dpkg-checkbuilddeps: error: Unmet build dependencies: libpcre2-dev default-jdk | openjdk-10-jdk
W: Unmet build-dependency in source
*** 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
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building r-base using existing ./r-base_3.6.1.orig.tar.gz
dpkg-source: info: building r-base in r-base_3.6.1-2~bustercran.0.debian.tar.xz
dpkg-source: info: building r-base in r-base_3.6.1-2~bustercran.0.dsc
I: Generating source changes file for original dsc
dpkg-genchanges: warning: the current version (3.6.1-2~bustercran.0) is earlier than the previous one (3.6.1-2)
dpkg-genchanges: info: including full source code in upload
W: cgroups are not available on the host, not using them.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Jul  9 06:18:19 CEST 2019
I: pbuilder-time-stamp: 1562645899
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/buster-i386-base.tgz]
I: copying local configuration
I: Installing apt-lines
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Obtaining the cached apt archive contents
I: Copying source file
I: copying [../r-base_3.6.1-2~bustercran.0.dsc]
I: copying [../r-base_3.6.1.orig.tar.gz]
I: copying [../r-base_3.6.1-2~bustercran.0.debian.tar.xz]
I: Extracting source
dpkg-source: warning: extracting unsigned source package (r-base_3.6.1-2~bustercran.0.dsc)
dpkg-source: info: extracting r-base in r-base-3.6.1
dpkg-source: info: unpacking r-base_3.6.1.orig.tar.gz
dpkg-source: info: unpacking r-base_3.6.1-2~bustercran.0.debian.tar.xz
I: using fakeroot in build.
I: Installing the build-deps
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre2-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk | openjdk-10-jdk, mpack, bash-completion
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 12146 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on gfortran (>= 4:4.1.0); however:
  Package gfortran is not installed.
 pbuilder-satisfydepends-dummy depends on libblas-dev; however:
  Package libblas-dev is not installed.
 pbuilder-satisfydepends-dummy depends on liblapack-dev (>= 3.1.1); however:
  Package liblapack-dev is not installed.
 pbuilder-satisfydepends-dummy depends on tcl8.6-dev; however:
  Package tcl8.6-dev is not installed.
 pbuilder-satisfydepends-dummy depends on tk8.6-dev; however:
  Package tk8.6-dev is not installed.
 pbuilder-satisfydepends-dummy depends on bison; however:
  Package bison is not installed.
 pbuilder-satisfydepends-dummy depends on groff-base; however:
  Package groff-base is not installed.
 pbuilder-satisfydepends-dummy depends on libncurses5-dev; however:
  Package libncurses5-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libreadline-dev; however:
  Package libreadline-dev is not installed.
 pbuilder-satisfydepends-dummy depends on debhelper (>= 7.2.3); however:
  Package debhelper is not installed.
 pbuilder-satisfydepends-dummy depends on texinfo (>= 4.1-2); however:
  Package texinfo is not installed.
 pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
  Package libbz2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on liblzma-dev; however:
  Package liblzma-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libpcre2-dev; however:
  Package libpcre2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libpcre3-dev; however:
  Package libpcre3-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libcurl4-openssl-dev | libcurl4-dev; however:
  Package libcurl4-openssl-dev is not installed.
  Package libcurl4-dev is not installed.
 pbuilder-satisfydepends-dummy depends on xdg-utils; however:
  Package xdg-utils is not installed.
 pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
  Package zlib1g-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libpng-dev; however:
  Package libpng-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libjpeg-dev; however:
  Package libjpeg-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libx11-dev; however:
  Package libx11-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libxt-dev; however:
  Package libxt-dev is not installed.
 pbuilder-satisfydepends-dummy depends on x11proto-core-dev; however:
  Package x11proto-core-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libpango1.0-dev; however:
  Package libpango1.0-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libcairo2-dev; however:
  Package libcairo2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libtiff5-dev; however:
  Package libtiff5-dev is not installed.
 pbuilder-satisfydepends-dummy depends on xvfb; however:
  Package xvfb is not installed.
 pbuilder-satisfydepends-dummy depends on xauth; however:
  Package xauth is not installed.
 pbuilder-satisfydepends-dummy depends on xfonts-base; however:
  Package xfonts-base is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-base; however:
  Package texlive-base is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-latex-base; however:
  Package texlive-latex-base is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-generic-recommended; however:
  Package texlive-generic-recommended is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however:
  Package texlive-fonts-recommended is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-fonts-extra; however:
  Package texlive-fonts-extra is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-extra-utils; however:
  Package texlive-extra-utils is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however:
  Package texlive-latex-recommended is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however:
  Package texlive-latex-extra is not installed.
 pbuilder-satisfydepends-dummy depends on default-jdk | openjdk-10-jdk; however:
  Package default-jdk is not installed.
  Package openjdk-10-jdk is not installed.
 pbuilder-satisfydepends-dummy depends on mpack; however:
  Package mpack is not installed.
 pbuilder-satisfydepends-dummy depends on bash-completion; however:
  Package bash-completion is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  adwaita-icon-theme{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bison{a} bsdmainutils{a} ca-certificates{a} ca-certificates-java{a} dbus{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dmsetup{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} gir1.2-freedesktop{a} gir1.2-glib-2.0{a} gir1.2-harfbuzz-0.0{a} gir1.2-pango-1.0{a} glib-networking{a} glib-networking-common{a} glib-networking-services{a} groff-base{a} gsettings-desktop-schemas{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} icu-devtools{a} intltool-debian{a} java-common{a} libapparmor1{a} libarchive-zip-perl{a} libargon2-1{a} libasound2{a} libasound2-data{a} libatk-bridge2.0-0{a} libatk1.0-0{a} libatk1.0-data{a} libatspi2.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbison-dev{a} libblas-dev{a} libblas3{a} libblkid-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcap2{a} libcolord2{a} libcroco3{a} libcryptsetup12{a} libcups2{a} libcupsimage2{a} libcurl4{a} libcurl4-openssl-dev{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdevmapper1.02.1{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} libepoxy0{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontconfig1-dev{a} libfontenc1{a} libfreetype6{a} libfreetype6-dev{a} libfribidi-dev{a} libfribidi0{a} libgdk-pixbuf2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran-8-dev{a} libgfortran5{a} libgif7{a} libgirepository-1.0-1{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgraphite2-dev{a} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libgtk-3-0{a} libgtk-3-common{a} libharfbuzz-dev{a} libharfbuzz-gobject0{a} libharfbuzz-icu0{a} libharfbuzz0b{a} libice-dev{a} libice6{a} libicu-dev{a} libicu63{a} libidn11{a} libijs-0.35{a} libip4tc0{a} libjbig-dev{a} libjbig0{a} libjbig2dec0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjson-c3{a} libjson-glib-1.0-0{a} libjson-glib-1.0-common{a} libk5crypto3{a} libkeyutils1{a} libkmod2{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} libllvm7{a} liblzma-dev{a} liblzo2-2{a} libmagic-mgc{a} libmagic1{a} libmime-charset-perl{a} libmount-dev{a} libmpdec2{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpam-systemd{a} libpango-1.0-0{a} libpango1.0-dev{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpangoxft-1.0-0{a} libpaper-utils{a} libpaper1{a} libpciaccess0{a} libpcre16-3{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-8-0{a} libpcre2-dev{a} libpcre2-posix0{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpng-dev{a} libpng16-16{a} libpotrace0{a} libproxy1v5{a} libpsl5{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline-dev{a} libreadline7{a} librest-0.7-0{a} librsvg2-2{a} librsvg2-common{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsensors-config{a} libsensors5{a} libsepol1-dev{a} libsigsegv2{a} libsm-dev{a} libsm6{a} libsombok3{a} libsoup-gnome2.4-1{a} libsoup2.4-1{a} libssh2-1{a} libssl1.1{a} libsynctex2{a} libtcl8.6{a} libteckit0{a} libtexlua52{a} libtexlua53{a} libtexluajit2{a} libtext-unidecode-perl{a} libthai-data{a} libthai0{a} libtiff-dev{a} libtiff5{a} libtiff5-dev{a} libtiffxx5{a} libtk8.6{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{a} libunwind8{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwebp6{a} libwoff1{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb-sync1{a} libxcb1{a} libxcb1-dev{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes3{a} libxfont2{a} libxft-dev{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxkbfile1{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml2{a} libxmu6{a} libxmuu1{a} libxpm4{a} libxrandr2{a} libxrender-dev{a} libxrender1{a} libxshmfence1{a} libxss-dev{a} libxss1{a} libxt-dev{a} libxt6{a} libxtst6{a} libxxf86vm1{a} libxxhash0{a} libzzip-0-13{a} lsb-base{a} m4{a} man-db{a} mime-support{a} mpack{a} openjdk-11-jdk{a} openjdk-11-jdk-headless{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openssl{a} pango1.0-tools{a} pkg-config{a} po-debconf{a} poppler-data{a} preview-latex-style{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} shared-mime-info{a} systemd{a} systemd-sysv{a} t1utils{a} tcl8.6{a} tcl8.6-dev{a} tex-common{a} texinfo{a} texlive-base{a} texlive-binaries{a} texlive-extra-utils{a} texlive-fonts-extra{a} texlive-fonts-recommended{a} texlive-generic-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} texlive-plain-generic{a} tk8.6{a} tk8.6-dev{a} ucf{a} uuid-dev{a} x11-common{a} x11-xkb-utils{a} x11proto-core-dev{a} x11proto-dev{a} x11proto-scrnsaver-dev{a} x11proto-xext-dev{a} xauth{a} xdg-utils{a} xfonts-base{a} xfonts-encodings{a} xfonts-utils{a} xkb-data{a} xorg-sgml-doctools{a} xserver-common{a} xtrans-dev{a} xvfb{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  at-spi2-core bzip2-doc curl deepin-terminal eterm fonts-adf-accanthis fonts-adf-berenis fonts-adf-gillius fonts-adf-universalis fonts-cabin fonts-comfortaa fonts-croscore fonts-crosextra-caladea fonts-crosextra-carlito fonts-dejavu-extra fonts-droid-fallback fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga fonts-gfs-solomos fonts-go fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobstertwo fonts-noto-hinted fonts-noto-mono fonts-oflb-asana-math fonts-open-sans fonts-roboto-unhinted fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix freetype2-doc ghostscript gnome-terminal kitty konsole krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libcupsfilters1 libfile-homedir-perl libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libgpm2 libgtk-3-bin liblog-log4perl-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libnss-systemd libpng-tools libsasl2-modules libwww-perl libx11-protocol-perl libxml-sax-expat-perl libyaml-tiny-perl lilyterm lmodern lxterminal lynx mate-terminal mlterm mlterm-tiny pterm publicsuffix qterminal ruby rxvt-unicode sakura stterm terminator terminology termit tex-gyre texlive-fonts-extra-links tilix tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs xfce4-terminal xiterm+thai xterm 
0 packages upgraded, 372 newly installed, 0 to remove and 0 not upgraded.
Need to get 1120 kB/1036 MB of archives. After unpacking 2683 MB will be used.
Writing extended state information...
Get: 1 http://ftp.de.debian.org/debian buster/main i386 libpcre2-32-0 i386 10.32-5 [194 kB]
Get: 2 http://ftp.de.debian.org/debian buster/main i386 libpcre2-8-0 i386 10.32-5 [214 kB]
Get: 3 http://ftp.de.debian.org/debian buster/main i386 libpcre2-posix0 i386 10.32-5 [38.8 kB]
Get: 4 http://ftp.de.debian.org/debian buster/main i386 libpcre2-dev i386 10.32-5 [672 kB]
Fetched 1120 kB in 1s (1298 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libapparmor1:i386.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12146 files and directories currently installed.)
Preparing to unpack .../00-libapparmor1_2.13.2-10_i386.deb ...
Unpacking libapparmor1:i386 (2.13.2-10) ...
Selecting previously unselected package libcap2:i386.
Preparing to unpack .../01-libcap2_1%3a2.25-2_i386.deb ...
Unpacking libcap2:i386 (1:2.25-2) ...
Selecting previously unselected package libargon2-1:i386.
Preparing to unpack .../02-libargon2-1_0~20171227-0.2_i386.deb ...
Unpacking libargon2-1:i386 (0~20171227-0.2) ...
Selecting previously unselected package dmsetup.
Preparing to unpack .../03-dmsetup_2%3a1.02.155-2_i386.deb ...
Unpacking dmsetup (2:1.02.155-2) ...
Selecting previously unselected package libdevmapper1.02.1:i386.
Preparing to unpack .../04-libdevmapper1.02.1_2%3a1.02.155-2_i386.deb ...
Unpacking libdevmapper1.02.1:i386 (2:1.02.155-2) ...
Selecting previously unselected package libjson-c3:i386.
Preparing to unpack .../05-libjson-c3_0.12.1+ds-2_i386.deb ...
Unpacking libjson-c3:i386 (0.12.1+ds-2) ...
Selecting previously unselected package libssl1.1:i386.
Preparing to unpack .../06-libssl1.1_1.1.1b-2_i386.deb ...
Unpacking libssl1.1:i386 (1.1.1b-2) ...
Selecting previously unselected package libcryptsetup12:i386.
Preparing to unpack .../07-libcryptsetup12_2%3a2.1.0-3_i386.deb ...
Unpacking libcryptsetup12:i386 (2:2.1.0-3) ...
Selecting previously unselected package libidn11:i386.
Preparing to unpack .../08-libidn11_1.33-2.2_i386.deb ...
Unpacking libidn11:i386 (1.33-2.2) ...
Selecting previously unselected package libip4tc0:i386.
Preparing to unpack .../09-libip4tc0_1.8.2-4_i386.deb ...
Unpacking libip4tc0:i386 (1.8.2-4) ...
Selecting previously unselected package libkmod2:i386.
Preparing to unpack .../10-libkmod2_26-1_i386.deb ...
Unpacking libkmod2:i386 (26-1) ...
Selecting previously unselected package systemd.
Preparing to unpack .../11-systemd_241-3_i386.deb ...
Unpacking systemd (241-3) ...
Setting up libapparmor1:i386 (2.13.2-10) ...
Setting up libcap2:i386 (1:2.25-2) ...
Setting up libargon2-1:i386 (0~20171227-0.2) ...
Setting up libjson-c3:i386 (0.12.1+ds-2) ...
Setting up libssl1.1:i386 (1.1.1b-2) ...
Setting up libidn11:i386 (1.33-2.2) ...
Setting up libip4tc0:i386 (1.8.2-4) ...
Setting up libkmod2:i386 (26-1) ...
Setting up libdevmapper1.02.1:i386 (2:1.02.155-2) ...
Setting up libcryptsetup12:i386 (2:2.1.0-3) ...
Setting up systemd (241-3) ...
Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service -> /lib/systemd/system/getty@.service.
Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target -> /lib/systemd/system/remote-fs.target.
Created symlink /etc/systemd/system/dbus-org.freedesktop.timesync1.service -> /lib/systemd/system/systemd-timesyncd.service.
Created symlink /etc/systemd/system/sysinit.target.wants/systemd-timesyncd.service -> /lib/systemd/system/systemd-timesyncd.service.
Initializing machine ID from random generator.
Setting up dmsetup (2:1.02.155-2) ...
Selecting previously unselected package systemd-sysv.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13003 files and directories currently installed.)
Preparing to unpack .../00-systemd-sysv_241-3_i386.deb ...
Unpacking systemd-sysv (241-3) ...
Selecting previously unselected package libbsd0:i386.
Preparing to unpack .../01-libbsd0_0.9.1-2_i386.deb ...
Unpacking libbsd0:i386 (0.9.1-2) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../02-bsdmainutils_11.1.2+b1_i386.deb ...
Unpacking bsdmainutils (11.1.2+b1) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../03-libuchardet0_0.0.6-3_i386.deb ...
Unpacking libuchardet0:i386 (0.0.6-3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../04-groff-base_1.22.4-3_i386.deb ...
Unpacking groff-base (1.22.4-3) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../05-libpipeline1_1.5.1-2_i386.deb ...
Unpacking libpipeline1:i386 (1.5.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../06-man-db_2.8.5-2_i386.deb ...
Unpacking man-db (2.8.5-2) ...
Selecting previously unselected package libpython2.7-minimal:i386.
Preparing to unpack .../07-libpython2.7-minimal_2.7.16-2_i386.deb ...
Unpacking libpython2.7-minimal:i386 (2.7.16-2) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../08-python2.7-minimal_2.7.16-2_i386.deb ...
Unpacking python2.7-minimal (2.7.16-2) ...
Selecting previously unselected package python2-minimal.
Preparing to unpack .../09-python2-minimal_2.7.16-1_i386.deb ...
Unpacking python2-minimal (2.7.16-1) ...
Selecting previously unselected package python-minimal.
Preparing to unpack .../10-python-minimal_2.7.16-1_i386.deb ...
Unpacking python-minimal (2.7.16-1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../11-mime-support_3.62_all.deb ...
Unpacking mime-support (3.62) ...
Selecting previously unselected package libexpat1:i386.
Preparing to unpack .../12-libexpat1_2.2.6-1_i386.deb ...
Unpacking libexpat1:i386 (2.2.6-1) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../13-readline-common_7.0-5_all.deb ...
Unpacking readline-common (7.0-5) ...
Selecting previously unselected package libreadline7:i386.
Preparing to unpack .../14-libreadline7_7.0-5_i386.deb ...
Unpacking libreadline7:i386 (7.0-5) ...
Selecting previously unselected package libpython2.7-stdlib:i386.
Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2_i386.deb ...
Unpacking libpython2.7-stdlib:i386 (2.7.16-2) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../16-python2.7_2.7.16-2_i386.deb ...
Unpacking python2.7 (2.7.16-2) ...
Selecting previously unselected package libpython2-stdlib:i386.
Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_i386.deb ...
Unpacking libpython2-stdlib:i386 (2.7.16-1) ...
Selecting previously unselected package libpython-stdlib:i386.
Preparing to unpack .../18-libpython-stdlib_2.7.16-1_i386.deb ...
Unpacking libpython-stdlib:i386 (2.7.16-1) ...
Setting up libpython2.7-minimal:i386 (2.7.16-2) ...
Setting up python2.7-minimal (2.7.16-2) ...
Setting up python2-minimal (2.7.16-1) ...
Selecting previously unselected package python2.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 14475 files and directories currently installed.)
Preparing to unpack .../python2_2.7.16-1_i386.deb ...
Unpacking python2 (2.7.16-1) ...
Setting up python-minimal (2.7.16-1) ...
Selecting previously unselected package python.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 14508 files and directories currently installed.)
Preparing to unpack .../python_2.7.16-1_i386.deb ...
Unpacking python (2.7.16-1) ...
Selecting previously unselected package poppler-data.
Preparing to unpack .../poppler-data_0.4.9-2_all.deb ...
Unpacking poppler-data (0.4.9-2) ...
Selecting previously unselected package libpython3.7-minimal:i386.
Preparing to unpack .../libpython3.7-minimal_3.7.3~rc1-1_i386.deb ...
Unpacking libpython3.7-minimal:i386 (3.7.3~rc1-1) ...
Selecting previously unselected package python3.7-minimal.
Preparing to unpack .../python3.7-minimal_3.7.3~rc1-1_i386.deb ...
Unpacking python3.7-minimal (3.7.3~rc1-1) ...
Setting up libpython3.7-minimal:i386 (3.7.3~rc1-1) ...
Setting up libexpat1:i386 (2.2.6-1) ...
Setting up python3.7-minimal (3.7.3~rc1-1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 15279 files and directories currently installed.)
Preparing to unpack .../python3-minimal_3.7.2-1_i386.deb ...
Unpacking python3-minimal (3.7.2-1) ...
Selecting previously unselected package libmpdec2:i386.
Preparing to unpack .../libmpdec2_2.4.2-2_i386.deb ...
Unpacking libmpdec2:i386 (2.4.2-2) ...
Selecting previously unselected package libpython3.7-stdlib:i386.
Preparing to unpack .../libpython3.7-stdlib_3.7.3~rc1-1_i386.deb ...
Unpacking libpython3.7-stdlib:i386 (3.7.3~rc1-1) ...
Selecting previously unselected package python3.7.
Preparing to unpack .../python3.7_3.7.3~rc1-1_i386.deb ...
Unpacking python3.7 (3.7.3~rc1-1) ...
Selecting previously unselected package libpython3-stdlib:i386.
Preparing to unpack .../libpython3-stdlib_3.7.2-1_i386.deb ...
Unpacking libpython3-stdlib:i386 (3.7.2-1) ...
Setting up python3-minimal (3.7.2-1) ...
Selecting previously unselected package python3.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 15691 files and directories currently installed.)
Preparing to unpack .../000-python3_3.7.2-1_i386.deb ...
Unpacking python3 (3.7.2-1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../001-sensible-utils_0.0.12_all.deb ...
Unpacking sensible-utils (0.0.12) ...
Selecting previously unselected package ucf.
Preparing to unpack .../002-ucf_3.0038+nmu1_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0038+nmu1) ...
Selecting previously unselected package tex-common.
Preparing to unpack .../003-tex-common_6.11_all.deb ...
Unpacking tex-common (6.11) ...
Selecting previously unselected package bash-completion.
Preparing to unpack .../004-bash-completion_1%3a2.8-6_all.deb ...
Unpacking bash-completion (1:2.8-6) ...
Selecting previously unselected package libdbus-1-3:i386.
Preparing to unpack .../005-libdbus-1-3_1.12.12-1_i386.deb ...
Unpacking libdbus-1-3:i386 (1.12.12-1) ...
Selecting previously unselected package dbus.
Preparing to unpack .../006-dbus_1.12.12-1_i386.deb ...
Unpacking dbus (1.12.12-1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../007-libmagic-mgc_1%3a5.35-4_i386.deb ...
Unpacking libmagic-mgc (1:5.35-4) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../008-libmagic1_1%3a5.35-4_i386.deb ...
Unpacking libmagic1:i386 (1:5.35-4) ...
Selecting previously unselected package file.
Preparing to unpack .../009-file_1%3a5.35-4_i386.deb ...
Unpacking file (1:5.35-4) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../010-gettext-base_0.19.8.1-9_i386.deb ...
Unpacking gettext-base (0.19.8.1-9) ...
Selecting previously unselected package libpam-systemd:i386.
Preparing to unpack .../011-libpam-systemd_241-3_i386.deb ...
Unpacking libpam-systemd:i386 (241-3) ...
Selecting previously unselected package hicolor-icon-theme.
Preparing to unpack .../012-hicolor-icon-theme_0.17-2_all.deb ...
Unpacking hicolor-icon-theme (0.17-2) ...
Selecting previously unselected package libglib2.0-0:i386.
Preparing to unpack .../013-libglib2.0-0_2.58.3-1_i386.deb ...
Unpacking libglib2.0-0:i386 (2.58.3-1) ...
Selecting previously unselected package libjpeg62-turbo:i386.
Preparing to unpack .../014-libjpeg62-turbo_1%3a1.5.2-2+b1_i386.deb ...
Unpacking libjpeg62-turbo:i386 (1:1.5.2-2+b1) ...
Selecting previously unselected package libpng16-16:i386.
Preparing to unpack .../015-libpng16-16_1.6.36-5_i386.deb ...
Unpacking libpng16-16:i386 (1.6.36-5) ...
Selecting previously unselected package libjbig0:i386.
Preparing to unpack .../016-libjbig0_2.1-3.1+b2_i386.deb ...
Unpacking libjbig0:i386 (2.1-3.1+b2) ...
Selecting previously unselected package libwebp6:i386.
Preparing to unpack .../017-libwebp6_0.6.1-2_i386.deb ...
Unpacking libwebp6:i386 (0.6.1-2) ...
Selecting previously unselected package libtiff5:i386.
Preparing to unpack .../018-libtiff5_4.0.10-4_i386.deb ...
Unpacking libtiff5:i386 (4.0.10-4) ...
Selecting previously unselected package libxau6:i386.
Preparing to unpack .../019-libxau6_1%3a1.0.8-1+b2_i386.deb ...
Unpacking libxau6:i386 (1:1.0.8-1+b2) ...
Selecting previously unselected package libxdmcp6:i386.
Preparing to unpack .../020-libxdmcp6_1%3a1.1.2-3_i386.deb ...
Unpacking libxdmcp6:i386 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:i386.
Preparing to unpack .../021-libxcb1_1.13.1-2_i386.deb ...
Unpacking libxcb1:i386 (1.13.1-2) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../022-libx11-data_2%3a1.6.7-1_all.deb ...
Unpacking libx11-data (2:1.6.7-1) ...
Selecting previously unselected package libx11-6:i386.
Preparing to unpack .../023-libx11-6_2%3a1.6.7-1_i386.deb ...
Unpacking libx11-6:i386 (2:1.6.7-1) ...
Selecting previously unselected package libicu63:i386.
Preparing to unpack .../024-libicu63_63.1-6_i386.deb ...
Unpacking libicu63:i386 (63.1-6) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../025-libxml2_2.9.4+dfsg1-7+b3_i386.deb ...
Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ...
Selecting previously unselected package shared-mime-info.
Preparing to unpack .../026-shared-mime-info_1.10-1_i386.deb ...
Unpacking shared-mime-info (1.10-1) ...
Selecting previously unselected package libgdk-pixbuf2.0-common.
Preparing to unpack .../027-libgdk-pixbuf2.0-common_2.38.1+dfsg-1_all.deb ...
Unpacking libgdk-pixbuf2.0-common (2.38.1+dfsg-1) ...
Selecting previously unselected package libgdk-pixbuf2.0-0:i386.
Preparing to unpack .../028-libgdk-pixbuf2.0-0_2.38.1+dfsg-1_i386.deb ...
Unpacking libgdk-pixbuf2.0-0:i386 (2.38.1+dfsg-1) ...
Selecting previously unselected package gtk-update-icon-cache.
Preparing to unpack .../029-gtk-update-icon-cache_3.24.5-1_i386.deb ...
No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed.
Unpacking gtk-update-icon-cache (3.24.5-1) ...
Selecting previously unselected package libfreetype6:i386.
Preparing to unpack .../030-libfreetype6_2.9.1-3_i386.deb ...
Unpacking libfreetype6:i386 (2.9.1-3) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../031-fonts-dejavu-core_2.37-1_all.deb ...
Unpacking fonts-dejavu-core (2.37-1) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../032-fontconfig-config_2.13.1-2_all.deb ...
Unpacking fontconfig-config (2.13.1-2) ...
Selecting previously unselected package libfontconfig1:i386.
Preparing to unpack .../033-libfontconfig1_2.13.1-2_i386.deb ...
Unpacking libfontconfig1:i386 (2.13.1-2) ...
Selecting previously unselected package libpixman-1-0:i386.
Preparing to unpack .../034-libpixman-1-0_0.36.0-1_i386.deb ...
Unpacking libpixman-1-0:i386 (0.36.0-1) ...
Selecting previously unselected package libxcb-render0:i386.
Preparing to unpack .../035-libxcb-render0_1.13.1-2_i386.deb ...
Unpacking libxcb-render0:i386 (1.13.1-2) ...
Selecting previously unselected package libxcb-shm0:i386.
Preparing to unpack .../036-libxcb-shm0_1.13.1-2_i386.deb ...
Unpacking libxcb-shm0:i386 (1.13.1-2) ...
Selecting previously unselected package libxext6:i386.
Preparing to unpack .../037-libxext6_2%3a1.3.3-1+b2_i386.deb ...
Unpacking libxext6:i386 (2:1.3.3-1+b2) ...
Selecting previously unselected package libxrender1:i386.
Preparing to unpack .../038-libxrender1_1%3a0.9.10-1_i386.deb ...
Unpacking libxrender1:i386 (1:0.9.10-1) ...
Selecting previously unselected package libcairo2:i386.
Preparing to unpack .../039-libcairo2_1.16.0-4_i386.deb ...
Unpacking libcairo2:i386 (1.16.0-4) ...
Selecting previously unselected package libcroco3:i386.
Preparing to unpack .../040-libcroco3_0.6.12-3_i386.deb ...
Unpacking libcroco3:i386 (0.6.12-3) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../041-fontconfig_2.13.1-2_i386.deb ...
Unpacking fontconfig (2.13.1-2) ...
Selecting previously unselected package libfribidi0:i386.
Preparing to unpack .../042-libfribidi0_1.0.5-3.1_i386.deb ...
Unpacking libfribidi0:i386 (1.0.5-3.1) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../043-libthai-data_0.1.28-2_all.deb ...
Unpacking libthai-data (0.1.28-2) ...
Selecting previously unselected package libdatrie1:i386.
Preparing to unpack .../044-libdatrie1_0.2.12-2_i386.deb ...
Unpacking libdatrie1:i386 (0.2.12-2) ...
Selecting previously unselected package libthai0:i386.
Preparing to unpack .../045-libthai0_0.1.28-2_i386.deb ...
Unpacking libthai0:i386 (0.1.28-2) ...
Selecting previously unselected package libpango-1.0-0:i386.
Preparing to unpack .../046-libpango-1.0-0_1.42.4-6_i386.deb ...
Unpacking libpango-1.0-0:i386 (1.42.4-6) ...
Selecting previously unselected package libgraphite2-3:i386.
Preparing to unpack .../047-libgraphite2-3_1.3.13-7_i386.deb ...
Unpacking libgraphite2-3:i386 (1.3.13-7) ...
Selecting previously unselected package libharfbuzz0b:i386.
Preparing to unpack .../048-libharfbuzz0b_2.3.1-1_i386.deb ...
Unpacking libharfbuzz0b:i386 (2.3.1-1) ...
Selecting previously unselected package libpangoft2-1.0-0:i386.
Preparing to unpack .../049-libpangoft2-1.0-0_1.42.4-6_i386.deb ...
Unpacking libpangoft2-1.0-0:i386 (1.42.4-6) ...
Selecting previously unselected package libpangocairo-1.0-0:i386.
Preparing to unpack .../050-libpangocairo-1.0-0_1.42.4-6_i386.deb ...
Unpacking libpangocairo-1.0-0:i386 (1.42.4-6) ...
Selecting previously unselected package librsvg2-2:i386.
Preparing to unpack .../051-librsvg2-2_2.44.10-2.1_i386.deb ...
Unpacking librsvg2-2:i386 (2.44.10-2.1) ...
Selecting previously unselected package librsvg2-common:i386.
Preparing to unpack .../052-librsvg2-common_2.44.10-2.1_i386.deb ...
Unpacking librsvg2-common:i386 (2.44.10-2.1) ...
Selecting previously unselected package adwaita-icon-theme.
Preparing to unpack .../053-adwaita-icon-theme_3.30.1-1_all.deb ...
Unpacking adwaita-icon-theme (3.30.1-1) ...
Selecting previously unselected package libsigsegv2:i386.
Preparing to unpack .../054-libsigsegv2_2.12-2_i386.deb ...
Unpacking libsigsegv2:i386 (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../055-m4_1.4.18-2_i386.deb ...
Unpacking m4 (1.4.18-2) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../056-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../057-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../058-automake_1%3a1.16.1-4_all.deb ...
Unpacking automake (1:1.16.1-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../059-autopoint_0.19.8.1-9_all.deb ...
Unpacking autopoint (0.19.8.1-9) ...
Selecting previously unselected package libbison-dev:i386.
Preparing to unpack .../060-libbison-dev_2%3a3.3.2.dfsg-1_i386.deb ...
Unpacking libbison-dev:i386 (2:3.3.2.dfsg-1) ...
Selecting previously unselected package bison.
Preparing to unpack .../061-bison_2%3a3.3.2.dfsg-1_i386.deb ...
Unpacking bison (2:3.3.2.dfsg-1) ...
Selecting previously unselected package openssl.
Preparing to unpack .../062-openssl_1.1.1b-2_i386.deb ...
Unpacking openssl (1.1.1b-2) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../063-ca-certificates_20190110_all.deb ...
Unpacking ca-certificates (20190110) ...
Selecting previously unselected package java-common.
Preparing to unpack .../064-java-common_0.71_all.deb ...
Unpacking java-common (0.71) ...
Selecting previously unselected package libavahi-common-data:i386.
Preparing to unpack .../065-libavahi-common-data_0.7-4+b1_i386.deb ...
Unpacking libavahi-common-data:i386 (0.7-4+b1) ...
Selecting previously unselected package libavahi-common3:i386.
Preparing to unpack .../066-libavahi-common3_0.7-4+b1_i386.deb ...
Unpacking libavahi-common3:i386 (0.7-4+b1) ...
Selecting previously unselected package libavahi-client3:i386.
Preparing to unpack .../067-libavahi-client3_0.7-4+b1_i386.deb ...
Unpacking libavahi-client3:i386 (0.7-4+b1) ...
Selecting previously unselected package libkeyutils1:i386.
Preparing to unpack .../068-libkeyutils1_1.6-6_i386.deb ...
Unpacking libkeyutils1:i386 (1.6-6) ...
Selecting previously unselected package libkrb5support0:i386.
Preparing to unpack .../069-libkrb5support0_1.17-2_i386.deb ...
Unpacking libkrb5support0:i386 (1.17-2) ...
Selecting previously unselected package libk5crypto3:i386.
Preparing to unpack .../070-libk5crypto3_1.17-2_i386.deb ...
Unpacking libk5crypto3:i386 (1.17-2) ...
Selecting previously unselected package libkrb5-3:i386.
Preparing to unpack .../071-libkrb5-3_1.17-2_i386.deb ...
Unpacking libkrb5-3:i386 (1.17-2) ...
Selecting previously unselected package libgssapi-krb5-2:i386.
Preparing to unpack .../072-libgssapi-krb5-2_1.17-2_i386.deb ...
Unpacking libgssapi-krb5-2:i386 (1.17-2) ...
Selecting previously unselected package libcups2:i386.
Preparing to unpack .../073-libcups2_2.2.10-6_i386.deb ...
Unpacking libcups2:i386 (2.2.10-6) ...
Selecting previously unselected package liblcms2-2:i386.
Preparing to unpack .../074-liblcms2-2_2.9-3_i386.deb ...
Unpacking liblcms2-2:i386 (2.9-3) ...
Selecting previously unselected package libnspr4:i386.
Preparing to unpack .../075-libnspr4_2%3a4.20-1_i386.deb ...
Unpacking libnspr4:i386 (2:4.20-1) ...
Selecting previously unselected package libnss3:i386.
Preparing to unpack .../076-libnss3_2%3a3.42.1-1_i386.deb ...
Unpacking libnss3:i386 (2:3.42.1-1) ...
Selecting previously unselected package libasound2-data.
Preparing to unpack .../077-libasound2-data_1.1.8-1_all.deb ...
Unpacking libasound2-data (1.1.8-1) ...
Selecting previously unselected package libasound2:i386.
Preparing to unpack .../078-libasound2_1.1.8-1_i386.deb ...
Unpacking libasound2:i386 (1.1.8-1) ...
Selecting previously unselected package libpcsclite1:i386.
Preparing to unpack .../079-libpcsclite1_1.8.24-1_i386.deb ...
Unpacking libpcsclite1:i386 (1.8.24-1) ...
Selecting previously unselected package libxi6:i386.
Preparing to unpack .../080-libxi6_2%3a1.7.9-1_i386.deb ...
Unpacking libxi6:i386 (2:1.7.9-1) ...
Selecting previously unselected package lsb-base.
Preparing to unpack .../081-lsb-base_10.2019031300_all.deb ...
Unpacking lsb-base (10.2019031300) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../082-x11-common_1%3a7.7+19_all.deb ...
Unpacking x11-common (1:7.7+19) ...
Selecting previously unselected package libxtst6:i386.
Preparing to unpack .../083-libxtst6_2%3a1.2.3-1_i386.deb ...
Unpacking libxtst6:i386 (2:1.2.3-1) ...
Selecting previously unselected package openjdk-11-jre-headless:i386.
Preparing to unpack .../084-openjdk-11-jre-headless_11.0.3+1-1_i386.deb ...
Unpacking openjdk-11-jre-headless:i386 (11.0.3+1-1) ...
Selecting previously unselected package default-jre-headless.
Preparing to unpack .../085-default-jre-headless_2%3a1.11-71_i386.deb ...
Unpacking default-jre-headless (2:1.11-71) ...
Selecting previously unselected package ca-certificates-java.
Preparing to unpack .../086-ca-certificates-java_20190405_all.deb ...
Unpacking ca-certificates-java (20190405) ...
Selecting previously unselected package dbus-user-session.
Preparing to unpack .../087-dbus-user-session_1.12.12-1_i386.deb ...
Unpacking dbus-user-session (1.12.12-1) ...
Selecting previously unselected package libdconf1:i386.
Preparing to unpack .../088-libdconf1_0.30.1-2_i386.deb ...
Unpacking libdconf1:i386 (0.30.1-2) ...
Selecting previously unselected package dconf-service.
Preparing to unpack .../089-dconf-service_0.30.1-2_i386.deb ...
Unpacking dconf-service (0.30.1-2) ...
Selecting previously unselected package dconf-gsettings-backend:i386.
Preparing to unpack .../090-dconf-gsettings-backend_0.30.1-2_i386.deb ...
Unpacking dconf-gsettings-backend:i386 (0.30.1-2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../091-libtool_2.4.6-9_all.deb ...
Unpacking libtool (2.4.6-9) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../092-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../093-libarchive-zip-perl_1.64-1_all.deb ...
Unpacking libarchive-zip-perl (1.64-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../094-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../095-dh-strip-nondeterminism_1.1.2-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.1.2-1) ...
Selecting previously unselected package libelf1:i386.
Preparing to unpack .../096-libelf1_0.176-1_i386.deb ...
Unpacking libelf1:i386 (0.176-1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../097-dwz_0.12-3_i386.deb ...
Unpacking dwz (0.12-3) ...
Selecting previously unselected package libncurses6:i386.
Preparing to unpack .../098-libncurses6_6.1+20181013-2_i386.deb ...
Unpacking libncurses6:i386 (6.1+20181013-2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../099-gettext_0.19.8.1-9_i386.deb ...
Unpacking gettext (0.19.8.1-9) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../100-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../101-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../102-debhelper_12.1.1_all.deb ...
Unpacking debhelper (12.1.1) ...
Selecting previously unselected package libatk1.0-data.
Preparing to unpack .../103-libatk1.0-data_2.30.0-2_all.deb ...
Unpacking libatk1.0-data (2.30.0-2) ...
Selecting previously unselected package libatk1.0-0:i386.
Preparing to unpack .../104-libatk1.0-0_2.30.0-2_i386.deb ...
Unpacking libatk1.0-0:i386 (2.30.0-2) ...
Selecting previously unselected package libatspi2.0-0:i386.
Preparing to unpack .../105-libatspi2.0-0_2.30.0-7_i386.deb ...
Unpacking libatspi2.0-0:i386 (2.30.0-7) ...
Selecting previously unselected package libatk-bridge2.0-0:i386.
Preparing to unpack .../106-libatk-bridge2.0-0_2.30.0-5_i386.deb ...
Unpacking libatk-bridge2.0-0:i386 (2.30.0-5) ...
Selecting previously unselected package libcairo-gobject2:i386.
Preparing to unpack .../107-libcairo-gobject2_1.16.0-4_i386.deb ...
Unpacking libcairo-gobject2:i386 (1.16.0-4) ...
Selecting previously unselected package libcolord2:i386.
Preparing to unpack .../108-libcolord2_1.4.3-4_i386.deb ...
Unpacking libcolord2:i386 (1.4.3-4) ...
Selecting previously unselected package libepoxy0:i386.
Preparing to unpack .../109-libepoxy0_1.5.3-0.1_i386.deb ...
Unpacking libepoxy0:i386 (1.5.3-0.1) ...
Selecting previously unselected package libjson-glib-1.0-common.
Preparing to unpack .../110-libjson-glib-1.0-common_1.4.4-2_all.deb ...
Unpacking libjson-glib-1.0-common (1.4.4-2) ...
Selecting previously unselected package libjson-glib-1.0-0:i386.
Preparing to unpack .../111-libjson-glib-1.0-0_1.4.4-2_i386.deb ...
Unpacking libjson-glib-1.0-0:i386 (1.4.4-2) ...
Selecting previously unselected package libpsl5:i386.
Preparing to unpack .../112-libpsl5_0.20.2-2_i386.deb ...
Unpacking libpsl5:i386 (0.20.2-2) ...
Selecting previously unselected package libproxy1v5:i386.
Preparing to unpack .../113-libproxy1v5_0.4.15-5_i386.deb ...
Unpacking libproxy1v5:i386 (0.4.15-5) ...
Selecting previously unselected package glib-networking-common.
Preparing to unpack .../114-glib-networking-common_2.58.0-2_all.deb ...
Unpacking glib-networking-common (2.58.0-2) ...
Selecting previously unselected package glib-networking-services.
Preparing to unpack .../115-glib-networking-services_2.58.0-2_i386.deb ...
Unpacking glib-networking-services (2.58.0-2) ...
Selecting previously unselected package gsettings-desktop-schemas.
Preparing to unpack .../116-gsettings-desktop-schemas_3.28.1-1_all.deb ...
Unpacking gsettings-desktop-schemas (3.28.1-1) ...
Selecting previously unselected package glib-networking:i386.
Preparing to unpack .../117-glib-networking_2.58.0-2_i386.deb ...
Unpacking glib-networking:i386 (2.58.0-2) ...
Selecting previously unselected package libsoup2.4-1:i386.
Preparing to unpack .../118-libsoup2.4-1_2.64.2-2_i386.deb ...
Unpacking libsoup2.4-1:i386 (2.64.2-2) ...
Selecting previously unselected package libsoup-gnome2.4-1:i386.
Preparing to unpack .../119-libsoup-gnome2.4-1_2.64.2-2_i386.deb ...
Unpacking libsoup-gnome2.4-1:i386 (2.64.2-2) ...
Selecting previously unselected package librest-0.7-0:i386.
Preparing to unpack .../120-librest-0.7-0_0.8.1-1_i386.deb ...
Unpacking librest-0.7-0:i386 (0.8.1-1) ...
Selecting previously unselected package libwayland-client0:i386.
Preparing to unpack .../121-libwayland-client0_1.16.0-1_i386.deb ...
Unpacking libwayland-client0:i386 (1.16.0-1) ...
Selecting previously unselected package libwayland-cursor0:i386.
Preparing to unpack .../122-libwayland-cursor0_1.16.0-1_i386.deb ...
Unpacking libwayland-cursor0:i386 (1.16.0-1) ...
Selecting previously unselected package libwayland-egl1:i386.
Preparing to unpack .../123-libwayland-egl1_1.16.0-1_i386.deb ...
Unpacking libwayland-egl1:i386 (1.16.0-1) ...
Selecting previously unselected package libxcomposite1:i386.
Preparing to unpack .../124-libxcomposite1_1%3a0.4.4-2_i386.deb ...
Unpacking libxcomposite1:i386 (1:0.4.4-2) ...
Selecting previously unselected package libxfixes3:i386.
Preparing to unpack .../125-libxfixes3_1%3a5.0.3-1_i386.deb ...
Unpacking libxfixes3:i386 (1:5.0.3-1) ...
Selecting previously unselected package libxcursor1:i386.
Preparing to unpack .../126-libxcursor1_1%3a1.1.15-2_i386.deb ...
Unpacking libxcursor1:i386 (1:1.1.15-2) ...
Selecting previously unselected package libxdamage1:i386.
Preparing to unpack .../127-libxdamage1_1%3a1.1.4-3+b3_i386.deb ...
Unpacking libxdamage1:i386 (1:1.1.4-3+b3) ...
Selecting previously unselected package libxinerama1:i386.
Preparing to unpack .../128-libxinerama1_2%3a1.1.4-2_i386.deb ...
Unpacking libxinerama1:i386 (2:1.1.4-2) ...
Selecting previously unselected package xkb-data.
Preparing to unpack .../129-xkb-data_2.26-2_all.deb ...
Unpacking xkb-data (2.26-2) ...
Selecting previously unselected package libxkbcommon0:i386.
Preparing to unpack .../130-libxkbcommon0_0.8.2-1_i386.deb ...
Unpacking libxkbcommon0:i386 (0.8.2-1) ...
Selecting previously unselected package libxrandr2:i386.
Preparing to unpack .../131-libxrandr2_2%3a1.5.1-1_i386.deb ...
Unpacking libxrandr2:i386 (2:1.5.1-1) ...
Selecting previously unselected package libgtk-3-common.
Preparing to unpack .../132-libgtk-3-common_3.24.5-1_all.deb ...
Unpacking libgtk-3-common (3.24.5-1) ...
Selecting previously unselected package libgtk-3-0:i386.
Preparing to unpack .../133-libgtk-3-0_3.24.5-1_i386.deb ...
Unpacking libgtk-3-0:i386 (3.24.5-1) ...
Selecting previously unselected package libglvnd0:i386.
Preparing to unpack .../134-libglvnd0_1.1.0-1_i386.deb ...
Unpacking libglvnd0:i386 (1.1.0-1) ...
Selecting previously unselected package libdrm-common.
Preparing to unpack .../135-libdrm-common_2.4.97-1_all.deb ...
Unpacking libdrm-common (2.4.97-1) ...
Selecting previously unselected package libdrm2:i386.
Preparing to unpack .../136-libdrm2_2.4.97-1_i386.deb ...
Unpacking libdrm2:i386 (2.4.97-1) ...
Selecting previously unselected package libglapi-mesa:i386.
Preparing to unpack .../137-libglapi-mesa_18.3.4-2_i386.deb ...
