cc7c1e54a23830224942 4921816 debug optional r-base-core-dbg_3.5.1-1_armhf.deb
 d4bf6c496fa8cd6afbe0a2efb9776c0a 23575560 gnu-r optional r-base-core_3.5.1-1_armhf.deb
 af3dfb327b472ae0640ca0056127c846 15213 gnu-r optional r-base_3.5.1-1_armhf.buildinfo
 c2e9c0bff1f7ef997de36453f63b884b 1798712 gnu-r optional r-mathlib_3.5.1-1_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


r-base-core-dbg_3.5.1-1_armhf.deb
---------------------------------

 new Debian package, version 2.0.
 size 4921816 bytes: control archive=2260 bytes.
    2557 bytes,    39 lines      control              
    2249 bytes,    22 lines      md5sums              
 Package: r-base-core-dbg
 Source: r-base
 Version: 3.5.1-1
 Architecture: armhf
 Maintainer: Dirk Eddelbuettel <edd@debian.org>
 Installed-Size: 5280
 Depends: r-base-core (= 3.5.1-1), r-base-dev (= 3.5.1-1)
 Section: debug
 Priority: optional
 Homepage: http://www.r-project.org/
 Description: GNU R debug symbols for statistical comp. language and environment
  R is a system for statistical computation and graphics.  It consists
  of a language plus a run-time environment with graphics, a debugger,
  access to certain system functions, and the ability to run programs
  stored in script files.
  .
  The design of R has been heavily influenced by two existing languages:
  Becker, Chambers & Wilks' S and Sussman's Scheme.  Whereas the
  resulting language is very similar in appearance to S, the underlying
  implementation and semantics are derived from Scheme.
  .
  The core of R is an interpreted computer language which allows
  branching and looping as well as modular programming using functions.
  Most of the user-visible functions in R are written in R.  It is
  possible for the user to interface to procedures written in the
  C, C++, or FORTRAN languages for efficiency, and many of R's core
  functions do so.  The R distribution contains functionality for a
  large number of statistical procedures and underlying applied math
  computations.  There is also a large set of functions which provide
  a flexible graphical environment for creating various kinds of data
  presentations.
  .
  Additionally, several thousand extension "packages" are available from
  CRAN, the Comprehensive R Archive Network, many also as Debian packages,
  named 'r-cran-<name>'.
  .
  This package contains debugging symbol tables for the binaries and dynamic
  libraries in the r-base-core package.
 Build-Ids: 0207db0237d2e98cd72cd2e802a8221634414b60 216423c8de1c1c0d6453ad8074eb72557a295793 3b0ec3dfac002d989a6f3f67c1b3ca19c8a72fa6 469791696a173fcedade4109f9ac64ed29ee4574 7704987bc3ba5d4b384f746a88ad8c9509760b9c 7c9313ebba5a919d1b9dddc4bf5030ba7fb4ed6f 817b9f654d5d8a95a4f13412555301cb06631b90 850dea281c656de9a175c54b0a0e0e752eb05de5 862489c89eb98a7015abdf0fca22b3b48381de27 8c5c9594fbc03c58a67f0d8b3e78f698a3975954 9a20556fb3046d071aad39d92731a348f52a8886 9b31f861b834db8d23578b3f208a4ba06c42cbe1 ad061759e5f88430899a3aa8bd69bee3e776243c bb338201397628677693d0849e8d118004dc4a63 bf6c6d380092517f7a4dde210da7fef720c1856b c2b964d7f906ca6cfd4b089fc6756f01d4d18123 ca1259ad9db8cccb081df57234d73f71c99ec0af d5771f027c818204255c0b86ea86cb32cb6ac0c7 e5ed32340939d0de09ddd3609fe07310c0305c70

drwxr-xr-x root/root         0 2018-07-02 10:08 ./
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/lib/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/lib/debug/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/lib/debug/.build-id/02/
-rw-r--r-- root/root    206108 2018-07-02 10:08 ./usr/lib/debug/.build-id/02/07db0237d2e98cd72cd2e802a8221634414b60.debug
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/lib/debug/.build-id/21/
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r-base-core_3.5.1-1_armhf.deb
-----------------------------