Unpacking libglapi-mesa:i386 (18.3.4-2) ...
Selecting previously unselected package libx11-xcb1:i386.
Preparing to unpack .../138-libx11-xcb1_2%3a1.6.7-1_i386.deb ...
Unpacking libx11-xcb1:i386 (2:1.6.7-1) ...
Selecting previously unselected package libxcb-dri2-0:i386.
Preparing to unpack .../139-libxcb-dri2-0_1.13.1-2_i386.deb ...
Unpacking libxcb-dri2-0:i386 (1.13.1-2) ...
Selecting previously unselected package libxcb-dri3-0:i386.
Preparing to unpack .../140-libxcb-dri3-0_1.13.1-2_i386.deb ...
Unpacking libxcb-dri3-0:i386 (1.13.1-2) ...
Selecting previously unselected package libxcb-glx0:i386.
Preparing to unpack .../141-libxcb-glx0_1.13.1-2_i386.deb ...
Unpacking libxcb-glx0:i386 (1.13.1-2) ...
Selecting previously unselected package libxcb-present0:i386.
Preparing to unpack .../142-libxcb-present0_1.13.1-2_i386.deb ...
Unpacking libxcb-present0:i386 (1.13.1-2) ...
Selecting previously unselected package libxcb-sync1:i386.
Preparing to unpack .../143-libxcb-sync1_1.13.1-2_i386.deb ...
Unpacking libxcb-sync1:i386 (1.13.1-2) ...
Selecting previously unselected package libxshmfence1:i386.
Preparing to unpack .../144-libxshmfence1_1.3-1_i386.deb ...
Unpacking libxshmfence1:i386 (1.3-1) ...
Selecting previously unselected package libxxf86vm1:i386.
Preparing to unpack .../145-libxxf86vm1_1%3a1.1.4-1+b2_i386.deb ...
Unpacking libxxf86vm1:i386 (1:1.1.4-1+b2) ...
Selecting previously unselected package libdrm-amdgpu1:i386.
Preparing to unpack .../146-libdrm-amdgpu1_2.4.97-1_i386.deb ...
Unpacking libdrm-amdgpu1:i386 (2.4.97-1) ...
Selecting previously unselected package libpciaccess0:i386.
Preparing to unpack .../147-libpciaccess0_0.14-1_i386.deb ...
Unpacking libpciaccess0:i386 (0.14-1) ...
Selecting previously unselected package libdrm-intel1:i386.
Preparing to unpack .../148-libdrm-intel1_2.4.97-1_i386.deb ...
Unpacking libdrm-intel1:i386 (2.4.97-1) ...
Selecting previously unselected package libdrm-nouveau2:i386.
Preparing to unpack .../149-libdrm-nouveau2_2.4.97-1_i386.deb ...
Unpacking libdrm-nouveau2:i386 (2.4.97-1) ...
Selecting previously unselected package libdrm-radeon1:i386.
Preparing to unpack .../150-libdrm-radeon1_2.4.97-1_i386.deb ...
Unpacking libdrm-radeon1:i386 (2.4.97-1) ...
Selecting previously unselected package libedit2:i386.
Preparing to unpack .../151-libedit2_3.1-20181209-1_i386.deb ...
Unpacking libedit2:i386 (3.1-20181209-1) ...
Selecting previously unselected package libllvm7:i386.
Preparing to unpack .../152-libllvm7_1%3a7.0.1-8_i386.deb ...
Unpacking libllvm7:i386 (1:7.0.1-8) ...
Selecting previously unselected package libsensors-config.
Preparing to unpack .../153-libsensors-config_1%3a3.5.0-3_all.deb ...
Unpacking libsensors-config (1:3.5.0-3) ...
Selecting previously unselected package libsensors5:i386.
Preparing to unpack .../154-libsensors5_1%3a3.5.0-3_i386.deb ...
Unpacking libsensors5:i386 (1:3.5.0-3) ...
Selecting previously unselected package libgl1-mesa-dri:i386.
Preparing to unpack .../155-libgl1-mesa-dri_18.3.4-2_i386.deb ...
Unpacking libgl1-mesa-dri:i386 (18.3.4-2) ...
Selecting previously unselected package libglx-mesa0:i386.
Preparing to unpack .../156-libglx-mesa0_18.3.4-2_i386.deb ...
Unpacking libglx-mesa0:i386 (18.3.4-2) ...
Selecting previously unselected package libglx0:i386.
Preparing to unpack .../157-libglx0_1.1.0-1_i386.deb ...
Unpacking libglx0:i386 (1.1.0-1) ...
Selecting previously unselected package libgl1:i386.
Preparing to unpack .../158-libgl1_1.1.0-1_i386.deb ...
Unpacking libgl1:i386 (1.1.0-1) ...
Selecting previously unselected package libgif7:i386.
Preparing to unpack .../159-libgif7_5.1.4-3_i386.deb ...
Unpacking libgif7:i386 (5.1.4-3) ...
Selecting previously unselected package openjdk-11-jre:i386.
Preparing to unpack .../160-openjdk-11-jre_11.0.3+1-1_i386.deb ...
Unpacking openjdk-11-jre:i386 (11.0.3+1-1) ...
Selecting previously unselected package default-jre.
Preparing to unpack .../161-default-jre_2%3a1.11-71_i386.deb ...
Unpacking default-jre (2:1.11-71) ...
Selecting previously unselected package openjdk-11-jdk-headless:i386.
Preparing to unpack .../162-openjdk-11-jdk-headless_11.0.3+1-1_i386.deb ...
Unpacking openjdk-11-jdk-headless:i386 (11.0.3+1-1) ...
Selecting previously unselected package default-jdk-headless.
Preparing to unpack .../163-default-jdk-headless_2%3a1.11-71_i386.deb ...
Unpacking default-jdk-headless (2:1.11-71) ...
Selecting previously unselected package openjdk-11-jdk:i386.
Preparing to unpack .../164-openjdk-11-jdk_11.0.3+1-1_i386.deb ...
Unpacking openjdk-11-jdk:i386 (11.0.3+1-1) ...
Selecting previously unselected package default-jdk.
Preparing to unpack .../165-default-jdk_2%3a1.11-71_i386.deb ...
Unpacking default-jdk (2:1.11-71) ...
Selecting previously unselected package fonts-lmodern.
Preparing to unpack .../166-fonts-lmodern_2.004.5-6_all.deb ...
Unpacking fonts-lmodern (2.004.5-6) ...
Selecting previously unselected package libgfortran5:i386.
Preparing to unpack .../167-libgfortran5_8.3.0-6_i386.deb ...
Unpacking libgfortran5:i386 (8.3.0-6) ...
Selecting previously unselected package libgfortran-8-dev:i386.
Preparing to unpack .../168-libgfortran-8-dev_8.3.0-6_i386.deb ...
Unpacking libgfortran-8-dev:i386 (8.3.0-6) ...
Selecting previously unselected package gfortran-8.
Preparing to unpack .../169-gfortran-8_8.3.0-6_i386.deb ...
Unpacking gfortran-8 (8.3.0-6) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../170-gfortran_4%3a8.3.0-1_i386.deb ...
Unpacking gfortran (4:8.3.0-1) ...
Selecting previously unselected package libgirepository-1.0-1:i386.
Preparing to unpack .../171-libgirepository-1.0-1_1.58.3-2_i386.deb ...
Unpacking libgirepository-1.0-1:i386 (1.58.3-2) ...
Selecting previously unselected package gir1.2-glib-2.0:i386.
Preparing to unpack .../172-gir1.2-glib-2.0_1.58.3-2_i386.deb ...
Unpacking gir1.2-glib-2.0:i386 (1.58.3-2) ...
Selecting previously unselected package gir1.2-freedesktop:i386.
Preparing to unpack .../173-gir1.2-freedesktop_1.58.3-2_i386.deb ...
Unpacking gir1.2-freedesktop:i386 (1.58.3-2) ...
Selecting previously unselected package libharfbuzz-gobject0:i386.
Preparing to unpack .../174-libharfbuzz-gobject0_2.3.1-1_i386.deb ...
Unpacking libharfbuzz-gobject0:i386 (2.3.1-1) ...
Selecting previously unselected package gir1.2-harfbuzz-0.0:i386.
Preparing to unpack .../175-gir1.2-harfbuzz-0.0_2.3.1-1_i386.deb ...
Unpacking gir1.2-harfbuzz-0.0:i386 (2.3.1-1) ...
Selecting previously unselected package libxft2:i386.
Preparing to unpack .../176-libxft2_2.3.2-2_i386.deb ...
Unpacking libxft2:i386 (2.3.2-2) ...
Selecting previously unselected package libpangoxft-1.0-0:i386.
Preparing to unpack .../177-libpangoxft-1.0-0_1.42.4-6_i386.deb ...
Unpacking libpangoxft-1.0-0:i386 (1.42.4-6) ...
Selecting previously unselected package gir1.2-pango-1.0:i386.
Preparing to unpack .../178-gir1.2-pango-1.0_1.42.4-6_i386.deb ...
Unpacking gir1.2-pango-1.0:i386 (1.42.4-6) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../179-icu-devtools_63.1-6_i386.deb ...
Unpacking icu-devtools (63.1-6) ...
Selecting previously unselected package libblas3:i386.
Preparing to unpack .../180-libblas3_3.8.0-2_i386.deb ...
Unpacking libblas3:i386 (3.8.0-2) ...
Selecting previously unselected package libblas-dev:i386.
Preparing to unpack .../181-libblas-dev_3.8.0-2_i386.deb ...
Unpacking libblas-dev:i386 (3.8.0-2) ...
Selecting previously unselected package uuid-dev:i386.
Preparing to unpack .../182-uuid-dev_2.33.1-0.1_i386.deb ...
Unpacking uuid-dev:i386 (2.33.1-0.1) ...
Selecting previously unselected package libblkid-dev:i386.
Preparing to unpack .../183-libblkid-dev_2.33.1-0.1_i386.deb ...
Unpacking libblkid-dev:i386 (2.33.1-0.1) ...
Selecting previously unselected package libbrotli1:i386.
Preparing to unpack .../184-libbrotli1_1.0.7-2_i386.deb ...
Unpacking libbrotli1:i386 (1.0.7-2) ...
Selecting previously unselected package libbz2-dev:i386.
Preparing to unpack .../185-libbz2-dev_1.0.6-9_i386.deb ...
Unpacking libbz2-dev:i386 (1.0.6-9) ...
Selecting previously unselected package liblzo2-2:i386.
Preparing to unpack .../186-liblzo2-2_2.10-0.1_i386.deb ...
Unpacking liblzo2-2:i386 (2.10-0.1) ...
Selecting previously unselected package libcairo-script-interpreter2:i386.
Preparing to unpack .../187-libcairo-script-interpreter2_1.16.0-4_i386.deb ...
Unpacking libcairo-script-interpreter2:i386 (1.16.0-4) ...
Selecting previously unselected package libexpat1-dev:i386.
Preparing to unpack .../188-libexpat1-dev_2.2.6-1_i386.deb ...
Unpacking libexpat1-dev:i386 (2.2.6-1) ...
Selecting previously unselected package zlib1g-dev:i386.
Preparing to unpack .../189-zlib1g-dev_1%3a1.2.11.dfsg-1_i386.deb ...
Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-1) ...
Selecting previously unselected package libpng-dev:i386.
Preparing to unpack .../190-libpng-dev_1.6.36-5_i386.deb ...
Unpacking libpng-dev:i386 (1.6.36-5) ...
Selecting previously unselected package libfreetype6-dev:i386.
Preparing to unpack .../191-libfreetype6-dev_2.9.1-3_i386.deb ...
Unpacking libfreetype6-dev:i386 (2.9.1-3) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../192-pkg-config_0.29-6_i386.deb ...
Unpacking pkg-config (0.29-6) ...
Selecting previously unselected package libfontconfig1-dev:i386.
Preparing to unpack .../193-libfontconfig1-dev_2.13.1-2_i386.deb ...
Unpacking libfontconfig1-dev:i386 (2.13.1-2) ...
Selecting previously unselected package xorg-sgml-doctools.
Preparing to unpack .../194-xorg-sgml-doctools_1%3a1.11-1_all.deb ...
Unpacking xorg-sgml-doctools (1:1.11-1) ...
Selecting previously unselected package x11proto-dev.
Preparing to unpack .../195-x11proto-dev_2018.4-4_all.deb ...
Unpacking x11proto-dev (2018.4-4) ...
Selecting previously unselected package x11proto-core-dev.
Preparing to unpack .../196-x11proto-core-dev_2018.4-4_all.deb ...
Unpacking x11proto-core-dev (2018.4-4) ...
Selecting previously unselected package libxau-dev:i386.
Preparing to unpack .../197-libxau-dev_1%3a1.0.8-1+b2_i386.deb ...
Unpacking libxau-dev:i386 (1:1.0.8-1+b2) ...
Selecting previously unselected package libxdmcp-dev:i386.
Preparing to unpack .../198-libxdmcp-dev_1%3a1.1.2-3_i386.deb ...
Unpacking libxdmcp-dev:i386 (1:1.1.2-3) ...
Selecting previously unselected package xtrans-dev.
Preparing to unpack .../199-xtrans-dev_1.3.5-1_all.deb ...
Unpacking xtrans-dev (1.3.5-1) ...
Selecting previously unselected package libpthread-stubs0-dev:i386.
Preparing to unpack .../200-libpthread-stubs0-dev_0.4-1_i386.deb ...
Unpacking libpthread-stubs0-dev:i386 (0.4-1) ...
Selecting previously unselected package libxcb1-dev:i386.
Preparing to unpack .../201-libxcb1-dev_1.13.1-2_i386.deb ...
Unpacking libxcb1-dev:i386 (1.13.1-2) ...
Selecting previously unselected package libx11-dev:i386.
Preparing to unpack .../202-libx11-dev_2%3a1.6.7-1_i386.deb ...
Unpacking libx11-dev:i386 (2:1.6.7-1) ...
Selecting previously unselected package libxrender-dev:i386.
Preparing to unpack .../203-libxrender-dev_1%3a0.9.10-1_i386.deb ...
Unpacking libxrender-dev:i386 (1:0.9.10-1) ...
Selecting previously unselected package x11proto-xext-dev.
Preparing to unpack .../204-x11proto-xext-dev_2018.4-4_all.deb ...
Unpacking x11proto-xext-dev (2018.4-4) ...
Selecting previously unselected package libxext-dev:i386.
Preparing to unpack .../205-libxext-dev_2%3a1.3.3-1+b2_i386.deb ...
Unpacking libxext-dev:i386 (2:1.3.3-1+b2) ...
Selecting previously unselected package libice6:i386.
Preparing to unpack .../206-libice6_2%3a1.0.9-2_i386.deb ...
Unpacking libice6:i386 (2:1.0.9-2) ...
Selecting previously unselected package libsm6:i386.
Preparing to unpack .../207-libsm6_2%3a1.2.3-1_i386.deb ...
Unpacking libsm6:i386 (2:1.2.3-1) ...
Selecting previously unselected package libice-dev:i386.
Preparing to unpack .../208-libice-dev_2%3a1.0.9-2_i386.deb ...
Unpacking libice-dev:i386 (2:1.0.9-2) ...
Selecting previously unselected package libsm-dev:i386.
Preparing to unpack .../209-libsm-dev_2%3a1.2.3-1_i386.deb ...
Unpacking libsm-dev:i386 (2:1.2.3-1) ...
Selecting previously unselected package libpixman-1-dev:i386.
Preparing to unpack .../210-libpixman-1-dev_0.36.0-1_i386.deb ...
Unpacking libpixman-1-dev:i386 (0.36.0-1) ...
Selecting previously unselected package libxcb-render0-dev:i386.
Preparing to unpack .../211-libxcb-render0-dev_1.13.1-2_i386.deb ...
Unpacking libxcb-render0-dev:i386 (1.13.1-2) ...
Selecting previously unselected package libxcb-shm0-dev:i386.
Preparing to unpack .../212-libxcb-shm0-dev_1.13.1-2_i386.deb ...
Unpacking libxcb-shm0-dev:i386 (1.13.1-2) ...
Selecting previously unselected package libffi-dev:i386.
Preparing to unpack .../213-libffi-dev_3.2.1-9_i386.deb ...
Unpacking libffi-dev:i386 (3.2.1-9) ...
Selecting previously unselected package libglib2.0-data.
Preparing to unpack .../214-libglib2.0-data_2.58.3-1_all.deb ...
Unpacking libglib2.0-data (2.58.3-1) ...
Selecting previously unselected package libglib2.0-bin.
Preparing to unpack .../215-libglib2.0-bin_2.58.3-1_i386.deb ...
Unpacking libglib2.0-bin (2.58.3-1) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../216-python3-lib2to3_3.7.3~rc1-1_all.deb ...
Unpacking python3-lib2to3 (3.7.3~rc1-1) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../217-python3-distutils_3.7.3~rc1-1_all.deb ...
Unpacking python3-distutils (3.7.3~rc1-1) ...
Selecting previously unselected package libglib2.0-dev-bin.
Preparing to unpack .../218-libglib2.0-dev-bin_2.58.3-1_i386.deb ...
Unpacking libglib2.0-dev-bin (2.58.3-1) ...
Selecting previously unselected package libmount-dev:i386.
Preparing to unpack .../219-libmount-dev_2.33.1-0.1_i386.deb ...
Unpacking libmount-dev:i386 (2.33.1-0.1) ...
Selecting previously unselected package libpcre16-3:i386.
Preparing to unpack .../220-libpcre16-3_2%3a8.39-12_i386.deb ...
Unpacking libpcre16-3:i386 (2:8.39-12) ...
Selecting previously unselected package libpcre32-3:i386.
Preparing to unpack .../221-libpcre32-3_2%3a8.39-12_i386.deb ...
Unpacking libpcre32-3:i386 (2:8.39-12) ...
Selecting previously unselected package libpcrecpp0v5:i386.
Preparing to unpack .../222-libpcrecpp0v5_2%3a8.39-12_i386.deb ...
Unpacking libpcrecpp0v5:i386 (2:8.39-12) ...
Selecting previously unselected package libpcre3-dev:i386.
Preparing to unpack .../223-libpcre3-dev_2%3a8.39-12_i386.deb ...
Unpacking libpcre3-dev:i386 (2:8.39-12) ...
Selecting previously unselected package libsepol1-dev:i386.
Preparing to unpack .../224-libsepol1-dev_2.8-1_i386.deb ...
Unpacking libsepol1-dev:i386 (2.8-1) ...
Selecting previously unselected package libselinux1-dev:i386.
Preparing to unpack .../225-libselinux1-dev_2.8-1+b1_i386.deb ...
Unpacking libselinux1-dev:i386 (2.8-1+b1) ...
Selecting previously unselected package libglib2.0-dev:i386.
Preparing to unpack .../226-libglib2.0-dev_2.58.3-1_i386.deb ...
Unpacking libglib2.0-dev:i386 (2.58.3-1) ...
Selecting previously unselected package libcairo2-dev:i386.
Preparing to unpack .../227-libcairo2-dev_1.16.0-4_i386.deb ...
Unpacking libcairo2-dev:i386 (1.16.0-4) ...
Selecting previously unselected package libcupsimage2:i386.
Preparing to unpack .../228-libcupsimage2_2.2.10-6_i386.deb ...
Unpacking libcupsimage2:i386 (2.2.10-6) ...
Selecting previously unselected package libsasl2-modules-db:i386.
Preparing to unpack .../229-libsasl2-modules-db_2.1.27+dfsg-1_i386.deb ...
Unpacking libsasl2-modules-db:i386 (2.1.27+dfsg-1) ...
Selecting previously unselected package libsasl2-2:i386.
Preparing to unpack .../230-libsasl2-2_2.1.27+dfsg-1_i386.deb ...
Unpacking libsasl2-2:i386 (2.1.27+dfsg-1) ...
Selecting previously unselected package libldap-common.
Preparing to unpack .../231-libldap-common_2.4.47+dfsg-3_all.deb ...
Unpacking libldap-common (2.4.47+dfsg-3) ...
Selecting previously unselected package libldap-2.4-2:i386.
Preparing to unpack .../232-libldap-2.4-2_2.4.47+dfsg-3_i386.deb ...
Unpacking libldap-2.4-2:i386 (2.4.47+dfsg-3) ...
Selecting previously unselected package libnghttp2-14:i386.
Preparing to unpack .../233-libnghttp2-14_1.36.0-2_i386.deb ...
Unpacking libnghttp2-14:i386 (1.36.0-2) ...
Selecting previously unselected package librtmp1:i386.
Preparing to unpack .../234-librtmp1_2.4+20151223.gitfa8646d.1-2_i386.deb ...
Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2) ...
Selecting previously unselected package libssh2-1:i386.
Preparing to unpack .../235-libssh2-1_1.8.0-2.1_i386.deb ...
Unpacking libssh2-1:i386 (1.8.0-2.1) ...
Selecting previously unselected package libcurl4:i386.
Preparing to unpack .../236-libcurl4_7.64.0-2_i386.deb ...
Unpacking libcurl4:i386 (7.64.0-2) ...
Selecting previously unselected package libcurl4-openssl-dev:i386.
Preparing to unpack .../237-libcurl4-openssl-dev_7.64.0-2_i386.deb ...
Unpacking libcurl4-openssl-dev:i386 (7.64.0-2) ...
Selecting previously unselected package libfontenc1:i386.
Preparing to unpack .../238-libfontenc1_1%3a1.1.3-1+b2_i386.deb ...
Unpacking libfontenc1:i386 (1:1.1.3-1+b2) ...
Selecting previously unselected package libfribidi-dev:i386.
Preparing to unpack .../239-libfribidi-dev_1.0.5-3.1_i386.deb ...
Unpacking libfribidi-dev:i386 (1.0.5-3.1) ...
Selecting previously unselected package libgraphite2-dev:i386.
Preparing to unpack .../240-libgraphite2-dev_1.3.13-7_i386.deb ...
Unpacking libgraphite2-dev:i386 (1.3.13-7) ...
Selecting previously unselected package libgs9-common.
Preparing to unpack .../241-libgs9-common_9.27~dfsg-1_all.deb ...
Unpacking libgs9-common (9.27~dfsg-1) ...
Selecting previously unselected package libijs-0.35:i386.
Preparing to unpack .../242-libijs-0.35_0.35-13_i386.deb ...
Unpacking libijs-0.35:i386 (0.35-13) ...
Selecting previously unselected package libjbig2dec0:i386.
Preparing to unpack .../243-libjbig2dec0_0.16-1_i386.deb ...
Unpacking libjbig2dec0:i386 (0.16-1) ...
Selecting previously unselected package libopenjp2-7:i386.
Preparing to unpack .../244-libopenjp2-7_2.3.0-2_i386.deb ...
Unpacking libopenjp2-7:i386 (2.3.0-2) ...
Selecting previously unselected package libpaper1:i386.
Preparing to unpack .../245-libpaper1_1.1.26_i386.deb ...
Unpacking libpaper1:i386 (1.1.26) ...
Selecting previously unselected package libgs9:i386.
Preparing to unpack .../246-libgs9_9.27~dfsg-1_i386.deb ...
Unpacking libgs9:i386 (9.27~dfsg-1) ...
Selecting previously unselected package libharfbuzz-icu0:i386.
Preparing to unpack .../247-libharfbuzz-icu0_2.3.1-1_i386.deb ...
Unpacking libharfbuzz-icu0:i386 (2.3.1-1) ...
Selecting previously unselected package libicu-dev:i386.
Preparing to unpack .../248-libicu-dev_63.1-6_i386.deb ...
Unpacking libicu-dev:i386 (63.1-6) ...
Selecting previously unselected package libharfbuzz-dev:i386.
Preparing to unpack .../249-libharfbuzz-dev_2.3.1-1_i386.deb ...
Unpacking libharfbuzz-dev:i386 (2.3.1-1) ...
Selecting previously unselected package libjbig-dev:i386.
Preparing to unpack .../250-libjbig-dev_2.1-3.1+b2_i386.deb ...
Unpacking libjbig-dev:i386 (2.1-3.1+b2) ...
Selecting previously unselected package libjpeg62-turbo-dev:i386.
Preparing to unpack .../251-libjpeg62-turbo-dev_1%3a1.5.2-2+b1_i386.deb ...
Unpacking libjpeg62-turbo-dev:i386 (1:1.5.2-2+b1) ...
Selecting previously unselected package libjpeg-dev.
Preparing to unpack .../252-libjpeg-dev_1%3a1.5.2-2_all.deb ...
Unpacking libjpeg-dev (1:1.5.2-2) ...
Selecting previously unselected package libkpathsea6:i386.
Preparing to unpack .../253-libkpathsea6_2018.20181218.49446-1_i386.deb ...
Unpacking libkpathsea6:i386 (2018.20181218.49446-1) ...
Selecting previously unselected package liblapack3:i386.
Preparing to unpack .../254-liblapack3_3.8.0-2_i386.deb ...
Unpacking liblapack3:i386 (3.8.0-2) ...
Selecting previously unselected package liblapack-dev:i386.
Preparing to unpack .../255-liblapack-dev_3.8.0-2_i386.deb ...
Unpacking liblapack-dev:i386 (3.8.0-2) ...
Selecting previously unselected package liblzma-dev:i386.
Preparing to unpack .../256-liblzma-dev_5.2.4-1_i386.deb ...
Unpacking liblzma-dev:i386 (5.2.4-1) ...
Selecting previously unselected package libmime-charset-perl.
Preparing to unpack .../257-libmime-charset-perl_1.012.2-1_all.deb ...
Unpacking libmime-charset-perl (1.012.2-1) ...
Selecting previously unselected package libncurses-dev:i386.
Preparing to unpack .../258-libncurses-dev_6.1+20181013-2_i386.deb ...
Unpacking libncurses-dev:i386 (6.1+20181013-2) ...
Selecting previously unselected package libncurses5-dev:i386.
Preparing to unpack .../259-libncurses5-dev_6.1+20181013-2_i386.deb ...
Unpacking libncurses5-dev:i386 (6.1+20181013-2) ...
Selecting previously unselected package libxft-dev:i386.
Preparing to unpack .../260-libxft-dev_2.3.2-2_i386.deb ...
Unpacking libxft-dev:i386 (2.3.2-2) ...
Selecting previously unselected package pango1.0-tools.
Preparing to unpack .../261-pango1.0-tools_1.42.4-6_i386.deb ...
Unpacking pango1.0-tools (1.42.4-6) ...
Selecting previously unselected package libpango1.0-dev:i386.
Preparing to unpack .../262-libpango1.0-dev_1.42.4-6_i386.deb ...
Unpacking libpango1.0-dev:i386 (1.42.4-6) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../263-libpaper-utils_1.1.26_i386.deb ...
Unpacking libpaper-utils (1.1.26) ...
Selecting previously unselected package libpcre2-16-0:i386.
Preparing to unpack .../264-libpcre2-16-0_10.32-5_i386.deb ...
Unpacking libpcre2-16-0:i386 (10.32-5) ...
Selecting previously unselected package libpcre2-32-0:i386.
Preparing to unpack .../265-libpcre2-32-0_10.32-5_i386.deb ...
Unpacking libpcre2-32-0:i386 (10.32-5) ...
Selecting previously unselected package libpcre2-8-0:i386.
Preparing to unpack .../266-libpcre2-8-0_10.32-5_i386.deb ...
Unpacking libpcre2-8-0:i386 (10.32-5) ...
Selecting previously unselected package libpcre2-posix0:i386.
Preparing to unpack .../267-libpcre2-posix0_10.32-5_i386.deb ...
Unpacking libpcre2-posix0:i386 (10.32-5) ...
Selecting previously unselected package libpcre2-dev:i386.
Preparing to unpack .../268-libpcre2-dev_10.32-5_i386.deb ...
Unpacking libpcre2-dev:i386 (10.32-5) ...
Selecting previously unselected package libpotrace0:i386.
Preparing to unpack .../269-libpotrace0_1.15-1_i386.deb ...
Unpacking libpotrace0:i386 (1.15-1) ...
Selecting previously unselected package libptexenc1:i386.
Preparing to unpack .../270-libptexenc1_2018.20181218.49446-1_i386.deb ...
Unpacking libptexenc1:i386 (2018.20181218.49446-1) ...
Selecting previously unselected package libreadline-dev:i386.
Preparing to unpack .../271-libreadline-dev_7.0-5_i386.deb ...
Unpacking libreadline-dev:i386 (7.0-5) ...
Selecting previously unselected package libsombok3:i386.
Preparing to unpack .../272-libsombok3_2.4.0-2_i386.deb ...
Unpacking libsombok3:i386 (2.4.0-2) ...
Selecting previously unselected package libsynctex2:i386.
Preparing to unpack .../273-libsynctex2_2018.20181218.49446-1_i386.deb ...
Unpacking libsynctex2:i386 (2018.20181218.49446-1) ...
Selecting previously unselected package libtcl8.6:i386.
Preparing to unpack .../274-libtcl8.6_8.6.9+dfsg-2_i386.deb ...
Unpacking libtcl8.6:i386 (8.6.9+dfsg-2) ...
Selecting previously unselected package libteckit0:i386.
Preparing to unpack .../275-libteckit0_2.5.8+ds2-5_i386.deb ...
Unpacking libteckit0:i386 (2.5.8+ds2-5) ...
Selecting previously unselected package libtexlua52:i386.
Preparing to unpack .../276-libtexlua52_2018.20181218.49446-1_i386.deb ...
Unpacking libtexlua52:i386 (2018.20181218.49446-1) ...
Selecting previously unselected package libtexlua53:i386.
Preparing to unpack .../277-libtexlua53_2018.20181218.49446-1_i386.deb ...
Unpacking libtexlua53:i386 (2018.20181218.49446-1) ...
Selecting previously unselected package libtexluajit2:i386.
Preparing to unpack .../278-libtexluajit2_2018.20181218.49446-1_i386.deb ...
Unpacking libtexluajit2:i386 (2018.20181218.49446-1) ...
Selecting previously unselected package libtext-unidecode-perl.
Preparing to unpack .../279-libtext-unidecode-perl_1.30-1_all.deb ...
Unpacking libtext-unidecode-perl (1.30-1) ...
Selecting previously unselected package libtiffxx5:i386.
Preparing to unpack .../280-libtiffxx5_4.0.10-4_i386.deb ...
Unpacking libtiffxx5:i386 (4.0.10-4) ...
Selecting previously unselected package libtiff-dev:i386.
Preparing to unpack .../281-libtiff-dev_4.0.10-4_i386.deb ...
Unpacking libtiff-dev:i386 (4.0.10-4) ...
Selecting previously unselected package libtiff5-dev.
Preparing to unpack .../282-libtiff5-dev_4.0.10-4_i386.deb ...
Unpacking libtiff5-dev (4.0.10-4) ...
Selecting previously unselected package libxss1:i386.
Preparing to unpack .../283-libxss1_1%3a1.2.3-1_i386.deb ...
Unpacking libxss1:i386 (1:1.2.3-1) ...
Selecting previously unselected package libtk8.6:i386.
Preparing to unpack .../284-libtk8.6_8.6.9-2_i386.deb ...
Unpacking libtk8.6:i386 (8.6.9-2) ...
Selecting previously unselected package libunicode-linebreak-perl.
Preparing to unpack .../285-libunicode-linebreak-perl_0.0.20190101-1_i386.deb ...
Unpacking libunicode-linebreak-perl (0.0.20190101-1) ...
Selecting previously unselected package libunwind8:i386.
Preparing to unpack .../286-libunwind8_1.2.1-9_i386.deb ...
Unpacking libunwind8:i386 (1.2.1-9) ...
Selecting previously unselected package libwoff1:i386.
Preparing to unpack .../287-libwoff1_1.0.2-1_i386.deb ...
Unpacking libwoff1:i386 (1.0.2-1) ...
Selecting previously unselected package libxt6:i386.
Preparing to unpack .../288-libxt6_1%3a1.1.5-1+b3_i386.deb ...
Unpacking libxt6:i386 (1:1.1.5-1+b3) ...
Selecting previously unselected package libxmu6:i386.
Preparing to unpack .../289-libxmu6_2%3a1.1.2-2+b3_i386.deb ...
Unpacking libxmu6:i386 (2:1.1.2-2+b3) ...
Selecting previously unselected package libxpm4:i386.
Preparing to unpack .../290-libxpm4_1%3a3.5.12-1_i386.deb ...
Unpacking libxpm4:i386 (1:3.5.12-1) ...
Selecting previously unselected package libxaw7:i386.
Preparing to unpack .../291-libxaw7_2%3a1.0.13-1+b2_i386.deb ...
Unpacking libxaw7:i386 (2:1.0.13-1+b2) ...
Selecting previously unselected package libxfont2:i386.
Preparing to unpack .../292-libxfont2_1%3a2.0.3-1_i386.deb ...
Unpacking libxfont2:i386 (1:2.0.3-1) ...
Selecting previously unselected package libxkbfile1:i386.
Preparing to unpack .../293-libxkbfile1_1%3a1.0.9-2+b11_i386.deb ...
Unpacking libxkbfile1:i386 (1:1.0.9-2+b11) ...
Selecting previously unselected package libxml-namespacesupport-perl.
Preparing to unpack .../294-libxml-namespacesupport-perl_1.12-1_all.deb ...
Unpacking libxml-namespacesupport-perl (1.12-1) ...
Selecting previously unselected package libxml-sax-base-perl.
Preparing to unpack .../295-libxml-sax-base-perl_1.09-1_all.deb ...
Unpacking libxml-sax-base-perl (1.09-1) ...
Selecting previously unselected package libxml-sax-perl.
Preparing to unpack .../296-libxml-sax-perl_1.00+dfsg-1_all.deb ...
Unpacking libxml-sax-perl (1.00+dfsg-1) ...
Selecting previously unselected package libxml-libxml-perl.
Preparing to unpack .../297-libxml-libxml-perl_2.0134+dfsg-1_i386.deb ...
Unpacking libxml-libxml-perl (2.0134+dfsg-1) ...
Selecting previously unselected package libxmuu1:i386.
Preparing to unpack .../298-libxmuu1_2%3a1.1.2-2+b3_i386.deb ...
Unpacking libxmuu1:i386 (2:1.1.2-2+b3) ...
Selecting previously unselected package x11proto-scrnsaver-dev.
Preparing to unpack .../299-x11proto-scrnsaver-dev_2018.4-4_all.deb ...
Unpacking x11proto-scrnsaver-dev (2018.4-4) ...
Selecting previously unselected package libxss-dev:i386.
Preparing to unpack .../300-libxss-dev_1%3a1.2.3-1_i386.deb ...
Unpacking libxss-dev:i386 (1:1.2.3-1) ...
Selecting previously unselected package libxt-dev:i386.
Preparing to unpack .../301-libxt-dev_1%3a1.1.5-1+b3_i386.deb ...
Unpacking libxt-dev:i386 (1:1.1.5-1+b3) ...
Selecting previously unselected package libxxhash0:i386.
Preparing to unpack .../302-libxxhash0_0.6.5-2_i386.deb ...
Unpacking libxxhash0:i386 (0.6.5-2) ...
Selecting previously unselected package libzzip-0-13:i386.
Preparing to unpack .../303-libzzip-0-13_0.13.62-3.2_i386.deb ...
Unpacking libzzip-0-13:i386 (0.13.62-3.2) ...
Selecting previously unselected package mpack.
Preparing to unpack .../304-mpack_1.6-8.2_i386.deb ...
Unpacking mpack (1.6-8.2) ...
Selecting previously unselected package preview-latex-style.
Preparing to unpack .../305-preview-latex-style_11.91-2_all.deb ...
Unpacking preview-latex-style (11.91-2) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../306-t1utils_1.41-3_i386.deb ...
Unpacking t1utils (1.41-3) ...
Selecting previously unselected package tcl8.6.
Preparing to unpack .../307-tcl8.6_8.6.9+dfsg-2_i386.deb ...
Unpacking tcl8.6 (8.6.9+dfsg-2) ...
Selecting previously unselected package tcl8.6-dev:i386.
Preparing to unpack .../308-tcl8.6-dev_8.6.9+dfsg-2_i386.deb ...
Unpacking tcl8.6-dev:i386 (8.6.9+dfsg-2) ...
Selecting previously unselected package texinfo.
Preparing to unpack .../309-texinfo_6.5.0.dfsg.1-4+b1_i386.deb ...
Unpacking texinfo (6.5.0.dfsg.1-4+b1) ...
Selecting previously unselected package texlive-binaries.
Preparing to unpack .../310-texlive-binaries_2018.20181218.49446-1_i386.deb ...
Unpacking texlive-binaries (2018.20181218.49446-1) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../311-xdg-utils_1.1.3-1_all.deb ...
Unpacking xdg-utils (1.1.3-1) ...
Selecting previously unselected package texlive-base.
Preparing to unpack .../312-texlive-base_2018.20190227-2_all.deb ...
Unpacking texlive-base (2018.20190227-2) ...
Selecting previously unselected package texlive-latex-base.
Preparing to unpack .../313-texlive-latex-base_2018.20190227-2_all.deb ...
Unpacking texlive-latex-base (2018.20190227-2) ...
Selecting previously unselected package texlive-extra-utils.
Preparing to unpack .../314-texlive-extra-utils_2018.20190227-2_all.deb ...
Unpacking texlive-extra-utils (2018.20190227-2) ...
Selecting previously unselected package texlive-fonts-extra.
Preparing to unpack .../315-texlive-fonts-extra_2018.20190227-2_all.deb ...
Unpacking texlive-fonts-extra (2018.20190227-2) ...
Selecting previously unselected package texlive-fonts-recommended.
Preparing to unpack .../316-texlive-fonts-recommended_2018.20190227-2_all.deb ...
Unpacking texlive-fonts-recommended (2018.20190227-2) ...
Selecting previously unselected package texlive-plain-generic.
Preparing to unpack .../317-texlive-plain-generic_2018.20190227-2_all.deb ...
Unpacking texlive-plain-generic (2018.20190227-2) ...
Selecting previously unselected package texlive-generic-recommended.
Preparing to unpack .../318-texlive-generic-recommended_2018.20190227-2_all.deb ...
Unpacking texlive-generic-recommended (2018.20190227-2) ...
Selecting previously unselected package texlive-latex-recommended.
Preparing to unpack .../319-texlive-latex-recommended_2018.20190227-2_all.deb ...
Unpacking texlive-latex-recommended (2018.20190227-2) ...
Selecting previously unselected package texlive-pictures.
Preparing to unpack .../320-texlive-pictures_2018.20190227-2_all.deb ...
Unpacking texlive-pictures (2018.20190227-2) ...
Selecting previously unselected package texlive-latex-extra.
Preparing to unpack .../321-texlive-latex-extra_2018.20190227-2_all.deb ...
Unpacking texlive-latex-extra (2018.20190227-2) ...
Selecting previously unselected package tk8.6.
Preparing to unpack .../322-tk8.6_8.6.9-2_i386.deb ...
Unpacking tk8.6 (8.6.9-2) ...
Selecting previously unselected package tk8.6-dev:i386.
Preparing to unpack .../323-tk8.6-dev_8.6.9-2_i386.deb ...
Unpacking tk8.6-dev:i386 (8.6.9-2) ...
Selecting previously unselected package x11-xkb-utils.
Preparing to unpack .../324-x11-xkb-utils_7.7+4_i386.deb ...
Unpacking x11-xkb-utils (7.7+4) ...
Selecting previously unselected package xauth.
Preparing to unpack .../325-xauth_1%3a1.0.10-1_i386.deb ...
Unpacking xauth (1:1.0.10-1) ...
Selecting previously unselected package xfonts-encodings.
Preparing to unpack .../326-xfonts-encodings_1%3a1.0.4-2_all.deb ...
Unpacking xfonts-encodings (1:1.0.4-2) ...
Selecting previously unselected package xfonts-utils.
Preparing to unpack .../327-xfonts-utils_1%3a7.7+6_i386.deb ...
Unpacking xfonts-utils (1:7.7+6) ...
Selecting previously unselected package xfonts-base.
Preparing to unpack .../328-xfonts-base_1%3a1.0.5_all.deb ...
Unpacking xfonts-base (1:1.0.5) ...
Selecting previously unselected package xserver-common.
Preparing to unpack .../329-xserver-common_2%3a1.20.3-1_all.deb ...
Unpacking xserver-common (2:1.20.3-1) ...
Selecting previously unselected package xvfb.
Preparing to unpack .../330-xvfb_2%3a1.20.3-1_i386.deb ...
Unpacking xvfb (2:1.20.3-1) ...
Setting up libgs9-common (9.27~dfsg-1) ...
Setting up libpcrecpp0v5:i386 (2:8.39-12) ...
Setting up libpipeline1:i386 (1.5.1-2) ...
Setting up libgraphite2-3:i386 (1.3.13-7) ...
Setting up liblcms2-2:i386 (2.9-3) ...
Setting up libpixman-1-0:i386 (0.36.0-1) ...
Setting up lsb-base (10.2019031300) ...
Setting up libx11-xcb1:i386 (2:1.6.7-1) ...
Setting up libpciaccess0:i386 (0.14-1) ...
Setting up systemd-sysv (241-3) ...
Setting up libxau6:i386 (1:1.0.8-1+b2) ...
Setting up libkeyutils1:i386 (1.6-6) ...
Setting up libproxy1v5:i386 (0.4.15-5) ...
Setting up libpsl5:i386 (0.20.2-2) ...
Setting up libpixman-1-dev:i386 (0.36.0-1) ...
Setting up mime-support (3.62) ...
Setting up libtexlua52:i386 (2018.20181218.49446-1) ...
Setting up libpcre16-3:i386 (2:8.39-12) ...
Setting up hicolor-icon-theme (0.17-2) ...
Setting up libbison-dev:i386 (2:3.3.2.dfsg-1) ...
Setting up java-common (0.71) ...
Setting up libdatrie1:i386 (0.2.12-2) ...
Setting up libmagic-mgc (1:5.35-4) ...
Setting up mpack (1.6-8.2) ...
Setting up libtexlua53:i386 (2018.20181218.49446-1) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libglib2.0-0:i386 (2.58.3-1) ...
Setting up libglvnd0:i386 (1.1.0-1) ...
Setting up libijs-0.35:i386 (0.35-13) ...
Setting up libtexluajit2:i386 (2018.20181218.49446-1) ...
Setting up libbrotli1:i386 (1.0.7-2) ...
Setting up libgdk-pixbuf2.0-common (2.38.1+dfsg-1) ...
Setting up x11-common (1:7.7+19) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
[....] Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix[?25l7[ ok 8[?12l[?25h.
Setting up libsensors-config (1:3.5.0-3) ...
Setting up libnghttp2-14:i386 (1.36.0-2) ...
Setting up libmagic1:i386 (1:5.35-4) ...
Setting up libsepol1-dev:i386 (2.8-1) ...
Setting up libxml-namespacesupport-perl (1.12-1) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up xkb-data (2.26-2) ...
Setting up liblzo2-2:i386 (2.10-0.1) ...
Setting up libzzip-0-13:i386 (0.13.62-3.2) ...
Setting up file (1:5.35-4) ...
Setting up libffi-dev:i386 (3.2.1-9) ...
Setting up libldap-common (2.4.47+dfsg-3) ...
Setting up libunwind8:i386 (1.2.1-9) ...
Setting up libpthread-stubs0-dev:i386 (0.4-1) ...
Setting up libjbig0:i386 (2.1-3.1+b2) ...
Setting up libpcre2-16-0:i386 (10.32-5) ...
Setting up libcolord2:i386 (1.4.3-4) ...
Setting up libicu63:i386 (63.1-6) ...
Setting up poppler-data (0.4.9-2) ...
Setting up libkrb5support0:i386 (1.17-2) ...
Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-1) ...
Setting up libdconf1:i386 (0.30.1-2) ...
Setting up libasound2-data (1.1.8-1) ...
Setting up libxml-sax-base-perl (1.09-1) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up libgraphite2-dev:i386 (1.3.13-7) ...
Setting up libfontenc1:i386 (1:1.1.3-1+b2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libpcre2-32-0:i386 (10.32-5) ...
Setting up libglib2.0-data (2.58.3-1) ...
Setting up libexpat1-dev:i386 (2.2.6-1) ...
Setting up libjpeg62-turbo:i386 (1:1.5.2-2+b1) ...
Setting up libx11-data (2:1.6.7-1) ...
Setting up libjpeg62-turbo-dev:i386 (1:1.5.2-2+b1) ...
Setting up libepoxy0:i386 (1.5.3-0.1) ...
Setting up libnspr4:i386 (2:4.20-1) ...
Setting up libjbig2dec0:i386 (0.16-1) ...
Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2) ...
Setting up libteckit0:i386 (2.5.8+ds2-5) ...
Setting up bash-completion (1:2.8-6) ...
Setting up uuid-dev:i386 (2.33.1-0.1) ...
Setting up libavahi-common-data:i386 (0.7-4+b1) ...
Setting up libncurses6:i386 (6.1+20181013-2) ...
Setting up libdbus-1-3:i386 (1.12.12-1) ...
Setting up dbus (1.12.12-1) ...
Running in chroot, ignoring request.
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libsigsegv2:i386 (2.12-2) ...
Setting up xfonts-encodings (1:1.0.4-2) ...
Setting up libfribidi0:i386 (1.0.5-3.1) ...
Setting up t1utils (1.41-3) ...
Setting up libpng16-16:i386 (1.6.36-5) ...
Setting up libpcre32-3:i386 (2:8.39-12) ...
Setting up libtcl8.6:i386 (8.6.9+dfsg-2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up libwebp6:i386 (0.6.1-2) ...
Setting up icu-devtools (63.1-6) ...
Setting up pkg-config (0.29-6) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libpcsclite1:i386 (1.8.24-1) ...
Setting up libsensors5:i386 (1:3.5.0-3) ...
Setting up libpcre2-8-0:i386 (10.32-5) ...
Setting up libk5crypto3:i386 (1.17-2) ...
Setting up libglapi-mesa:i386 (18.3.4-2) ...
Setting up libkpathsea6:i386 (2018.20181218.49446-1) ...
Setting up libsasl2-2:i386 (2.1.27+dfsg-1) ...
Setting up libgfortran5:i386 (8.3.0-6) ...
Setting up liblzma-dev:i386 (5.2.4-1) ...
Setting up libgif7:i386 (5.1.4-3) ...
Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-1) ...
Setting up libatk1.0-data (2.30.0-2) ...
Setting up sensible-utils (0.0.12) ...
Setting up libxshmfence1:i386 (1.3-1) ...
Setting up libmime-charset-perl (1.012.2-1) ...
Setting up libxxhash0:i386 (0.6.5-2) ...
Setting up libuchardet0:i386 (0.0.6-3) ...
Setting up libasound2:i386 (1.1.8-1) ...
Setting up libpam-systemd:i386 (241-3) ...
Setting up fonts-lmodern (2.004.5-6) ...
Setting up libopenjp2-7:i386 (2.3.0-2) ...
Setting up libthai-data (0.1.28-2) ...
Setting up libgirepository-1.0-1:i386 (1.58.3-2) ...
Setting up libssh2-1:i386 (1.8.0-2.1) ...
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up libjson-glib-1.0-common (1.4.4-2) ...
Setting up libatk1.0-0:i386 (2.30.0-2) ...
Setting up libkrb5-3:i386 (1.17-2) ...
Setting up libtiff5:i386 (4.0.10-4) ...
Setting up libwayland-egl1:i386 (1.16.0-1) ...
Setting up libmpdec2:i386 (2.4.2-2) ...
Setting up glib-networking-common (2.58.0-2) ...
Setting up libtext-unidecode-perl (1.30-1) ...
Setting up openssl (1.1.1b-2) ...
Setting up libbsd0:i386 (0.9.1-2) ...
Setting up libdrm-common (2.4.97-1) ...
Setting up libelf1:i386 (0.176-1) ...
Setting up readline-common (7.0-5) ...
Setting up libicu-dev:i386 (63.1-6) ...
Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ...
Setting up xdg-utils (1.1.3-1) ...
Setting up libsynctex2:i386 (2018.20181218.49446-1) ...
Setting up libreadline7:i386 (7.0-5) ...
Setting up libtiffxx5:i386 (4.0.10-4) ...
Setting up libbz2-dev:i386 (1.0.6-9) ...
Setting up libxkbcommon0:i386 (0.8.2-1) ...
Setting up libpotrace0:i386 (1.15-1) ...
Setting up libwayland-client0:i386 (1.16.0-1) ...
Setting up x11proto-dev (2018.4-4) ...
Setting up libfile-stripnondeterminism-perl (1.1.2-1) ...
Setting up glib-networking-services (2.58.0-2) ...
Setting up libblkid-dev:i386 (2.33.1-0.1) ...
Setting up libgfortran-8-dev:i386 (8.3.0-6) ...
Setting up libice6:i386 (2:1.0.9-2) ...
Setting up libxdmcp6:i386 (1:1.1.2-3) ...
Setting up libpython3.7-stdlib:i386 (3.7.3~rc1-1) ...
Setting up tcl8.6 (8.6.9+dfsg-2) ...
Setting up libncurses-dev:i386 (6.1+20181013-2) ...
Setting up libxcb1:i386 (1.13.1-2) ...
Setting up libxau-dev:i386 (1:1.0.8-1+b2) ...
Setting up libwoff1:i386 (1.0.2-1) ...
Setting up libice-dev:i386 (2:1.0.9-2) ...
Setting up libtool (2.4.6-9) ...
Setting up libxcb-render0:i386 (1.13.1-2) ...
Setting up libpcre3-dev:i386 (2:8.39-12) ...
Setting up gfortran-8 (8.3.0-6) ...
Setting up libfribidi-dev:i386 (1.0.5-3.1) ...
Setting up libxcb-glx0:i386 (1.13.1-2) ...
Setting up tcl8.6-dev:i386 (8.6.9+dfsg-2) ...
Setting up libedit2:i386 (3.1-20181209-1) ...
Setting up libpng-dev:i386 (1.6.36-5) ...
Setting up libavahi-common3:i386 (0.7-4+b1) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up libjbig-dev:i386 (2.1-3.1+b2) ...
Setting up libglib2.0-bin (2.58.3-1) ...
Setting up libldap-2.4-2:i386 (2.4.47+dfsg-3) ...
Setting up m4 (1.4.18-2) ...
Setting up libnss3:i386 (2:3.42.1-1) ...
Setting up libxcb-shm0:i386 (1.13.1-2) ...
Setting up libreadline-dev:i386 (7.0-5) ...
Setting up gfortran (4:8.3.0-1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libjson-glib-1.0-0:i386 (1.4.4-2) ...
Setting up libpython2.7-stdlib:i386 (2.7.16-2) ...
Setting up libxcb-present0:i386 (1.13.1-2) ...
Setting up libthai0:i386 (0.1.28-2) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up dbus-user-session (1.12.12-1) ...
Setting up libxdmcp-dev:i386 (1:1.1.2-3) ...
Setting up libblas3:i386 (3.8.0-2) ...
update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode
Setting up libptexenc1:i386 (2018.20181218.49446-1) ...
Setting up libpcre2-posix0:i386 (10.32-5) ...
Setting up libfreetype6:i386 (2.9.1-3) ...
Setting up libtiff-dev:i386 (4.0.10-4) ...
Setting up libxcb-sync1:i386 (1.13.1-2) ...
Setting up x11proto-core-dev (2018.4-4) ...
Setting up shared-mime-info (1.10-1) ...
Setting up bsdmainutils (11.1.2+b1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:i386 (1.17-2) ...
Setting up libcroco3:i386 (0.6.12-3) ...
Setting up ucf (3.0038+nmu1) ...
Setting up gir1.2-glib-2.0:i386 (1.58.3-2) ...
Setting up autoconf (2.69-11) ...
Setting up libxcb-dri2-0:i386 (1.13.1-2) ...
Setting up x11proto-xext-dev (2018.4-4) ...
Setting up libdrm2:i386 (2.4.97-1) ...
Setting up dwz (0.12-3) ...
Setting up groff-base (1.22.4-3) ...
Setting up libwayland-cursor0:i386 (1.16.0-1) ...
Setting up libncurses5-dev:i386 (6.1+20181013-2) ...
Setting up bison (2:3.3.2.dfsg-1) ...
update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode
Setting up libcurl4:i386 (7.64.0-2) ...
Setting up libllvm7:i386 (1:7.0.1-8) ...
Setting up libx11-6:i386 (2:1.6.7-1) ...
Setting up libharfbuzz0b:i386 (2.3.1-1) ...
Setting up libxkbfile1:i386 (1:1.0.9-2+b11) ...
Setting up x11proto-scrnsaver-dev (2018.4-4) ...
Setting up libxcomposite1:i386 (1:0.4.4-2) ...
Setting up libsm6:i386 (2:1.2.3-1) ...
Setting up libxfont2:i386 (1:2.0.3-1) ...
Setting up libavahi-client3:i386 (0.7-4+b1) ...
Setting up libmount-dev:i386 (2.33.1-0.1) ...
Setting up libxmuu1:i386 (2:1.1.2-2+b3) ...
Setting up libblas-dev:i386 (3.8.0-2) ...
update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode
Setting up libpython3-stdlib:i386 (3.7.2-1) ...
Setting up libdrm-amdgpu1:i386 (2.4.97-1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libxcb-dri3-0:i386 (1.13.1-2) ...
Setting up libpaper1:i386 (1.1.26) ...

Creating config file /etc/papersize with new version
Setting up python3.7 (3.7.3~rc1-1) ...
Setting up liblapack3:i386 (3.8.0-2) ...
update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode
Setting up libdrm-nouveau2:i386 (2.4.97-1) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libharfbuzz-icu0:i386 (2.3.1-1) ...
Setting up libxcb1-dev:i386 (1.13.1-2) ...
Setting up libxpm4:i386 (1:3.5.12-1) ...
Setting up libpcre2-dev:i386 (10.32-5) ...
Setting up python2.7 (2.7.16-2) ...
Setting up libxrender1:i386 (1:0.9.10-1) ...
Setting up libpython2-stdlib:i386 (2.7.16-1) ...
Setting up libsombok3:i386 (2.4.0-2) ...
Setting up libsm-dev:i386 (2:1.2.3-1) ...
Setting up libselinux1-dev:i386 (2.8-1+b1) ...
Setting up libdrm-radeon1:i386 (2.4.97-1) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up libdrm-intel1:i386 (2.4.97-1) ...
Setting up libgl1-mesa-dri:i386 (18.3.4-2) ...
Setting up libx11-dev:i386 (2:1.6.7-1) ...
Setting up libxext6:i386 (2:1.3.3-1+b2) ...
Setting up libtiff5-dev (4.0.10-4) ...
Setting up dconf-service (0.30.1-2) ...
Setting up python3 (3.7.2-1) ...
Setting up libharfbuzz-gobject0:i386 (2.3.1-1) ...
Setting up libpaper-utils (1.1.26) ...
Setting up libatspi2.0-0:i386 (2.30.0-7) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up man-db (2.8.5-2) ...
Building database of manual pages ...
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libxml-sax-perl (1.00+dfsg-1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...

Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up gir1.2-harfbuzz-0.0:i386 (2.3.1-1) ...
Setting up python2 (2.7.16-1) ...
Setting up libfreetype6-dev:i386 (2.9.1-3) ...
Setting up libxxf86vm1:i386 (1:1.1.4-1+b2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up tex-common (6.11) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up libatk-bridge2.0-0:i386 (2.30.0-5) ...
Setting up libxcb-shm0-dev:i386 (1.13.1-2) ...
Setting up libpython-stdlib:i386 (2.7.16-1) ...
Setting up xfonts-base (1:1.0.5) ...
Setting up libxfixes3:i386 (1:5.0.3-1) ...
Setting up libcurl4-openssl-dev:i386 (7.64.0-2) ...
Setting up libunicode-linebreak-perl (0.0.20190101-1) ...
Setting up libgdk-pixbuf2.0-0:i386 (2.38.1+dfsg-1) ...
Setting up libxinerama1:i386 (2:1.1.4-2) ...
Setting up liblapack-dev:i386 (3.8.0-2) ...
update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode
Setting up libxrandr2:i386 (2:1.5.1-1) ...
Setting up libxcb-render0-dev:i386 (1.13.1-2) ...
Setting up libxt6:i386 (1:1.1.5-1+b3) ...
Setting up libxext-dev:i386 (2:1.3.3-1+b2) ...
Setting up libxml-libxml-perl (2.0134+dfsg-1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libcups2:i386 (2.2.10-6) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libxss1:i386 (1:1.2.3-1) ...
Setting up libfontconfig1:i386 (2.13.1-2) ...
Setting up python3-lib2to3 (3.7.3~rc1-1) ...
Setting up python (2.7.16-1) ...
Setting up libxrender-dev:i386 (1:0.9.10-1) ...
Setting up python3-distutils (3.7.3~rc1-1) ...
Setting up libglib2.0-dev-bin (2.58.3-1) ...
Setting up gtk-update-icon-cache (3.24.5-1) ...
Setting up fontconfig (2.13.1-2) ...
Regenerating fonts cache... done.
Setting up libxft2:i386 (2.3.2-2) ...
Setting up libxmu6:i386 (2:1.1.2-2+b3) ...
Setting up libfontconfig1-dev:i386 (2.13.1-2) ...
Setting up libxdamage1:i386 (1:1.1.4-3+b3) ...
Setting up libxi6:i386 (2:1.7.9-1) ...
Setting up dconf-gsettings-backend:i386 (0.30.1-2) ...
Setting up libxtst6:i386 (2:1.2.3-1) ...
Setting up po-debconf (1.0.21) ...
Setting up preview-latex-style (11.91-2) ...
Setting up libtk8.6:i386 (8.6.9-2) ...
Setting up libxcursor1:i386 (1:1.1.15-2) ...
Setting up libpango-1.0-0:i386 (1.42.4-6) ...
Setting up libxaw7:i386 (2:1.0.13-1+b2) ...
Setting up libxss-dev:i386 (1:1.2.3-1) ...
Setting up libcairo2:i386 (1.16.0-4) ...
Setting up libcupsimage2:i386 (2.2.10-6) ...
Setting up libglib2.0-dev:i386 (2.58.3-1) ...
Setting up libxt-dev:i386 (1:1.1.5-1+b3) ...
Setting up texinfo (6.5.0.dfsg.1-4+b1) ...
Running mktexlsr. This may take some time. ... done.
Setting up libcairo-gobject2:i386 (1.16.0-4) ...
Setting up libpangoft2-1.0-0:i386 (1.42.4-6) ...
Setting up libgtk-3-common (3.24.5-1) ...
Setting up libpangocairo-1.0-0:i386 (1.42.4-6) ...
Setting up libxft-dev:i386 (2.3.2-2) ...
Setting up libcairo-script-interpreter2:i386 (1.16.0-4) ...
Setting up gsettings-desktop-schemas (3.28.1-1) ...
Setting up tk8.6 (8.6.9-2) ...
Setting up libharfbuzz-dev:i386 (2.3.1-1) ...
Setting up gir1.2-freedesktop:i386 (1.58.3-2) ...
Setting up libglx-mesa0:i386 (18.3.4-2) ...
Setting up libgs9:i386 (9.27~dfsg-1) ...
Setting up libpangoxft-1.0-0:i386 (1.42.4-6) ...
Setting up libglx0:i386 (1.1.0-1) ...
Setting up x11-xkb-utils (7.7+4) ...
Setting up pango1.0-tools (1.42.4-6) ...
Setting up librsvg2-2:i386 (2.44.10-2.1) ...
Setting up gir1.2-pango-1.0:i386 (1.42.4-6) ...
Setting up libgl1:i386 (1.1.0-1) ...
Setting up librsvg2-common:i386 (2.44.10-2.1) ...
Setting up tk8.6-dev:i386 (8.6.9-2) ...
Setting up texlive-binaries (2018.20181218.49446-1) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Setting up libcairo2-dev:i386 (1.16.0-4) ...
Setting up xserver-common (2:1.20.3-1) ...
Setting up glib-networking:i386 (2.58.0-2) ...
Setting up texlive-base (2018.20190227-2) ...
tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex
tl-paper: setting paper size for dvipdfmx to letter: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for dvips to letter: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for pdftex to letter: /var/lib/texmf/tex/generic/config/pdftexconfig.tex
tl-paper: setting paper size for xdvi to letter: /var/lib/texmf/xdvi/XDvi-paper
Setting up libsoup2.4-1:i386 (2.64.2-2) ...
Setting up xvfb (2:1.20.3-1) ...
Setting up texlive-plain-generic (2018.20190227-2) ...
Setting up texlive-latex-base (2018.20190227-2) ...
Setting up adwaita-icon-theme (3.30.1-1) ...
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 texlive-extra-utils (2018.20190227-2) ...
Setting up texlive-fonts-extra (2018.20190227-2) ...
Setting up libpango1.0-dev:i386 (1.42.4-6) ...
Setting up texlive-latex-recommended (2018.20190227-2) ...
Setting up texlive-generic-recommended (2018.20190227-2) ...
Setting up texlive-pictures (2018.20190227-2) ...
Setting up texlive-fonts-recommended (2018.20190227-2) ...
Setting up libsoup-gnome2.4-1:i386 (2.64.2-2) ...
Setting up librest-0.7-0:i386 (0.8.1-1) ...
Setting up libgtk-3-0:i386 (3.24.5-1) ...
Setting up texlive-latex-extra (2018.20190227-2) ...
Setting up default-jre-headless (2:1.11-71) ...
Setting up openjdk-11-jre-headless:i386 (11.0.3+1-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
OpenJDK Client VM warning: Ignoring option PermSize; support was removed in 8.0
Setting up debhelper (12.1.1) ...
Setting up openjdk-11-jre:i386 (11.0.3+1-1) ...
Setting up openjdk-11-jdk-headless:i386 (11.0.3+1-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jre (2:1.11-71) ...
Setting up dh-autoreconf (19) ...
Setting up default-jdk-headless (2:1.11-71) ...
Setting up dh-strip-nondeterminism (1.1.2-1) ...
Setting up openjdk-11-jdk:i386 (11.0.3+1-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up ca-certificates-java (20190405) ...
head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:QuoVadis_Root_CA.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:EC-ACC.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:LuxTrust_Global_Root_2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:Certigna.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:EE_Certification_Centre_Root_CA.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:SecureTrust_CA.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:Izenpe.com.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:ACCVRAIZ1.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:Secure_Global_CA.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:AffirmTrust_Commercial.pem
done.
Setting up default-jdk (2:1.11-71) ...
Processing triggers for systemd (241-3) ...
Processing triggers for libc-bin (2.28-10) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...