 new Debian package, version 2.0.
 size 23575560 bytes: control archive=23960 bytes.
      93 bytes,     5 lines      conffiles            
    2782 bytes,    44 lines      control              
   73500 bytes,   933 lines      md5sums              
    2426 bytes,    68 lines   *  postinst             #!/bin/sh
     207 bytes,     5 lines   *  postrm               #!/bin/sh
     857 bytes,    37 lines   *  preinst              #!/bin/sh
     879 bytes,    29 lines   *  prerm                #!/bin/sh
 Package: r-base-core
 Source: r-base
 Version: 3.5.1-1
 Architecture: armhf
 Maintainer: Dirk Eddelbuettel <edd@debian.org>
 Installed-Size: 36290
 Depends: zip, unzip, libpaper-utils, xdg-utils, libblas3 | libblas.so.3, libbz2-1.0, libc6 (>= 2.27), libcairo2 (>= 1.6.0), libcurl4 (>= 7.28.0), libgfortran4 (>= 7), libglib2.0-0 (>= 2.12.0), libgomp1 (>= 4.9), libice6 (>= 1:1.0.0), libicu60 (>= 60.1-1~), libjpeg62-turbo (>= 1.3.1), liblapack3 | liblapack.so.3, liblzma5 (>= 5.1.1alpha+20120614), libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libpcre3, libpng16-16 (>= 1.6.2-1), libreadline7 (>= 6.0), libsm6, libtcl8.6 (>= 8.6.0), libtiff5 (>= 4.0.3), libtk8.6 (>= 8.6.0), libx11-6, libxext6, libxss1, libxt6, zlib1g (>= 1:1.1.4), ucf (>= 3.0), ca-certificates
 Recommends: r-recommended, r-base-dev, r-doc-html
 Suggests: ess, r-doc-info | r-doc-pdf, r-mathlib, r-base-html
 Conflicts: r-base-latex, r-cran-rcompgen, r-gnome
 Replaces: r-base (<= 1.4.1-1), r-base-latex (<= 2.9.2-4), r-cran-rcompgen (<= 0.1-17-1), r-gnome (<= 2.3.1), r-recommended (<< 1.9.0)
 Provides: r-api-3.5, r-base-latex, r-cran-rcompgen, r-gnome
 Section: gnu-r
 Priority: optional
 Homepage: http://www.r-project.org/
 Description: GNU R core of statistical computation and graphics system
  R is a system for statistical computation and graphics.  It consists
  of a language plus a run-time environment with graphics, a debugger,
  access to certain system functions, and the ability to run programs
  stored in script files.
  .
  The design of R has been heavily influenced by two existing languages:
  Becker, Chambers & Wilks' S and Sussman's Scheme.  Whereas the
  resulting language is very similar in appearance to S, the underlying
  implementation and semantics are derived from Scheme.
  .
  The core of R is an interpreted computer language which allows
  branching and looping as well as modular programming using functions.
  Most of the user-visible functions in R are written in R.  It is
  possible for the user to interface to procedures written in the
  C, C++, or FORTRAN languages for efficiency, and many of R's core
  functions do so.  The R distribution contains functionality for a
  large number of statistical procedures and underlying applied math
  computations.  There is also a large set of functions which provide
  a flexible graphical environment for creating various kinds of data
  presentations.
  .
  Additionally, 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 core GNU R system from which only the optional
  documentation packages r-base-html, r-doc-html, r-doc-pdf and r-doc-info
  have been split off to somewhat reduce the size of this package.

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drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/applications/
-rw-r--r-- root/root       213 2018-07-02 10:08 ./usr/share/applications/R.desktop
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/bash-completion/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/bash-completion/completions/
-rw-r--r-- root/root     13596 2018-04-16 22:27 ./usr/share/bash-completion/completions/R
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/doc/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/doc/r-base-core/
-rw-r--r-- root/root     35933 2014-03-12 23:03 ./usr/share/doc/r-base-core/NEWS.0.gz
-rw-r--r-- root/root    108753 2014-03-12 23:03 ./usr/share/doc/r-base-core/NEWS.1.gz
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lrwxrwxrwx root/root         0 2018-07-02 10:08 ./usr/share/doc/r-base-core/NEWS.gz -> changelog.gz
-rw-r--r-- root/root    534843 2018-07-02 10:08 ./usr/share/doc/r-base-core/NEWS.pdf.gz
-rw-r--r-- root/root    444939 2018-07-02 10:08 ./usr/share/doc/r-base-core/NEWS.rds.gz
-rw-r--r-- root/root      2739 2018-04-16 22:27 ./usr/share/doc/r-base-core/README.Atlas.gz
-rw-r--r-- root/root      2107 2016-10-04 09:14 ./usr/share/doc/r-base-core/README.gz
-rw-r--r-- root/root      3026 2018-04-16 22:27 ./usr/share/doc/r-base-core/README.mathlib
-rw-r--r-- root/root     31987 2018-07-02 10:08 ./usr/share/doc/r-base-core/changelog.Debian.gz
-rw-r--r-- root/root     95930 2018-07-02 10:08 ./usr/share/doc/r-base-core/changelog.gz
-rw-r--r-- root/root     20761 2018-04-16 22:27 ./usr/share/doc/r-base-core/copyright
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lrwxrwxrwx root/root         0 2018-07-02 10:08 ./usr/share/doc/r-base-core/library -> ../../../lib/R/library
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drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/lintian/
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drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/man/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/man/man1/
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r-mathlib_3.5.1-1_armhf.deb
---------------------------