done.
done.
Processing triggers for libgdk-pixbuf2.0-0:i386 (2.38.1+dfsg-1) ...
Processing triggers for tex-common (6.11) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  libfakeroot
The following NEW packages will be installed:
  fakeroot libfakeroot
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/134 kB of archives.
After this operation, 369 kB of additional disk space will be used.
Selecting previously unselected package libfakeroot:i386.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 125633 files and directories currently installed.)
Preparing to unpack .../libfakeroot_1.23-1_i386.deb ...
Unpacking libfakeroot:i386 (1.23-1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.23-1_i386.deb ...
Unpacking fakeroot (1.23-1) ...
Setting up libfakeroot:i386 (1.23-1) ...
Setting up fakeroot (1.23-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Processing triggers for man-db (2.8.5-2) ...
Processing triggers for libc-bin (2.28-10) ...
I: Copying back the cached apt archive contents
I: new cache content 'libpcre2-8-0_10.32-5_i386.deb' added
I: new cache content 'libpcre2-dev_10.32-5_i386.deb' added
I: new cache content 'libpcre2-posix0_10.32-5_i386.deb' added
I: new cache content 'libpcre2-32-0_10.32-5_i386.deb' added
I: Building the package
I: Running cd /build/r-base-3.6.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc  -sa
dpkg-buildpackage: info: source package r-base
dpkg-buildpackage: info: source version 3.6.1-2~bustercran.0
dpkg-buildpackage: info: source distribution buster-cran
dpkg-buildpackage: info: source changed by Johannes Ranke <jranke@uni-bremen.de>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 fakeroot debian/rules clean
*** clean ***
dh_testdir
dh_testroot
rm -f	configure-stamp \
	build-stamp build-indep-stamp build-arch-stamp \
	make-stamp make-arch-stamp make-indep-stamp \
	install-indep-stamp install-arch-stamp \
	check-stamp
[ ! -f Makefile ] || /usr/bin/make distclean
rm -f `find . -name "*~"`
rm -rf debian/tmp debian/files* core debian/substvars
rm -f doc/html/function.html doc/html/packages.html
rm -f modules/*.so src/unix/Rscript
dh_clean
 dpkg-source -b .
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building r-base using existing ./r-base_3.6.1.orig.tar.gz
dpkg-source: info: building r-base in r-base_3.6.1-2~bustercran.0.debian.tar.xz
dpkg-source: info: building r-base in r-base_3.6.1-2~bustercran.0.dsc
 debian/rules build
*** configure ***
#automake
#autoconf
dh_testdir
R_SHELL=/bin/bash				\
        mkdir_p="/bin/mkdir -p"                         \
MKDIR_P="/bin/mkdir -p"                         \
R_TEXI2DVICMD=emulation				\
R_PAPERSIZE=letter				\
R_BROWSER=xdg-open				\
R_BZIPCMD=/bin/bzip2				\
R_GZIPCMD="/bin/gzip -n"			\
PAGER=/usr/bin/pager				\
PERL=/usr/bin/perl				\
JAVA_HOME=/usr/lib/jvm/default-java             \
R_UNZIPCMD=/usr/bin/unzip			\
R_ZIPCMD=/usr/bin/zip				\
R_PRINTCMD=/usr/bin/lpr				\
TAR=/bin/tar					\
LIBnn=lib					\
AWK=/usr/bin/awk                                \
DD=/bin/dd					\
GREP=/bin/grep					\
FGREP="/bin/grep -F"				\
EGREP="/bin/grep -E"				\
SED=/bin/sed					\
GETWD="/bin/pwd"				\
CC="gcc -std=gnu99"					\
CXX=g++						\
F77=gfortran					\
FC=gfortran					\
CFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"				\
CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"				\
FFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong"				\
FCFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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 i686-linux-gnu
configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking whether ln -s works... yes
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for /usr/bin/pager... /usr/bin/pager
checking for /bin/tar... /bin/tar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for texi2any... /usr/bin/texi2any
checking whether texi2any version is at least 5.1... yes
checking for ginstall-info... no
checking for install-info... no
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... found zi4.sty
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip -n
checking for bzip2... /bin/bzip2
using default browser ... xdg-open
checking for acroread... no
checking for acroread4... no
checking for xdg-open... /usr/bin/xdg-open
checking for working aclocal... found
checking for working autoconf... found
checking for working autoheader... found
checking for bison... bison -y
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc -std=gnu99 needs -traditional... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... gcc -std=gnu99 -E
looking for a modern Fortran compiler
checking whether we are using the GNU Fortran 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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g can compile C++ code... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc -std=gnu99 accepts -fvisibility... yes
checking whether g++ accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking whether g++ can compile ObjC++... no
checking whether  can compile ObjC++... no
checking for Objective C++ compiler... no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... /usr/bin/awk
checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... yes
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking for tilde_expand_word... 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 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... 12
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes
checking for gcc -std=gnu99 option to support OpenMP... -fopenmp
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran...  -L/usr/lib/gcc/i686-linux-gnu/8 -L/usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/8/../../.. -lgfortran -lm -lquadmath
checking how to get verbose linking output from gcc -std=gnu99... -v
checking for C libraries of gcc -std=gnu99...  -L/usr/lib/gcc/i686-linux-gnu/8 -L/usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/8/../../.. -lgcc_s
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking whether gfortran appends underscores to external names... yes
checking whether gfortran appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether gfortran and gcc -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 whether we can compute ObjC Make dependencies... no
checking if need -fno-optimize-sibling-calls for gfortran... yes
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 g++ -std=gnu++11 option to support OpenMP... -fopenmp
checking for option providing pthread_kill... none required
checking whether POSIX threads are supported... 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 sgemm_ in -lopenblas... 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 pcre2.h usability... yes
checking pcre2.h presence... yes
checking for pcre2.h... yes
checking for pcre2_compile_8 in -lpcre2-8... yes
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 7.64.0
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 for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for gfortran option to support OpenMP... (cached) -fopenmp
checking whether NLS is requested... yes

Configuring src/extra/intl directory
checking for a 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... 3.3.2, ok
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking 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/javareconf
config.status: creating src/scripts/mkinstalldirs
config.status: creating src/scripts/pager
config.status: creating src/scripts/rtags
config.status: creating src/unix/Makefile
config.status: creating tests/Makefile
config.status: creating tests/Embedding/Makefile
config.status: creating tests/Examples/Makefile
config.status: creating tools/Makefile
config.status: creating src/include/config.h
config.status: executing libtool commands
config.status: executing stamp-h commands
configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib

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

  Source directory:            .
  Installation directory:      /usr

  C compiler:                  gcc -std=gnu99  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  Fortran fixed-form compiler: gfortran -fno-optimize-sibling-calls -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong

  Default C++ compiler:        g++ -std=gnu++11  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
  Fortran free-form compiler:  gfortran -fno-optimize-sibling-calls -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"			\
		CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g"			\
		FFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong"			\
		FCFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong"			\
		CC="gcc -std=gnu99"				\
		CXX=g++			\
		F77=gfortran			\
		LDFLAGS="-Wl,-z,relro"			\
		PKG_BUILT_STAMP=""""	\
		R_GZIPCMD="/bin/gzip -n"		\
		R
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/m4'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/m4'
make[2]: Entering directory '/build/r-base-3.6.1/tools'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tools'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/html'
make[3]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/etc'
make[2]: Leaving directory '/build/r-base-3.6.1/etc'
make[2]: Entering directory '/build/r-base-3.6.1/share'
make[2]: Leaving directory '/build/r-base-3.6.1/share'
make[2]: Entering directory '/build/r-base-3.6.1/src'
make[3]: Entering directory '/build/r-base-3.6.1/src/scripts'
creating src/scripts/R.fe
make[4]: Entering directory '/build/r-base-3.6.1/src/scripts'
mkdir -p -- ../../bin
make[4]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Entering directory '/build/r-base-3.6.1/src/include'
mkdir -p -- ../../include
make[4]: Entering directory '/build/r-base-3.6.1/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[4]: Leaving directory '/build/r-base-3.6.1/src/include/R_ext'
make[3]: Leaving directory '/build/r-base-3.6.1/src/include'
make[3]: Entering directory '/build/r-base-3.6.1/src/extra'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
making regcomp.d from regcomp.c
making regerror.d from regerror.c
making regexec.d from regexec.c
making tre-ast.d from tre-ast.c
making tre-compile.d from tre-compile.c
making tre-match-approx.d from tre-match-approx.c
making tre-match-backtrack.d from tre-match-backtrack.c
making tre-match-parallel.d from tre-match-parallel.c
making tre-mem.d from tre-mem.c
making tre-parse.d from tre-parse.c
making tre-stack.d from tre-stack.c
making xmalloc.d from xmalloc.c
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c xmalloc.c -o xmalloc.o
ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o
ranlib libtre.a
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[3]: Leaving directory '/build/r-base-3.6.1/src/extra'
make[3]: Entering directory '/build/r-base-3.6.1/src/appl'
making integrate.d from integrate.c
making interv.d from interv.c
making maxcol.d from maxcol.c
making optim.d from optim.c
making pretty.d from pretty.c
making uncmin.d from uncmin.c
make[4]: Entering directory '/build/r-base-3.6.1/src/appl'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uncmin.c -o uncmin.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dchdc.f -o dchdc.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dpbfa.f -o dpbfa.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dpbsl.f -o dpbsl.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dpoco.f -o dpoco.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dpodi.f -o dpodi.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dpofa.f -o dpofa.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dposl.f -o dposl.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dqrdc.f -o dqrdc.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dqrls.f -o dqrls.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dqrsl.f -o dqrsl.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dqrutl.f -o dqrutl.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dsvdc.f -o dsvdc.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dtrco.f -o dtrco.o
gfortran -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c dtrsl.f -o dtrsl.o
ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o 
ranlib libappl.a
make[4]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Entering directory '/build/r-base-3.6.1/src/nmath'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
make[4]: Entering directory '/build/r-base-3.6.1/src/nmath'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signrank.c -o signrank.o
ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
ranlib libnmath.a
make[4]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Entering directory '/build/r-base-3.6.1/src/unix'
config.status: creating src/unix/Makefile
making Rembedded.d from Rembedded.c
making dynload.d from dynload.c
making system.d from system.c
making sys-unix.d from sys-unix.c
making sys-std.d from sys-std.c
making X11.d from X11.c
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c X11.c -o X11.o
ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o
ranlib libunix.a
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/build/r-base-3.6.1"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Entering directory '/build/r-base-3.6.1/src/main'
config.status: creating src/main/Makefile
making CommandLineArgs.d from CommandLineArgs.c
making Rdynload.d from Rdynload.c
making Renviron.d from Renviron.c
making RNG.d from RNG.c
making agrep.d from agrep.c
making altclasses.d from altclasses.c
making altrep.d from altrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making radixsort.d from radixsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making g_alab_her.d from g_alab_her.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making g_her_glyph.d from g_her_glyph.c
making Rmain.d from Rmain.c
making alloca.d from alloca.c
making mkdtemp.d from mkdtemp.c
making strdup.d from strdup.c
making strncasecmp.d from strncasecmp.c
make[4]: Entering directory '/build/r-base-3.6.1/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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c altclasses.c -o altclasses.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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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 -fno-optimize-sibling-calls -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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 altclasses.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 -lquadmath   -lreadline  -lpcre2-8 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
mkdir -p -- /build/r-base-3.6.1/bin/exec
mkdir -p -- /build/r-base-3.6.1/lib
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmain.c -o Rmain.o
gcc -std=gnu99 -Wl,--export-dynamic -fopenmp  -L"../../lib" -Wl,-z,relro -o R.bin Rmain.o  -lR 
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Entering directory '/build/r-base-3.6.1/src/modules'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
making Rhttpd.d from Rhttpd.c
making Rsock.d from Rsock.c
making internet.d from internet.c
making libcurl.d from libcurl.c
making nanoftp.d from nanoftp.c
making nanohttp.d from nanohttp.c
making sock.d from sock.c
making sockconn.d from sockconn.c
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include   -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fvisibility=hidden -c sockconn.c -o sockconn.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR  
make[6]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
mkdir -p -- /build/r-base-3.6.1/modules
make[6]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
making Lapack.d from Lapack.c
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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 -lquadmath
make[6]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[6]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
making devX11.d from devX11.c
making rotated.d from rotated.c
making rbitmap.d from rbitmap.c
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devX11.c -o devX11.o
gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rotated.c -o rotated.o
gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/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=/build/r-base-3.6.1=. -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/i386-linux-gnu -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dataentry.c -o dataentry.o
gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt  -lR -lm 
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[3]: Leaving directory '/build/r-base-3.6.1/src/modules'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
mkdir -p -- ../../library
make[4]: Entering directory '/build/r-base-3.6.1/src/library/profile'
building system startup profile
mkdir -p -- ../../../library/base/R
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/profile'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/translations'
building package 'translations'
mkdir -p -- ../../../library/translations
make[5]: Entering directory '/build/r-base-3.6.1/src/library/translations'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
building package 'base'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/base'
mkdir -p -- ../../../library/base/demo
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
building package 'tools'
mkdir -p -- ../../../library/tools
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
mkdir -p -- ../../../library/tools/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramRd.c -o gramRd.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
mkdir -p -- ../../../../library/tools/libs
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
building package 'compiler'
mkdir -p -- ../../../library/compiler
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
mkdir -p -- ../../../library/compiler/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
byte-compiling package 'compiler'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
byte-compiling package 'base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
byte-compiling package 'tools'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/utils'
building package 'utils'
mkdir -p -- ../../../library/utils
mkdir -p -- ../../../library/utils/doc
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
mkdir -p -- ../../../library/utils/R
mkdir -p -- ../../../library/utils/Sweave
mkdir -p -- ../../../library/utils/misc
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[6]: Entering directory '/build/r-base-3.6.1/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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
mkdir -p -- ../../../../library/utils/libs
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
byte-compiling package 'utils'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
mkdir -p -- ../../../library/grDevices/R
mkdir -p -- ../../../library/grDevices/afm
mkdir -p -- ../../../library/grDevices/enc
mkdir -p -- ../../../library/grDevices/icc
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[6]: Entering directory '/build/r-base-3.6.1/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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devQuartz.c -o devQuartz.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
mkdir -p -- ../../../../library/grDevices/libs
make[8]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
making cairoBM.d from cairoBM.c
make[9]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: Entering directory '/build/r-base-3.6.1/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/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../../../src/modules/X11  -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cairoBM.c -o cairoBM.o
gcc -std=gnu99 -shared -L"../../../../../lib" -Wl,-z,relro -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm 
make[10]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
byte-compiling package 'grDevices'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
building package 'graphics'
mkdir -p -- ../../../library/graphics
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
mkdir -p -- ../../../library/graphics/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[6]: Entering directory '/build/r-base-3.6.1/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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stem.c -o stem.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
mkdir -p -- ../../../../library/graphics/libs
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
byte-compiling package 'graphics'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats'
building package 'stats'
mkdir -p -- ../../../library/stats
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
mkdir -p -- ../../../library/stats/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making 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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c influence.c -o influence.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c bsplvd.f -o bsplvd.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c bvalue.f -o bvalue.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c bvalus.f -o bvalus.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c loessf.f -o loessf.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c ppr.f -o ppr.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c qsbart.f -o qsbart.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c sgram.f -o sgram.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c sinerp.f -o sinerp.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c sslvrg.f -o sslvrg.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c stxwx.f -o stxwx.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c hclust.f -o hclust.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c kmns.f -o kmns.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c eureka.f -o eureka.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -c stl.f -o stl.o
gfortran -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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 -lquadmath -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
byte-compiling package 'stats'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[5]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
mkdir -p -- ../../../../library/methods/libs
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
byte-compiling 'methods'
initializing class and method definitions ... done
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
mkdir -p -- ../../../library/grid/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making matrix.d from matrix.c
making register.d from register.c
making state.d from state.c
making unit.d from unit.c
making util.d from util.c
making viewport.d from viewport.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG    -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c viewport.c -o viewport.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
mkdir -p -- ../../../../library/grid/libs
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
byte-compiling package 'grid'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/splines'
building package 'splines'
mkdir -p -- ../../../library/splines
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
mkdir -p -- ../../../library/splines/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
making splines.d from splines.c
gcc -std=gnu99 -I"../../../../include" -DNDEBUG    -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
mkdir -p -- ../../../../library/splines/libs
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
byte-compiling package 'splines'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
mkdir -p -- ../../../library/stats4/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
byte-compiling package 'stats4'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
gcc -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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/i386-linux-gnu -ltcl8.6 -L/usr/lib/i386-linux-gnu -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
mkdir -p -- ../../../../library/tcltk/libs
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
byte-compiling package 'tcltk'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
building package 'parallel'
mkdir -p -- ../../../library/parallel
mkdir -p -- ../../../library/parallel/doc
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
mkdir -p -- ../../../library/parallel/R
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[6]: Entering directory '/build/r-base-3.6.1/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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fork.c -o fork.o
gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR
make[7]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
mkdir -p -- ../../../../library/parallel/libs
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
byte-compiling package 'parallel'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src'
make[2]: Entering directory '/build/r-base-3.6.1/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tests'
you should 'make docs' now ...
make[1]: Leaving directory '/build/r-base-3.6.1'
(cd src/nmath/standalone;				\
	/usr/bin/make	CFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"		\
		CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"	\
		FFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -D_REENTRANT"	\
		CC="gcc -std=gnu99"				\
		CXX=g++			\
		F77=gfortran			\
		R_GZIPCMD="/bin/gzip -n"		\
		libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.1 \
		shared static )
make[1]: Entering directory '/build/r-base-3.6.1/src/nmath/standalone'
(cd ../../include; /usr/bin/make Rmath.h)
make[2]: Entering directory '/build/r-base-3.6.1/src/include'
make[2]: 'Rmath.h' is up to date.
make[2]: Leaving directory '/build/r-base-3.6.1/src/include'
Copying source files
make[2]: Entering directory '/build/r-base-3.6.1/src/nmath/standalone'
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
making std_unif.d from std_unif.c
make[2]: Leaving directory '/build/r-base-3.6.1/src/nmath/standalone'
make[2]: Entering directory '/build/r-base-3.6.1/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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.lo
gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro -o libRmath.so -Wl,-soname,libRmath.so.1 mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm
make[2]: Leaving directory '/build/r-base-3.6.1/src/nmath/standalone'
make[2]: Entering directory '/build/r-base-3.6.1/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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -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=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.o
ar -cr libRmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o
ranlib libRmath.a
make[2]: Leaving directory '/build/r-base-3.6.1/src/nmath/standalone'
make[1]: Leaving directory '/build/r-base-3.6.1/src/nmath/standalone'
R_GZIPCMD="/bin/gzip -n" \
	/usr/bin/make docs R_CMD_BUILD_HELP_OPTS="--txt --example"
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/m4'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/m4'
make[2]: Entering directory '/build/r-base-3.6.1/tools'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tools'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/html'
make[3]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/etc'
make[2]: Leaving directory '/build/r-base-3.6.1/etc'
make[2]: Entering directory '/build/r-base-3.6.1/share'
make[2]: Leaving directory '/build/r-base-3.6.1/share'
make[2]: Entering directory '/build/r-base-3.6.1/src'
make[3]: Entering directory '/build/r-base-3.6.1/src/scripts'
make[4]: Entering directory '/build/r-base-3.6.1/src/scripts'
make[4]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Entering directory '/build/r-base-3.6.1/src/include'
make[4]: Entering directory '/build/r-base-3.6.1/src/include/R_ext'
make[4]: Nothing to be done for 'R'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/include/R_ext'
make[3]: Leaving directory '/build/r-base-3.6.1/src/include'
make[3]: Entering directory '/build/r-base-3.6.1/src/extra'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: 'Makedeps' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: 'libtre.a' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[3]: Leaving directory '/build/r-base-3.6.1/src/extra'
make[3]: Entering directory '/build/r-base-3.6.1/src/appl'
make[4]: Entering directory '/build/r-base-3.6.1/src/appl'
make[4]: 'libappl.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[4]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[4]: 'libnmath.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Entering directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
make[4]: 'libunix.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-z,relro -DR_HOME='"/build/r-base-3.6.1"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Entering directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
/build/r-base-3.6.1/lib/libR.so is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
/build/r-base-3.6.1/bin/exec/R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Entering directory '/build/r-base-3.6.1/src/modules'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: 'internet.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: 'lapack.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: 'R_X11.so' is up to date.
make[5]: 'R_de.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
/build/r-base-3.6.1/modules/R_X11.so is unchanged
/build/r-base-3.6.1/modules/R_de.so is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[3]: Leaving directory '/build/r-base-3.6.1/src/modules'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/profile'
building system startup profile
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/profile'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/translations'
building package 'translations'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/translations'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
building package 'base'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/base'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
building package 'tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
../../../../library/tools/libs/tools.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
building package 'compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/utils'
building package 'utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
all.R is unchanged
make[5]: Nothing to be done for 'iconvlist'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
../../../../library/utils/libs/utils.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
building package 'grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
../../../../library/grDevices/libs/grDevices.so is unchanged
make[8]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: 'cairo.so' is up to date.
make[10]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
building package 'graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
../../../../library/graphics/libs/graphics.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats'
building package 'stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
../../../../library/stats/libs/stats.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
building package 'datasets'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/methods'
building package 'methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
../../../../library/methods/libs/methods.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Nothing to be done for 'RfilesLazy'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grid'
building package 'grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
../../../../library/grid/libs/grid.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/splines'
building package 'splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
../../../../library/splines/libs/splines.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
building package 'stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
building package 'tcltk'
all.R is unchanged
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
../../../../library/tcltk/libs/tcltk.so is unchanged
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
building package 'parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
../../../../library/parallel/libs/parallel.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src'
make[2]: Entering directory '/build/r-base-3.6.1/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tests'
you should 'make docs' now ...
make[2]: Entering directory '/build/r-base-3.6.1/doc'
creating doc/NEWS
creating doc/NEWS.pdf
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
creating doc/manual/R-FAQ.html
creating doc/manual/version.texi
creating doc/manual/R-admin.html
creating doc/manual/R-data.html
creating doc/manual/R-exts.html
creating doc/manual/R-intro.html
creating doc/manual/R-ints.html
creating doc/manual/R-lang.html
make[4]: Entering directory '/build/r-base-3.6.1/doc/html'
make[4]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
installing parsed Rd
make[4]: Entering directory '/build/r-base-3.6.1/src/library'
  base
  stats
  utils
  methods
  graphics
  grDevices
  datasets
  grid
  tools
  tcltk
  splines
  stats4
  compiler
  parallel
make[4]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
building/updating package metadata ...
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
writing package indices
make[4]: Entering directory '/build/r-base-3.6.1/src/library'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src/library'
make[1]: Leaving directory '/build/r-base-3.6.1'
/usr/bin/make javaconf
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/m4'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/m4'
make[2]: Entering directory '/build/r-base-3.6.1/tools'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tools'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/html'
make[3]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/etc'
make[2]: Leaving directory '/build/r-base-3.6.1/etc'
make[2]: Entering directory '/build/r-base-3.6.1/share'
make[2]: Leaving directory '/build/r-base-3.6.1/share'
make[2]: Entering directory '/build/r-base-3.6.1/src'
make[3]: Entering directory '/build/r-base-3.6.1/src/scripts'
make[4]: Entering directory '/build/r-base-3.6.1/src/scripts'
make[4]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Entering directory '/build/r-base-3.6.1/src/include'
make[4]: Entering directory '/build/r-base-3.6.1/src/include/R_ext'
make[4]: Nothing to be done for 'R'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/include/R_ext'
make[3]: Leaving directory '/build/r-base-3.6.1/src/include'
make[3]: Entering directory '/build/r-base-3.6.1/src/extra'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: 'Makedeps' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: 'libtre.a' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[3]: Leaving directory '/build/r-base-3.6.1/src/extra'
make[3]: Entering directory '/build/r-base-3.6.1/src/appl'
make[4]: Entering directory '/build/r-base-3.6.1/src/appl'
make[4]: 'libappl.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[4]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[4]: 'libnmath.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Entering directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
make[4]: 'libunix.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-z,relro -DR_HOME='"/build/r-base-3.6.1"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Entering directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
/build/r-base-3.6.1/lib/libR.so is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
/build/r-base-3.6.1/bin/exec/R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Entering directory '/build/r-base-3.6.1/src/modules'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: 'internet.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: 'lapack.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: 'R_X11.so' is up to date.
make[5]: 'R_de.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
/build/r-base-3.6.1/modules/R_X11.so is unchanged
/build/r-base-3.6.1/modules/R_de.so is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[3]: Leaving directory '/build/r-base-3.6.1/src/modules'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/profile'
building system startup profile
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/profile'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/translations'
building package 'translations'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/translations'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
building package 'base'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/base'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
building package 'tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
../../../../library/tools/libs/tools.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
building package 'compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/utils'
building package 'utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
all.R is unchanged
make[5]: Nothing to be done for 'iconvlist'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
../../../../library/utils/libs/utils.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
building package 'grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
../../../../library/grDevices/libs/grDevices.so is unchanged
make[8]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: 'cairo.so' is up to date.
make[10]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
building package 'graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
../../../../library/graphics/libs/graphics.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats'
building package 'stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
../../../../library/stats/libs/stats.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
building package 'datasets'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/methods'
building package 'methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
../../../../library/methods/libs/methods.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Nothing to be done for 'RfilesLazy'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grid'
building package 'grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
../../../../library/grid/libs/grid.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/splines'
building package 'splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
../../../../library/splines/libs/splines.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
building package 'stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
building package 'tcltk'
all.R is unchanged
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
../../../../library/tcltk/libs/tcltk.so is unchanged
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
building package 'parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
../../../../library/parallel/libs/parallel.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src'
make[2]: Entering directory '/build/r-base-3.6.1/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tests'
make[2]: Entering directory '/build/r-base-3.6.1'
configuring Java ...
Java interpreter : /usr/lib/jvm/default-java/bin/java
Java version     : 11.0.3
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/client -ljvm
make[3]: Entering directory '/tmp/Rjavareconf.0uayqn'
gcc -std=gnu99 -I"/build/r-base-3.6.1/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/build/r-base-3.6.1/lib -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/client -ljvm -L/build/r-base-3.6.1/lib -lR
make[3]: Leaving directory '/tmp/Rjavareconf.0uayqn'


JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/lib/client
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/client -ljvm
Updating Java configuration in /build/r-base-3.6.1
Done.

make[2]: Leaving directory '/build/r-base-3.6.1'
make[1]: Leaving directory '/build/r-base-3.6.1'
touch make-arch-stamp
*** make-indep ***
/usr/bin/make -k docs
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/m4'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/m4'
make[2]: Entering directory '/build/r-base-3.6.1/tools'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tools'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/html'
make[3]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/etc'
make[2]: Leaving directory '/build/r-base-3.6.1/etc'
make[2]: Entering directory '/build/r-base-3.6.1/share'
make[2]: Leaving directory '/build/r-base-3.6.1/share'
make[2]: Entering directory '/build/r-base-3.6.1/src'
make[3]: Entering directory '/build/r-base-3.6.1/src/scripts'
make[4]: Entering directory '/build/r-base-3.6.1/src/scripts'
make[4]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Entering directory '/build/r-base-3.6.1/src/include'
make[4]: Entering directory '/build/r-base-3.6.1/src/include/R_ext'
make[4]: Nothing to be done for 'R'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/include/R_ext'
make[3]: Leaving directory '/build/r-base-3.6.1/src/include'
make[3]: Entering directory '/build/r-base-3.6.1/src/extra'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: 'Makedeps' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: 'libtre.a' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[3]: Leaving directory '/build/r-base-3.6.1/src/extra'
make[3]: Entering directory '/build/r-base-3.6.1/src/appl'
make[4]: Entering directory '/build/r-base-3.6.1/src/appl'
make[4]: 'libappl.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[4]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[4]: 'libnmath.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Entering directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
make[4]: 'libunix.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-z,relro -DR_HOME='"/build/r-base-3.6.1"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Entering directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
/build/r-base-3.6.1/lib/libR.so is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
/build/r-base-3.6.1/bin/exec/R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Entering directory '/build/r-base-3.6.1/src/modules'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: 'internet.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: 'lapack.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: 'R_X11.so' is up to date.
make[5]: 'R_de.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
/build/r-base-3.6.1/modules/R_X11.so is unchanged
/build/r-base-3.6.1/modules/R_de.so is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[3]: Leaving directory '/build/r-base-3.6.1/src/modules'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/profile'
building system startup profile
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/profile'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/translations'
building package 'translations'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/translations'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
building package 'base'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/base'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
building package 'tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
../../../../library/tools/libs/tools.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
building package 'compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/utils'
building package 'utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
all.R is unchanged
make[5]: Nothing to be done for 'iconvlist'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
../../../../library/utils/libs/utils.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
building package 'grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
../../../../library/grDevices/libs/grDevices.so is unchanged
make[8]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: 'cairo.so' is up to date.
make[10]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
building package 'graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
../../../../library/graphics/libs/graphics.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats'
building package 'stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
../../../../library/stats/libs/stats.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
building package 'datasets'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/methods'
building package 'methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
../../../../library/methods/libs/methods.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Nothing to be done for 'RfilesLazy'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grid'
building package 'grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
../../../../library/grid/libs/grid.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/splines'
building package 'splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
../../../../library/splines/libs/splines.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
building package 'stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
building package 'tcltk'
all.R is unchanged
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
../../../../library/tcltk/libs/tcltk.so is unchanged
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
building package 'parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
../../../../library/parallel/libs/parallel.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src'
make[2]: Entering directory '/build/r-base-3.6.1/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tests'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
make[4]: Entering directory '/build/r-base-3.6.1/doc/html'
make[4]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
installing parsed Rd
make[4]: Entering directory '/build/r-base-3.6.1/src/library'
  base
  stats
  utils
  methods
  graphics
  grDevices
  datasets
  grid
  tools
  tcltk
  splines
  stats4
  compiler
  parallel
make[4]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
building/updating package metadata ...
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
writing package indices
make[4]: Entering directory '/build/r-base-3.6.1/src/library'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src/library'
make[1]: Leaving directory '/build/r-base-3.6.1'
(cd doc/manual && /usr/bin/make html)
make[1]: Entering directory '/build/r-base-3.6.1/doc/manual'
make[2]: Entering directory '/build/r-base-3.6.1/doc/html'
make[2]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[1]: Leaving directory '/build/r-base-3.6.1/doc/manual'
/usr/bin/make info
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-exts.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-intro.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-ints.texi
/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-lang.texi
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[1]: Leaving directory '/build/r-base-3.6.1'
(cd doc/manual && \
	/usr/bin/make refman.pdf R-admin.pdf R-data.pdf R-exts.pdf \
		R-FAQ.pdf R-intro.pdf R-ints.pdf R-lang.pdf)
make[1]: Entering directory '/build/r-base-3.6.1/doc/manual'
creating doc/manual/version.tex
collecting LaTeX docs for package 'base' ...
Converting parsed Rd's to LaTeX ...........................................
collecting LaTeX docs for package 'tools' ...
Converting parsed Rd's to LaTeX ......
collecting LaTeX docs for package 'utils' ...
Converting parsed Rd's to LaTeX ...............
collecting LaTeX docs for package 'grDevices' ...
Converting parsed Rd's to LaTeX .......
collecting LaTeX docs for package 'graphics' ...
Converting parsed Rd's to LaTeX .......
collecting LaTeX docs for package 'stats' ...
Converting parsed Rd's to LaTeX ..............................
collecting LaTeX docs for package 'datasets' ...
Converting parsed Rd's to LaTeX ........
collecting LaTeX docs for package 'methods' ...
Converting parsed Rd's to LaTeX ........
collecting LaTeX docs for package 'grid' ...
Converting parsed Rd's to LaTeX .........
collecting LaTeX docs for package 'splines' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'stats4' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'tcltk' ...
Converting parsed Rd's to LaTeX .
collecting LaTeX docs for package 'compiler' ...
Converting parsed Rd's to LaTeX 
collecting LaTeX docs for package 'parallel' ...
Converting parsed Rd's to LaTeX .
PDF/LaTeX documentation: reference index ...
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./refman.tex
LaTeX2e <2018-12-01>
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2018/09/03 v1.4i Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file refman.idx
No file refman.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex
Chapter 1.
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2]
Underfull \hbox (badness 6995) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
/ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It

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

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

Underfull \hbox (badness 10000) in paragraph at lines 141--149
\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As

Underfull \hbox (badness 4995) in paragraph at lines 141--149
\T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi
4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 ,
[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] [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 1178--1181
[]\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 1953--1953
 []\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] [34] [35] [36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via

Underfull \hbox (badness 1102) in paragraph at lines 2392--2397
\T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim
-ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit

[38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52]
[53] [54] [55] [56] [57] [58] [59]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[60] [61] [62]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77]
[78]
Underfull \hbox (badness 2521) in paragraph at lines 5033--5035
[]\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
[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93]
[94] [95] [96]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6189--6189
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[97] [98] [99] [100] [101] [102]
Overfull \hbox (46.35893pt too wide) in paragraph at lines 6598--6600
[]\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 : 
[103] [104]
Underfull \hbox (badness 10000) in paragraph at lines 6746--6749
[]\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
[105] [106]
Underfull \hbox (badness 6063) in paragraph at lines 6928--6934
[]\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-


Underfull \hbox (badness 2343) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1708) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
s not rec-om-mended) when

Underfull \hbox (badness 1831) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
/10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
[107]
Underfull \hbox (badness 3568) in paragraph at lines 6990--6997
\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
[108] [109]
Underfull \vbox (badness 10000) has occurred while \output is active [110]
Underfull \vbox (badness 10000) has occurred while \output is active [111]
[112]
Underfull \hbox (badness 1077) in paragraph at lines 7307--7313
[]\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 7307--7313
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[113] [114] [115] [116] [117] [118]
Underfull \hbox (badness 2096) in paragraph at lines 7648--7652
\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 .
[119] [120]
Underfull \hbox (badness 2351) in paragraph at lines 7766--7769
[][][]\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 ,
[121] [122] [123] [124] [125]
Underfull \hbox (badness 4479) in paragraph at lines 8092--8102
[][][]\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),
[126] [127] [128] [129] [130] [131]
Underfull \hbox (badness 1629) in paragraph at lines 8539--8551
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

Underfull \hbox (badness 1609) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which

Underfull \hbox (badness 2426) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that 
value is on those OSes also used as an er-ror code.
[132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
Underfull \hbox (badness 1178) in paragraph at lines 9275--9279
[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154]
[155] [156] [157] [158] [159] [160]
Underfull \hbox (badness 1735) in paragraph at lines 10423--10427
\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 .
[161] [162] [163] [164] [165] [166] [167]
Underfull \hbox (badness 6396) in paragraph at lines 10862--10870
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 1946) in paragraph at lines 10862--10870
\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
[168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181] [182] [183] [184]
Underfull \hbox (badness 4569) in paragraph at lines 11978--11982
[]\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 11978--11982
\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
[185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196]
[197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208]
[209]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[210]
Underfull \hbox (badness 1565) in paragraph at lines 13712--13716
[][][]\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
[211]
Underfull \hbox (badness 4927) in paragraph at lines 13756--13758
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
[212]
Underfull \hbox (badness 3148) in paragraph at lines 13849--13854
[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
[213]
Underfull \hbox (badness 1466) in paragraph at lines 13896--13899
[]\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
[214] [215]
Underfull \hbox (badness 10000) in paragraph at lines 14015--14019
[][][]\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 14026--14029
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[216] [217] [218] [219]
Underfull \hbox (badness 3965) in paragraph at lines 14316--14320
[]\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,
[220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
[232]
Underfull \hbox (badness 4429) in paragraph at lines 15092--15095
[]\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
[233] [234]
Underfull \hbox (badness 10000) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

Underfull \hbox (badness 1215) in paragraph at lines 15198--15200
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

Underfull \hbox (badness 10000) in paragraph at lines 15220--15225
[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

Underfull \hbox (badness 1558) in paragraph at lines 15220--15225
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

Underfull \hbox (badness 10000) in paragraph at lines 15232--15236
[]\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