 new Debian package, version 2.0.
 size 1798712 bytes: control archive=2068 bytes.
    1781 bytes,    39 lines      control              
    1219 bytes,    18 lines      md5sums              
     369 bytes,    27 lines   *  postinst             #!/bin/sh
      21 bytes,     1 lines      shlibs               
      67 bytes,     2 lines      triggers             
 Package: r-mathlib
 Source: r-base
 Version: 3.5.1-1
 Architecture: armhf
 Maintainer: Dirk Eddelbuettel <edd@debian.org>
 Installed-Size: 2122
 Depends: libc6 (>= 2.23), libgomp1 (>= 4.2.1)
 Recommends: r-base-core (= 3.5.1-1), r-base-dev (= 3.5.1-1)
 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.

drwxr-xr-x root/root         0 2018-07-02 10:08 ./
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/include/
-rw-r--r-- root/root     17416 2018-07-02 10:08 ./usr/include/Rmath.h
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/lib/
-rw-r--r-- root/root    269394 2018-07-02 10:08 ./usr/lib/libRmath.a
lrwxrwxrwx root/root         0 2018-07-02 10:08 ./usr/lib/libRmath.so -> libRmath.so.1
lrwxrwxrwx root/root         0 2018-07-02 10:08 ./usr/lib/libRmath.so.1 -> libRmath.so.1.0.0
-rw-r--r-- root/root    145184 2018-07-02 10:08 ./usr/lib/libRmath.so.1.0.0
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/lib/pkgconfig/
-rw-r--r-- root/root       173 2018-07-02 10:08 ./usr/lib/pkgconfig/libRmath.pc
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/doc/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/doc/r-mathlib/
-rw-r--r-- root/root     35933 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.0.gz
-rw-r--r-- root/root    108753 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.1.gz
-rw-r--r-- root/root     96630 2018-03-07 23:02 ./usr/share/doc/r-mathlib/NEWS.2.Rd.gz
-rw-r--r-- root/root    229657 2018-03-25 22:02 ./usr/share/doc/r-mathlib/NEWS.2.gz
-rw-r--r-- root/root    104256 2018-06-21 22:02 ./usr/share/doc/r-mathlib/NEWS.Rd.gz
lrwxrwxrwx root/root         0 2018-07-02 10:08 ./usr/share/doc/r-mathlib/NEWS.gz -> changelog.gz
-rw-r--r-- root/root    534843 2018-07-02 10:08 ./usr/share/doc/r-mathlib/NEWS.pdf.gz
-rw-r--r-- root/root    444939 2018-07-02 10:08 ./usr/share/doc/r-mathlib/NEWS.rds.gz
-rw-r--r-- root/root      2107 2016-10-04 09:14 ./usr/share/doc/r-mathlib/README.gz
-rw-r--r-- root/root      3026 2018-04-16 22:27 ./usr/share/doc/r-mathlib/README.mathlib
-rw-r--r-- root/root     31987 2018-07-02 10:08 ./usr/share/doc/r-mathlib/changelog.Debian.gz
-rw-r--r-- root/root     95930 2018-07-02 10:08 ./usr/share/doc/r-mathlib/changelog.gz
-rw-r--r-- root/root     20761 2018-04-16 22:27 ./usr/share/doc/r-mathlib/copyright
drwxr-xr-x root/root         0 2018-07-02 10:08 ./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
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/lintian/
drwxr-xr-x root/root         0 2018-07-02 10:08 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       364 2018-04-16 22:27 ./usr/share/lintian/overrides/r-mathlib


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| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 315476
Build-Time: 1500
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1614
Job: r-base_3.5.1-1
Machine Architecture: armhf
Package: r-base
Package-Time: 3144
Source-Version: 3.5.1-1
Space: 315476
Status: successful
Version: 3.5.1-1
--------------------------------------------------------------------------------
Finished at 2018-07-07T09:27:09Z
Build needed 00:52:24, 315476k disk space
Raspbian Package Auto-Building

Build log for r-base (3.5.1-1) on armhf