Underfull \hbox (badness 2426) in paragraph at lines 15232--15236
\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[235]
Underfull \hbox (badness 2035) in paragraph at lines 15271--15275
[]\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 within
[236]
Underfull \vbox (badness 10000) has occurred while \output is active [237]
[238] [239] [240] [241] [242] [243] [244]
Underfull \hbox (badness 2452) in paragraph at lines 15870--15874
[]\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 15870--15874
\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
[245] [246] [247]
Underfull \hbox (badness 1092) in paragraph at lines 16043--16048
[][]\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
[248] [249] [250]
Underfull \hbox (badness 6741) in paragraph at lines 16293--16297
\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
 ,
[251] [252] [253] [254] [255] [256] [257] [258] [259]
Underfull \vbox (badness 3803) has occurred while \output is active [260]
Underfull \vbox (badness 10000) has occurred while \output is active [261]
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1478) in paragraph at lines 17582--17585
[]\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
[271] [272] [273] [274]
Underfull \hbox (badness 10000) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[275] [276] [277] [278] [279] [280] [281] [282] [283]
Underfull \hbox (badness 1442) in paragraph at lines 18437--18439
[]\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
[284]
Underfull \hbox (badness 2452) in paragraph at lines 18529--18545
[][][]\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 ,
[285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 1248) in paragraph at lines 18948--18951
[]\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 ,
[292] [293] [294] [295]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[296] [297] [298] [299] [300] [301]
Underfull \hbox (badness 1596) in paragraph at lines 19625--19630
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 2469) in paragraph at lines 20229--20234
[]\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 20243--20250
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[313]
Underfull \hbox (badness 10000) in paragraph at lines 20317--20321
[]\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 20317--20321
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[314] [315]
Underfull \hbox (badness 1014) in paragraph at lines 20487--20492
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
Underfull \hbox (badness 1264) in paragraph at lines 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[328]
Underfull \hbox (badness 4441) in paragraph at lines 21305--21308
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 6047) in paragraph at lines 22052--22054
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351]
[352] [353] [354] [355] [356]
Underfull \hbox (badness 1077) in paragraph at lines 23093--23099
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\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 .
[357] [358] [359] [360] [361] [362] [363] [364] [365]
Underfull \hbox (badness 2790) in paragraph at lines 23589--23592
[]\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 23589--23592
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[366] [367] [368] [369]
Underfull \hbox (badness 1194) in paragraph at lines 23871--23874
[]\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
[370] [371] [372]
Underfull \hbox (badness 2368) in paragraph at lines 24077--24083
[]\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 list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24077--24083
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[373] [374] [375] [376] [377] [378]
Underfull \hbox (badness 10000) in paragraph at lines 24459--24462
[]\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
[379] [380] [381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 25064--25066
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
[400]
Underfull \hbox (badness 1038) in paragraph at lines 25904--25912
[]\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 1735) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25913--25916
[]\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 25932--25934
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[401] [402]
Underfull \hbox (badness 2142) in paragraph at lines 26073--26077
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 26123--26128
[]\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
[403] [404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 26411--26417
[]\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 26411--26417
\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 26411--26417
\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 26424--26427
[]\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 26450--26452
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 26485--26490
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and
[407]
Underfull \hbox (badness 7203) in paragraph at lines 26503--26506
[]\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 10000) in paragraph at lines 26527--26532
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26527--26532
\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).
[408] [409] [410] [411] [412] [413] [414] [415]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[416]
Underfull \hbox (badness 7925) in paragraph at lines 27124--27128
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

Underfull \hbox (badness 1622) in paragraph at lines 27124--27128
[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

Underfull \hbox (badness 6125) in paragraph at lines 27129--27138
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427]
Underfull \hbox (badness 2726) in paragraph at lines 27850--27853
[]\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
[428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439]
[440] [441] [442] [443] [444] [445]
Underfull \vbox (badness 3803) has occurred while \output is active [446]
[447] [448] [449] [450] [451] [452] [453]
Underfull \hbox (badness 1533) in paragraph at lines 29541--29544
[]\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
[454] [455] [456]
Underfull \hbox (badness 1163) in paragraph at lines 29704--29715
[]\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
[457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468]
[469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 31250--31254
[]\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 31250--31254
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 31272--31274
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[481] [482] [483] [484] [485] [486] [487] [488] [489]
Underfull \hbox (badness 1655) in paragraph at lines 31828--31830
[]\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
[490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501]
[502] [503] [504] [505] [506]
Underfull \hbox (badness 2261) in paragraph at lines 32947--32952
[]\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
[507]
Underfull \hbox (badness 10000) in paragraph at lines 32974--32980
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1484) in paragraph at lines 32974--32980
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519]
[520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
[532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543]
[544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555]
Underfull \hbox (badness 1072) in paragraph at lines 36116--36120
[]\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 36121--36125
[]\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 36149--36155
[]\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 36149--36155
\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 36149--36155
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in

Underfull \hbox (badness 3009) in paragraph at lines 36161--36168
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 36161--36168
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 36161--36168
\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 36161--36168
\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
[556] [557] [558] [559] [560] [561]
Underfull \hbox (badness 1142) in paragraph at lines 36514--36520
[]\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 \T1/zi4/m/n/10 "%Y-%m-%d
[562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573]
[574] [575] [576] [577] [578] [579] [580] [581]
Underfull \hbox (badness 1565) in paragraph at lines 37787--37789
[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[582] [583] [584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 4967) in paragraph at lines 38386--38391
[]\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
[592] [593]
Underfull \hbox (badness 1616) in paragraph at lines 38499--38504
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
[594] [595] [596] [597]
Underfull \vbox (badness 10000) has occurred while \output is active [598]
[599] [600] [601] [602]
Underfull \hbox (badness 1472) in paragraph at lines 39025--39028
[]\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
[603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614]
[615]
Underfull \vbox (badness 3803) has occurred while \output is active [616]
Underfull \hbox (badness 10000) in paragraph at lines 39939--39943
[]\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., \T1/zi4/m/n/10
 length(bin) >
[617] [618] [619] [620]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[621] [622] [623]
Underfull \hbox (badness 10000) in paragraph at lines 40374--40378
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[624] [625] [626] [627] [628] [629] [630] [631] [632]
Underfull \hbox (badness 10000) in paragraph at lines 40987--40990
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
[633] [634] [635] [636] [637] [638]
Underfull \vbox (badness 10000) has occurred while \output is active [639]
[640] [641] [642] [643] [644] [645] [646]
Underfull \hbox (badness 1990) in paragraph at lines 41890--41898
[]\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 41890--41898
\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
[647] [648] [649] [650] [651] [652] [653] [654]
Underfull \hbox (badness 1917) in paragraph at lines 42396--42403
[]\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
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665]
Underfull \hbox (badness 3668) in paragraph at lines 43125--43127
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[666] [667]
Underfull \hbox (badness 2401) in paragraph at lines 43253--43257
[]\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
[668] [669] [670]
Underfull \hbox (badness 2111) in paragraph at lines 43442--43447
\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 10000) in paragraph at lines 43463--43468
[]\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
[671] [672] [673] [674] [675] [676] [677] [678] [679]
Underfull \hbox (badness 5417) in paragraph at lines 44045--44049
[]\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
[680]
Underfull \hbox (badness 10000) in paragraph at lines 44106--44110
[]\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
[681] [682]) (./compiler-pkg.tex
Chapter 2.
[683] [684] [685] [686]) (./datasets-pkg.tex
Chapter 3.
[687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698]
[699] [700] [701] [702] [703]
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.
[704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715]
[716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726]
Underfull \vbox (badness 1448) has occurred while \output is active [727]
[728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738]
Overfull \vbox (19.74611pt too high) has occurred while \output is active
[739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
[751] [752] [753] [754]
Underfull \vbox (badness 10000) has occurred while \output is active [755]
[756] [757] [758]
Underfull \vbox (badness 10000) has occurred while \output is active [759]
[760] [761] [762] [763] [764]
Overfull \vbox (18.9959pt too high) has occurred while \output is active
[765] [766] [767]) (./grDevices-pkg.tex [768]
Chapter 4.
[769] [770] [771] [772] [773]
Underfull \hbox (badness 3158) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

Underfull \hbox (badness 10000) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

Underfull \hbox (badness 1852) in paragraph at lines 298--303
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
[774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785]
[786]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\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
[787] [788] [789] [790]
Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
[]\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
[791] [792] [793]
Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
\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
[794] [795] [796] [797] [798] [799]
Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
\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 ,
[800] [801]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[802] [803] [804]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[805] [806] [807] [808] [809] [810] [811] [812] [813] [814]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829

[815] [816] [817] [818] [819] [820] [821] [822] [823]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[824] [825] [826] [827] [828]
Underfull \vbox (badness 10000) has occurred while \output is active [829]
Underfull \hbox (badness 10000) in paragraph at lines 3785--3788
[]\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
[830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

Underfull \hbox (badness 4181) in paragraph at lines 4514--4519
\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
[841]
Underfull \vbox (badness 10000) has occurred while \output is active [842]
[843]
Underfull \hbox (badness 1067) in paragraph at lines 4668--4675
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[844] [845] [846] [847]
Underfull \hbox (badness 1377) in paragraph at lines 4971--4976
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[848]
Underfull \hbox (badness 1418) in paragraph at lines 5047--5054
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[849] [850]
Underfull \hbox (badness 1377) in paragraph at lines 5176--5181
[]\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
[851]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\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
[852] [853]
Underfull \hbox (badness 2035) in paragraph at lines 5380--5389
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\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 ,
[854]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5448--5455
\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 .
[855] [856] [857]
Underfull \hbox (badness 1546) in paragraph at lines 5590--5598
[]\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 ,
[858] [859] [860] [861] [862] [863] [864] [865]
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877]
[878]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[879]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[880] [881] [882] [883] [884]
Underfull \hbox (badness 3780) in paragraph at lines 7345--7351
[]\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 ,
[885] [886] [887]
Underfull \hbox (badness 2680) in paragraph at lines 7546--7548
[]\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
[888] [889] [890]) (./graphics-pkg.tex
Chapter 5.
[891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902]
[903] [904] [905] [906] [907] [908] [909] [910] [911] [912]
Underfull \hbox (badness 4634) in paragraph at lines 1351--1354
[][][]\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 ,
[913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924]
[925] [926] [927] [928] [929]
Underfull \hbox (badness 1009) in paragraph at lines 2390--2397
\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
[930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941]
[942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952]
Underfull \vbox (badness 10000) has occurred while \output is active [953]
[954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965]
Underfull \hbox (badness 3229) in paragraph at lines 4534--4539
[]\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
[966] [967] [968] [969] [970]
Underfull \hbox (badness 10000) in paragraph at lines 4891--4897
[]\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 4891--4897
\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
[971]
Underfull \hbox (badness 10000) in paragraph at lines 5022--5025

[972]
Underfull \hbox (badness 10000) in paragraph at lines 5083--5085

[973 </build/r-base-3.6.1/library/graphics/help/figures/mai.pdf>] [974 </build/
r-base-3.6.1/library/graphics/help/figures/oma.pdf>] [975]
Underfull \hbox (badness 10000) in paragraph at lines 5273--5275
[]\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
[976]
Underfull \vbox (badness 3803) has occurred while \output is active [977]
[978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989]
[990] [991] [992] [993] [994] [995] [996] [997] [998]
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6751--6752
[][] 
[999] [1000 </build/r-base-3.6.1/library/graphics/help/figures/pch.pdf>]
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011]
[1012]
Underfull \hbox (badness 2012) in paragraph at lines 7576--7579
[]\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 poi
nt
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
[1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033]
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

Underfull \hbox (badness 10000) in paragraph at lines 8838--8840
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
[1034]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [1035] [1036] [1037] [1038])
(./grid-pkg.tex
Chapter 6.

Underfull \vbox (badness 10000) has occurred while \output is active [1039]
[1040] [1041] [1042] [1043] [1044] [1045] [1046]
Underfull \hbox (badness 2680) in paragraph at lines 483--486
[]\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
[1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056]
Underfull \hbox (badness 4279) in paragraph at lines 1064--1073
[][][]\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 ,
[1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067]
[1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078]
[1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089]
[1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100]
Underfull \vbox (badness 10000) has occurred while \output is active [1101]
[1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
[1113] [1114]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\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
[1115] [1116] [1117] [1118]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129]
[1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140]
[1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149]
Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
[]\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 \T1/zi4/m/n/10 depth
[1150] [1151] [1152] [1153]) (./methods-pkg.tex [1154]
Chapter 7.
[1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162]
Underfull \vbox (badness 3803) has occurred while \output is active [1163]
Underfull \vbox (badness 10000) has occurred while \output is active [1164]
[1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173]
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
[1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181]
Underfull \hbox (badness 2181) 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
[1182]
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
[1183] [1184] [1185]
Underfull \hbox (badness 2213) 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 =
[1186] [1187] [1188] [1189] [1190]
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
[1191] [1192]
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
[1193]
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
[1194] [1195] [1196] [1197] [1198] [1199] [1200]
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
[1201] [1202] [1203] [1204] [1205]
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
[1206]
Underfull \hbox (badness 10000) in paragraph at lines 3642--3651
[]\T1/ptm/m/n/10 The
[1207]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
[1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218]
Underfull \hbox (badness 1769) in paragraph at lines 4472--4478
[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228]
Underfull \vbox (badness 10000) has occurred while \output is active [1229]
[1230] [1231]
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
[1232]
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
[1233] [1234] [1235] [1236]
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
[1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244]
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
[1245] [1246] [1247] [1248]
Underfull \vbox (badness 10000) has occurred while \output is active [1249]
[1250] [1251] [1252]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}
                               [1253] [1254] [1255]pdfTeX warning (ext4): desti
nation with the same identifier (name{Rfn.Complex}) has been already used, dupl
icate ignored
<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}
                                                 [1256]
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
[1257] [1258] [1259]
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
[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281]
[1282] [1283] [1284] [1285] [1286]
Underfull \vbox (badness 10000) has occurred while \output is active [1287]
[1288] [1289] [1290] [1291] [1292] [1293] [1294]
Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1295] [1296] [1297] [1298] [1299] [1300] [1301]
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.,
[1302] [1303] [1304] [1305]) (./parallel-pkg.tex [1306]
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
[1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317]
[1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327]
Underfull \hbox (badness 3386) in paragraph at lines 1365--1368
[]\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
[1328] [1329] [1330]) (./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
[1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341]
[1342] [1343] [1344] [1345] [1346]) (./stats-pkg.tex
Chapter 10.
[1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
[1358] [1359] [1360]
Underfull \hbox (badness 1412) in paragraph at lines 875--877
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368]
Underfull \hbox (badness 2503) in paragraph at lines 1356--1359
[]\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 ,
[1369] [1370] [1371]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
[1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382]
[1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
[1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401]
Underfull \hbox (badness 2503) in paragraph at lines 3437--3440
[]\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 ,
[1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
[1413] [1414] [1415] [1416]
Underfull \hbox (badness 1127) in paragraph at lines 4351--4354
[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1417] [1418] [1419] [1420] [1421]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431]
Underfull \hbox (badness 2556) in paragraph at lines 5317--5320
[]\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 5334--5336
[]\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
[1432] [1433] [1434] [1435] [1436] [1437] [1438]
Underfull \hbox (badness 2503) in paragraph at lines 5726--5730
[]\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 ,
[1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
[1450] [1451]
Underfull \hbox (badness 7081) in paragraph at lines 6520--6523
[]\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 6524--6526
[]\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
[1452] [1453] [1454] [1455] [1456]
Underfull \vbox (badness 3803) has occurred while \output is active [1457]
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 7369--7372
[]\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
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
Underfull \vbox (badness 10000) has occurred while \output is active [1487]
[1488] [1489] [1490] [1491]
Underfull \hbox (badness 2626) in paragraph at lines 9048--9051
[]\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
[1492] [1493]
Underfull \hbox (badness 2503) in paragraph at lines 9155--9159
[]\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 ,
[1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504]
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516] [1517] [1518]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 10844--10847
[]\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,
[1519]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1526] [1527] [1528] [1529] [1530] [1531]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\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

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1532] [1533]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1534] [1535]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\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
[1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 \T1/zi4/m/n/10 SSinit =
[1546] [1547] [1548] [1549] [1550] [1551]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562]
[1563]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1574] [1575]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\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
[1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586]
[1587] [1588] [1589] [1590] [1591] [1592] [1593]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\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 ,
[1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\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
[1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612]
[1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623]
[1624] [1625] [1626] [1627] [1628] [1629]
Underfull \vbox (badness 10000) has occurred while \output is active [1630]
Underfull \vbox (badness 10000) has occurred while \output is active [1631]
[1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642]
[1643]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

Underfull \hbox (badness 1735) in paragraph at lines 18581--18584
[]\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
[1644]
Underfull \hbox (badness 2343) in paragraph at lines 18594--18598
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

Underfull \hbox (badness 3471) in paragraph at lines 18594--18598
\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18602--18606
[]\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
[1645] [1646] [1647]
Overfull \hbox (15.73795pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1648]
[1649] [1650] [1651] [1652] [1653] [1654]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1664] [1665] [1666] [1667]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1668] [1669] [1670] [1671] [1672] [1673] [1674]
Underfull \hbox (badness 2503) in paragraph at lines 20381--20384
[]\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 ,

Underfull \hbox (badness 3919) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
[1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685]
[1686] [1687] [1688] [1689] [1690] [1691] [1692]
Underfull \hbox (badness 10000) in paragraph at lines 21485--21491
[]\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 ,
[1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703]
[1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714]
[1715]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723]
Overfull \hbox (27.74408pt too wide) in paragraph at lines 23399--23399
 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1724] [1725] [1726] [1727] [1728]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 4205) in paragraph at lines 23650--23653
\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
[1729] [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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 \T1/zi4/m/n/10 y[j] =
[1738]
Underfull \hbox (badness 3690) in paragraph at lines 24287--24291
[][][]\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
[1739] [1740] [1741] [1742] [1743] [1744] [1745]
Underfull \vbox (badness 10000) has occurred while \output is active [1746]
[1747]
Underfull \hbox (badness 2165) in paragraph at lines 24777--24782
[]\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 ,
[1748] [1749] [1750]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
[1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761]
[1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772]
[1773] [1774]
Underfull \vbox (badness 10000) has occurred while \output is active [1775]
Underfull \hbox (badness 3514) in paragraph at lines 26556--26561
[]\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
[1776] [1777] [1778] [1779]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26790--26790
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1780]
Underfull \hbox (badness 3514) in paragraph at lines 26826--26832
[]\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
[1781] [1782] [1783] [1784]
Underfull \hbox (badness 3514) in paragraph at lines 27040--27045
[]\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
[1785] [1786]
Underfull \hbox (badness 3514) in paragraph at lines 27127--27132
[]\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
[1787]
Underfull \hbox (badness 3514) in paragraph at lines 27192--27197
[]\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
[1788] [1789]
Underfull \hbox (badness 3514) in paragraph at lines 27286--27291
[]\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
[1790]
Underfull \hbox (badness 6691) in paragraph at lines 27378--27383
[]\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
[1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799]
Underfull \hbox (badness 4024) in paragraph at lines 27908--27911
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
[1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809]
Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\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
[1810] [1811] [1812]
Underfull \hbox (badness 5431) in paragraph at lines 28724--28727
[]\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
[1813] [1814] [1815] [1816] [1817] [1818]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1819] [1820] [1821] [1822] [1823]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834]
[1835] [1836] [1837] [1838] [1839] [1840] [1841] [1842]
Underfull \hbox (badness 3557) in paragraph at lines 30470--30474
[]\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 \T1/zi4
/m/n/10 interval =
[1843] [1844] [1845]
Underfull \vbox (badness 10000) has occurred while \output is active [1846]
[1847] [1848]
Underfull \hbox (badness 1337) in paragraph at lines 30834--30838
[]\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
[1849] [1850] [1851] [1852] [1853] [1854] [1855] [1856] [1857]
Underfull \hbox (badness 1337) in paragraph at lines 31361--31365
[]\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
[1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867])
(./stats4-pkg.tex [1868]
Chapter 11.
[1869] [1870] [1871] [1872] [1873] [1874]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1875] [1876] [1877])
(./tcltk-pkg.tex [1878]
Chapter 12.
[1879] [1880] [1881] [1882] [1883] [1884] [1885]
Underfull \vbox (badness 10000) has occurred while \output is active [1886]
Underfull \vbox (badness 10000) has occurred while \output is active [1887]
Underfull \hbox (badness 1546) in paragraph at lines 664--671
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898]
[1899]) (./tools-pkg.tex [1900]
Chapter 13.
[1901]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 72.

[1902]
Underfull \hbox (badness 3039) in paragraph at lines 164--167
[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1903] [1904]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

Underfull \hbox (badness 4967) in paragraph at lines 285--298
\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1905] [1906]
Underfull \hbox (badness 3039) in paragraph at lines 389--391
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917]
[1918]
Underfull \hbox (badness 4441) in paragraph at lines 1139--1149
\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-
[1919]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
[1920]
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209
\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 ,
[1921] [1922] [1923] [1924] [1925]
Underfull \hbox (badness 2293) in paragraph at lines 1558--1560
[]\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
[1926] [1927]
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Underfull \hbox (badness 1082) in paragraph at lines 1703--1705
[]\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
[1928] [1929] [1930] [1931]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1932] [1933] [1934]
[1935] [1936]
Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202
 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1937] [1938] [1939]
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1940] [1941] [1942] [1943] [1944] [1945] [1946]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
(Font)              using `T1/zi4/m/n' instead on input line 2846.

[1947] [1948] [1949] [1950] [1951]
Underfull \hbox (badness 1424) in paragraph at lines 3128--3130
[]\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
[1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962]
Underfull \hbox (badness 10000) in paragraph at lines 3832--3834
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1963] [1964]
Underfull \hbox (badness 10000) in paragraph at lines 3971--3974
[]\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
[1965] [1966]
Underfull \hbox (badness 1137) in paragraph at lines 4073--4075
[]\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
[1967] [1968] [1969] [1970] [1971]
Underfull \hbox (badness 1796) in paragraph at lines 4381--4386
[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1972]
Underfull \hbox (badness 1838) in paragraph at lines 4455--4461
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

Underfull \hbox (badness 10000) in paragraph at lines 4455--4461
\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
[1973] [1974] [1975]
Underfull \hbox (badness 2197) in paragraph at lines 4671--4681
[]\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 :
[1976]
Underfull \hbox (badness 1571) in paragraph at lines 4734--4738
[]\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
[1977] [1978] [1979]) (./utils-pkg.tex [1980]
Chapter 14.
[1981]
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 ',
[1982] [1983] [1984] [1985] [1986]
Underfull \hbox (badness 10000) in paragraph at lines 376--381
\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
[1987] [1988] [1989] [1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\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 717--723
\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
[1992] [1993]
Underfull \hbox (badness 5847) in paragraph at lines 850--856
[]\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 850--856
\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
[1994]
Underfull \hbox (badness 3861) in paragraph at lines 918--923
[]\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 ,
[1995] [1996]
Underfull \hbox (badness 3323) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

Underfull \hbox (badness 3919) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 3735) in paragraph at lines 1089--1097
\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 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
[1997]
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1998] [1999]
Underfull \vbox (badness 3803) has occurred while \output is active [2000]
[2001] [2002] [2003] [2004]
Underfull \hbox (badness 1371) in paragraph at lines 1606--1608
[]\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
[2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Underfull \hbox (badness 2057) in paragraph at lines 2215--2217
[]\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
[2015] [2016] [2017] [2018] [2019] [2020]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [2021] [2022]
Underfull \hbox (badness 1748) in paragraph at lines 2733--2736
[]\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
[2023] [2024] [2025] [2026] [2027] [2028] [2029]
Underfull \hbox (badness 5388) in paragraph at lines 3142--3146
[]\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 [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

Underfull \hbox (badness 2285) in paragraph at lines 3147--3150
[]\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 =
[2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040]
Underfull \hbox (badness 1430) in paragraph at lines 3906--3914
[]\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
[2041]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\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
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [2056] [2057] [2058]
[2059] [2060] [2061] [2062] [2063]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073]
Underfull \hbox (badness 1371) in paragraph at lines 5996--5998
[]\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
[2074]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2075] [2076] [2077]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2078]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2079] [2080]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[2081] [2082] [2083]
Underfull \hbox (badness 1325) in paragraph at lines 6632--6636
[]\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

Underfull \hbox (badness 4726) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of
[2084]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[2085]
Underfull \hbox (badness 3219) in paragraph at lines 6792--6799
[]\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 6792--6799
\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 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

Underfull \hbox (badness 1596) in paragraph at lines 6792--6799
[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently

Underfull \hbox (badness 2932) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[2086]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,
[2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097]
[2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108]
[2109] [2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 8436--8438
[]\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 2310) in paragraph at lines 8458--8463
[]\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,
[2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119]
Underfull \hbox (badness 1248) in paragraph at lines 8982--8986
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[2120]
Underfull \hbox (badness 1789) in paragraph at lines 9060--9062
[]\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
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130]
Underfull \vbox (badness 10000) has occurred while \output is active [2131]
[2132] [2133]
Underfull \hbox (badness 1097) in paragraph at lines 9897--9900
[]\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
[2134] [2135]
Underfull \hbox (badness 3000) in paragraph at lines 10033--10038
[][][]\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 ;
[2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144]
Underfull \hbox (badness 2134) in paragraph at lines 10616--10621
[][][]\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 ;

Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 2469) in paragraph at lines 11165--11169
[]\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 11165--11169
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2154] [2155] [2156] [2157] [2158]
Underfull \hbox (badness 4060) in paragraph at lines 11496--11499
[]\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 11519--11519
 []\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 '[] 
[2159] [2160] [2161] [2162]
Underfull \hbox (badness 2150) in paragraph at lines 11758--11760
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2163] [2164] [2165] [2166]
Underfull \hbox (badness 10000) in paragraph at lines 11977--11981
[]\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 12008--12014
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2167] [2168] [2169]
Underfull \hbox (badness 1009) in paragraph at lines 12202--12214
[]\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

Underfull \hbox (badness 4779) in paragraph at lines 12239--12241
[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd
[2170]
Underfull \hbox (badness 1077) in paragraph at lines 12269--12276
\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2171] [2172] [2173] [2174] [2175] [2176]
Underfull \hbox (badness 3780) in paragraph at lines 12670--12674
[]\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 12686--12689
[]\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
[2177] [2178] [2179] [2180]
Underfull \hbox (badness 2302) in paragraph at lines 12891--12893
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2181] [2182] [2183] [2184]
Underfull \hbox (badness 10000) in paragraph at lines 13187--13192
[]\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 13196--13199
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2185] [2186]
Underfull \vbox (badness 10000) has occurred while \output is active [2187]
[2188] [2189] [2190] [2191]
Underfull \hbox (badness 2932) in paragraph at lines 13616--13623
[]\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,

Underfull \hbox (badness 1688) in paragraph at lines 13616--13623
\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2192] [2193] [2194] [2195] [2196]
Underfull \hbox (badness 6510) in paragraph at lines 13925--13929
[]\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 13932--13935
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 13932--13935
\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
[2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 10000) in paragraph at lines 14596--14601
[]\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 14596--14601
[][]\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 14602--14604
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2207]
Underfull \hbox (badness 10000) in paragraph at lines 14661--14664
[][][]\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 ,
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219]
Underfull \hbox (badness 10000) in paragraph at lines 15434--15436
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2220] [2221] [2222] [2223]) [2224]
No file refman.ind.
(./refman.aux)

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


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

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed 
one

pdfTeX warning (dest): name{Rfn.lmList} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparse.model.matrix} has been referenced but do
es not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nlsList} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/
texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4b.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr5.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/
fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on refman.pdf (2227 pages, 5567528 bytes).
Transcript written on refman.log.
This is makeindex, version 2.15 [TeX Live 2019/dev] (kpathsea + Thai support).
Scanning input file refman.idx.................done (13921 entries accepted, 34 rejected).
Sorting entries..................................................................................................................................................done (213790 comparisons).
Generating output file refman.ind................done (13715 lines written, 56 warnings).
Output written in refman.ind.
Transcript written in refman.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./refman.tex
LaTeX2e <2018-12-01>
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2018/09/03 v1.4i Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file refman.idx
(./refman.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./refman.out) (./refman.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] (./refman.toc
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] [3]
[4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]
[20] [21] [22] [23] [24] [25] [26] [27] [28] [29]) [30] (./base-pkg.tex
Chapter 1.
[1] [2]
Underfull \hbox (badness 6995) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
/ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It

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

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

Underfull \hbox (badness 10000) in paragraph at lines 141--149
\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As

Underfull \hbox (badness 4995) in paragraph at lines 141--149
\T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi
4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 ,
[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] [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 1178--1181
[]\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 1953--1953
 []\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] [34] [35] [36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via

Underfull \hbox (badness 1102) in paragraph at lines 2392--2397
\T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim
-ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit

[38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52]
[53] [54] [55] [56] [57] [58] [59]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[60] [61] [62]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77]
[78]
Underfull \hbox (badness 2521) in paragraph at lines 5033--5035
[]\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
[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93]
[94] [95] [96]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6189--6189
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[97] [98] [99] [100] [101] [102]
Overfull \hbox (46.35893pt too wide) in paragraph at lines 6598--6600
[]\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 : 
[103] [104]
Underfull \hbox (badness 10000) in paragraph at lines 6746--6749
[]\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
[105] [106]
Underfull \hbox (badness 6063) in paragraph at lines 6928--6934
[]\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-


Underfull \hbox (badness 2343) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1708) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
s not rec-om-mended) when

Underfull \hbox (badness 1831) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
/10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
[107]
Underfull \hbox (badness 3568) in paragraph at lines 6990--6997
\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
[108] [109]
Underfull \vbox (badness 10000) has occurred while \output is active [110]
Underfull \vbox (badness 10000) has occurred while \output is active [111]
[112]
Underfull \hbox (badness 1077) in paragraph at lines 7307--7313
[]\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 7307--7313
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[113] [114] [115] [116] [117] [118]
Underfull \hbox (badness 2096) in paragraph at lines 7648--7652
\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 .
[119] [120]
Underfull \hbox (badness 2351) in paragraph at lines 7766--7769
[][][]\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 ,
[121] [122] [123] [124] [125]
Underfull \hbox (badness 4479) in paragraph at lines 8092--8102
[][][]\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),
[126] [127] [128] [129] [130] [131]
Underfull \hbox (badness 1629) in paragraph at lines 8539--8551
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

Underfull \hbox (badness 1609) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which

Underfull \hbox (badness 2426) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that 
value is on those OSes also used as an er-ror code.
[132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
Underfull \hbox (badness 1178) in paragraph at lines 9275--9279
[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154]
[155] [156] [157] [158] [159] [160]
Underfull \hbox (badness 1735) in paragraph at lines 10423--10427
\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 .
[161] [162] [163] [164] [165] [166] [167]
Underfull \hbox (badness 6396) in paragraph at lines 10862--10870
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 1946) in paragraph at lines 10862--10870
\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
[168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181] [182] [183] [184]
Underfull \hbox (badness 4569) in paragraph at lines 11978--11982
[]\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 11978--11982
\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
[185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196]
[197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208]
[209]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[210]
Underfull \hbox (badness 1565) in paragraph at lines 13712--13716
[][][]\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
[211]
Underfull \hbox (badness 4927) in paragraph at lines 13756--13758
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
[212]
Underfull \hbox (badness 3148) in paragraph at lines 13849--13854
[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
[213]
Underfull \hbox (badness 1466) in paragraph at lines 13896--13899
[]\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
[214] [215]
Underfull \hbox (badness 10000) in paragraph at lines 14015--14019
[][][]\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 14026--14029
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[216] [217] [218] [219]
Underfull \hbox (badness 3965) in paragraph at lines 14316--14320
[]\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,
[220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
[232]
Underfull \hbox (badness 4429) in paragraph at lines 15092--15095
[]\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
[233] [234]
Underfull \hbox (badness 10000) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

Underfull \hbox (badness 1215) in paragraph at lines 15198--15200
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

Underfull \hbox (badness 10000) in paragraph at lines 15220--15225
[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

Underfull \hbox (badness 1558) in paragraph at lines 15220--15225
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

Underfull \hbox (badness 10000) in paragraph at lines 15232--15236
[]\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

Underfull \hbox (badness 2426) in paragraph at lines 15232--15236
\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[235]
Underfull \hbox (badness 2035) in paragraph at lines 15271--15275
[]\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 within
[236]
Underfull \vbox (badness 10000) has occurred while \output is active [237]
[238] [239] [240] [241] [242] [243] [244]
Underfull \hbox (badness 2452) in paragraph at lines 15870--15874
[]\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 15870--15874
\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
[245] [246] [247]
Underfull \hbox (badness 1092) in paragraph at lines 16043--16048
[][]\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
[248] [249] [250]
Underfull \hbox (badness 6741) in paragraph at lines 16293--16297
\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
 ,
[251] [252] [253] [254] [255] [256] [257] [258] [259]
Underfull \vbox (badness 3803) has occurred while \output is active [260]
Underfull \vbox (badness 10000) has occurred while \output is active [261]
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1478) in paragraph at lines 17582--17585
[]\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
[271] [272] [273] [274]
Underfull \hbox (badness 10000) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[275] [276] [277] [278] [279] [280] [281] [282] [283]
Underfull \hbox (badness 1442) in paragraph at lines 18437--18439
[]\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
[284]
Underfull \hbox (badness 2452) in paragraph at lines 18529--18545
[][][]\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 ,
[285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 1248) in paragraph at lines 18948--18951
[]\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 ,
[292] [293] [294] [295]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[296] [297] [298] [299] [300] [301]
Underfull \hbox (badness 1596) in paragraph at lines 19625--19630
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 2469) in paragraph at lines 20229--20234
[]\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 20243--20250
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[313]
Underfull \hbox (badness 10000) in paragraph at lines 20317--20321
[]\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 20317--20321
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[314] [315]
Underfull \hbox (badness 1014) in paragraph at lines 20487--20492
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
Underfull \hbox (badness 1264) in paragraph at lines 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[328]
Underfull \hbox (badness 4441) in paragraph at lines 21305--21308
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 6047) in paragraph at lines 22052--22054
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351]
[352] [353] [354] [355] [356]
Underfull \hbox (badness 1077) in paragraph at lines 23093--23099
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\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 .
[357] [358] [359] [360] [361] [362] [363] [364] [365]
Underfull \hbox (badness 2790) in paragraph at lines 23589--23592
[]\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 23589--23592
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[366] [367] [368] [369]
Underfull \hbox (badness 1194) in paragraph at lines 23871--23874
[]\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
[370] [371] [372]
Underfull \hbox (badness 2368) in paragraph at lines 24077--24083
[]\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 list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24077--24083
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[373] [374] [375] [376] [377] [378]
Underfull \hbox (badness 10000) in paragraph at lines 24459--24462
[]\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
[379] [380] [381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 25064--25066
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
[400]
Underfull \hbox (badness 1038) in paragraph at lines 25904--25912
[]\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 1735) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25913--25916
[]\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 25932--25934
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[401] [402]
Underfull \hbox (badness 2142) in paragraph at lines 26073--26077
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 26123--26128
[]\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
[403] [404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 26411--26417
[]\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 26411--26417
\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 26411--26417
\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 26424--26427
[]\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 26450--26452
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 26485--26490
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and
[407]
Underfull \hbox (badness 7203) in paragraph at lines 26503--26506
[]\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 10000) in paragraph at lines 26527--26532
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26527--26532
\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).
[408] [409] [410] [411] [412] [413] [414] [415]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[416]
Underfull \hbox (badness 7925) in paragraph at lines 27124--27128
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

Underfull \hbox (badness 1622) in paragraph at lines 27124--27128
[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

Underfull \hbox (badness 6125) in paragraph at lines 27129--27138
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427]
Underfull \hbox (badness 2726) in paragraph at lines 27850--27853
[]\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
[428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439]
[440] [441] [442] [443] [444] [445]
Underfull \vbox (badness 3803) has occurred while \output is active [446]
[447] [448] [449] [450] [451] [452] [453]
Underfull \hbox (badness 1533) in paragraph at lines 29541--29544
[]\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
[454] [455] [456]
Underfull \hbox (badness 1163) in paragraph at lines 29704--29715
[]\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
[457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468]
[469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 31250--31254
[]\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 31250--31254
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 31272--31274
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[481] [482] [483] [484] [485] [486] [487] [488] [489]
Underfull \hbox (badness 1655) in paragraph at lines 31828--31830
[]\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
[490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501]
[502] [503] [504] [505] [506]
Underfull \hbox (badness 2261) in paragraph at lines 32947--32952
[]\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
[507]
Underfull \hbox (badness 10000) in paragraph at lines 32974--32980
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1484) in paragraph at lines 32974--32980
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519]
[520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
[532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543]
[544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555]
Underfull \hbox (badness 1072) in paragraph at lines 36116--36120
[]\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 36121--36125
[]\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 36149--36155
[]\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 36149--36155
\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 36149--36155
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in

Underfull \hbox (badness 3009) in paragraph at lines 36161--36168
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 36161--36168
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 36161--36168
\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 36161--36168
\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
[556] [557] [558] [559] [560] [561]
Underfull \hbox (badness 1142) in paragraph at lines 36514--36520
[]\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 \T1/zi4/m/n/10 "%Y-%m-%d
[562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573]
[574] [575] [576] [577] [578] [579] [580] [581]
Underfull \hbox (badness 1565) in paragraph at lines 37787--37789
[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[582] [583] [584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 4967) in paragraph at lines 38386--38391
[]\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
[592] [593]
Underfull \hbox (badness 1616) in paragraph at lines 38499--38504
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
[594] [595] [596] [597]
Underfull \vbox (badness 10000) has occurred while \output is active [598]
[599] [600] [601] [602]
Underfull \hbox (badness 1472) in paragraph at lines 39025--39028
[]\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
[603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614]
[615]
Underfull \vbox (badness 3803) has occurred while \output is active [616]
Underfull \hbox (badness 10000) in paragraph at lines 39939--39943
[]\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., \T1/zi4/m/n/10
 length(bin) >
[617] [618] [619] [620]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[621] [622] [623]
Underfull \hbox (badness 10000) in paragraph at lines 40374--40378
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[624] [625] [626] [627] [628] [629] [630] [631] [632]
Underfull \hbox (badness 10000) in paragraph at lines 40987--40990
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
[633] [634] [635] [636] [637] [638]
Underfull \vbox (badness 10000) has occurred while \output is active [639]
[640] [641] [642] [643] [644] [645] [646]
Underfull \hbox (badness 1990) in paragraph at lines 41890--41898
[]\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 41890--41898
\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
[647] [648] [649] [650] [651] [652] [653] [654]
Underfull \hbox (badness 1917) in paragraph at lines 42396--42403
[]\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
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665]
Underfull \hbox (badness 3668) in paragraph at lines 43125--43127
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[666] [667]
Underfull \hbox (badness 2401) in paragraph at lines 43253--43257
[]\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
[668] [669] [670]
Underfull \hbox (badness 2111) in paragraph at lines 43442--43447
\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 10000) in paragraph at lines 43463--43468
[]\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
[671] [672] [673] [674] [675] [676] [677] [678] [679]
Underfull \hbox (badness 5417) in paragraph at lines 44045--44049
[]\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
[680]
Underfull \hbox (badness 10000) in paragraph at lines 44106--44110
[]\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
[681] [682]) (./compiler-pkg.tex
Chapter 2.
[683] [684] [685] [686]) (./datasets-pkg.tex
Chapter 3.
[687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698]
[699] [700] [701] [702] [703]
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.
[704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715]
[716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726]
Underfull \vbox (badness 1448) has occurred while \output is active [727]
[728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738]
Overfull \vbox (19.74611pt too high) has occurred while \output is active
[739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
[751] [752] [753] [754]
Underfull \vbox (badness 10000) has occurred while \output is active [755]
[756] [757] [758]
Underfull \vbox (badness 10000) has occurred while \output is active [759]
[760] [761] [762] [763] [764]
Overfull \vbox (18.9959pt too high) has occurred while \output is active
[765] [766] [767]) (./grDevices-pkg.tex [768]
Chapter 4.
[769] [770] [771] [772] [773]
Underfull \hbox (badness 3158) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

Underfull \hbox (badness 10000) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

Underfull \hbox (badness 1852) in paragraph at lines 298--303
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
[774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785]
[786]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\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
[787] [788] [789] [790]
Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
[]\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
[791] [792] [793]
Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
\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
[794] [795] [796] [797] [798] [799]
Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
\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 ,
[800] [801]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[802] [803] [804]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[805] [806] [807] [808] [809] [810] [811] [812] [813] [814]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829

[815] [816] [817] [818] [819] [820] [821] [822] [823]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[824] [825] [826] [827] [828]
Underfull \vbox (badness 10000) has occurred while \output is active [829]
Underfull \hbox (badness 10000) in paragraph at lines 3785--3788
[]\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
[830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

Underfull \hbox (badness 4181) in paragraph at lines 4514--4519
\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
[841]
Underfull \vbox (badness 10000) has occurred while \output is active [842]
[843]
Underfull \hbox (badness 1067) in paragraph at lines 4668--4675
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[844] [845] [846] [847]
Underfull \hbox (badness 1377) in paragraph at lines 4971--4976
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[848]
Underfull \hbox (badness 1418) in paragraph at lines 5047--5054
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[849] [850]
Underfull \hbox (badness 1377) in paragraph at lines 5176--5181
[]\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
[851]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\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
[852] [853]
Underfull \hbox (badness 2035) in paragraph at lines 5380--5389
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\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 ,
[854]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5448--5455
\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 .
[855] [856] [857]
Underfull \hbox (badness 1546) in paragraph at lines 5590--5598
[]\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 ,
[858] [859] [860] [861] [862] [863] [864] [865]
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877]
[878]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[879]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[880] [881] [882] [883] [884]
Underfull \hbox (badness 3780) in paragraph at lines 7345--7351
[]\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 ,
[885] [886] [887]
Underfull \hbox (badness 2680) in paragraph at lines 7546--7548
[]\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
[888] [889] [890]) (./graphics-pkg.tex
Chapter 5.
[891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902]
[903] [904] [905] [906] [907] [908] [909] [910] [911] [912]
Underfull \hbox (badness 4634) in paragraph at lines 1351--1354
[][][]\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 ,
[913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924]
[925] [926] [927] [928] [929]
Underfull \hbox (badness 1009) in paragraph at lines 2390--2397
\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
[930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941]
[942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952]
Underfull \vbox (badness 10000) has occurred while \output is active [953]
[954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965]
Underfull \hbox (badness 3229) in paragraph at lines 4534--4539
[]\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
[966] [967] [968] [969] [970]
Underfull \hbox (badness 10000) in paragraph at lines 4891--4897
[]\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 4891--4897
\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
[971]
Underfull \hbox (badness 10000) in paragraph at lines 5022--5025

[972]
Underfull \hbox (badness 10000) in paragraph at lines 5083--5085

[973 </build/r-base-3.6.1/library/graphics/help/figures/mai.pdf>] [974 </build/
r-base-3.6.1/library/graphics/help/figures/oma.pdf>] [975]
Underfull \hbox (badness 10000) in paragraph at lines 5273--5275
[]\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
[976]
Underfull \vbox (badness 3803) has occurred while \output is active [977]
[978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989]
[990] [991] [992] [993] [994] [995] [996] [997] [998]
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6751--6752
[][] 
[999] [1000 </build/r-base-3.6.1/library/graphics/help/figures/pch.pdf>]
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011]
[1012]
Underfull \hbox (badness 2012) in paragraph at lines 7576--7579
[]\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 poi
nt
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
[1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033]
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

Underfull \hbox (badness 10000) in paragraph at lines 8838--8840
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
[1034]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [1035] [1036] [1037] [1038])
(./grid-pkg.tex
Chapter 6.

Underfull \vbox (badness 10000) has occurred while \output is active [1039]
[1040] [1041] [1042] [1043] [1044] [1045] [1046]
Underfull \hbox (badness 2680) in paragraph at lines 483--486
[]\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
[1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056]
Underfull \hbox (badness 4279) in paragraph at lines 1064--1073
[][][]\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 ,
[1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067]
[1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078]
[1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089]
[1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100]
Underfull \vbox (badness 10000) has occurred while \output is active [1101]
[1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
[1113] [1114]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\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
[1115] [1116] [1117] [1118]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129]
[1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140]
[1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149]
Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
[]\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 \T1/zi4/m/n/10 depth
[1150] [1151] [1152] [1153]) (./methods-pkg.tex [1154]
Chapter 7.
[1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162]
Underfull \vbox (badness 3803) has occurred while \output is active [1163]
Underfull \vbox (badness 10000) has occurred while \output is active [1164]
[1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173]
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
[1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181]
Underfull \hbox (badness 2181) 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
[1182]
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
[1183] [1184] [1185]
Underfull \hbox (badness 2213) 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 =
[1186] [1187] [1188] [1189] [1190]
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
[1191] [1192]
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
[1193]
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
[1194] [1195] [1196] [1197] [1198] [1199] [1200]
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
[1201] [1202] [1203] [1204] [1205]
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
[1206]
Underfull \hbox (badness 10000) in paragraph at lines 3642--3651
[]\T1/ptm/m/n/10 The
[1207]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
[1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218]
Underfull \hbox (badness 1769) in paragraph at lines 4472--4478
[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228]
Underfull \vbox (badness 10000) has occurred while \output is active [1229]
[1230] [1231]
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
[1232]
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
[1233] [1234] [1235] [1236]
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
[1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244]
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
[1245] [1246] [1247] [1248]
Underfull \vbox (badness 10000) has occurred while \output is active [1249]
[1250] [1251] [1252]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}
                               [1253] [1254] [1255]pdfTeX warning (ext4): desti
nation with the same identifier (name{Rfn.Complex}) has been already used, dupl
icate ignored
<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}
                                                 [1256]
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
[1257] [1258] [1259]
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
[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281]
[1282] [1283] [1284] [1285] [1286]
Underfull \vbox (badness 10000) has occurred while \output is active [1287]
[1288] [1289] [1290] [1291] [1292] [1293] [1294]
Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1295] [1296] [1297] [1298] [1299] [1300] [1301]
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.,
[1302] [1303] [1304] [1305]) (./parallel-pkg.tex [1306]
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
[1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317]
[1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327]
Underfull \hbox (badness 3386) in paragraph at lines 1365--1368
[]\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
[1328] [1329] [1330]) (./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
[1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341]
[1342] [1343] [1344] [1345] [1346]) (./stats-pkg.tex
Chapter 10.
[1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
[1358] [1359] [1360]
Underfull \hbox (badness 1412) in paragraph at lines 875--877
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368]
Underfull \hbox (badness 2503) in paragraph at lines 1356--1359
[]\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 ,
[1369] [1370] [1371]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
[1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382]
[1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
[1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401]
Underfull \hbox (badness 2503) in paragraph at lines 3437--3440
[]\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 ,
[1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
[1413] [1414] [1415] [1416]
Underfull \hbox (badness 1127) in paragraph at lines 4351--4354
[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1417] [1418] [1419] [1420] [1421]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431]
Underfull \hbox (badness 2556) in paragraph at lines 5317--5320
[]\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 5334--5336
[]\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
[1432] [1433] [1434] [1435] [1436] [1437] [1438]
Underfull \hbox (badness 2503) in paragraph at lines 5726--5730
[]\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 ,
[1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
[1450] [1451]
Underfull \hbox (badness 7081) in paragraph at lines 6520--6523
[]\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 6524--6526
[]\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
[1452] [1453] [1454] [1455] [1456]
Underfull \vbox (badness 3803) has occurred while \output is active [1457]
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 7369--7372
[]\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
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
Underfull \vbox (badness 10000) has occurred while \output is active [1487]
[1488] [1489] [1490] [1491]
Underfull \hbox (badness 2626) in paragraph at lines 9048--9051
[]\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
[1492] [1493]
Underfull \hbox (badness 2503) in paragraph at lines 9155--9159
[]\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 ,
[1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504]
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516] [1517] [1518]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 10844--10847
[]\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,
[1519]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1526] [1527] [1528] [1529] [1530] [1531]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\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

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1532] [1533]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1534] [1535]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\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
[1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 \T1/zi4/m/n/10 SSinit =
[1546] [1547] [1548] [1549] [1550] [1551]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562]
[1563]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1574] [1575]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\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
[1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586]
[1587] [1588] [1589] [1590] [1591] [1592] [1593]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\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 ,
[1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\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
[1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612]
[1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623]
[1624] [1625] [1626] [1627] [1628] [1629]
Underfull \vbox (badness 10000) has occurred while \output is active [1630]
Underfull \vbox (badness 10000) has occurred while \output is active [1631]
[1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642]
[1643]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

Underfull \hbox (badness 1735) in paragraph at lines 18581--18584
[]\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
[1644]
Underfull \hbox (badness 2343) in paragraph at lines 18594--18598
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

Underfull \hbox (badness 3471) in paragraph at lines 18594--18598
\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18602--18606
[]\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
[1645] [1646] [1647]
Overfull \hbox (15.73795pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1648]
[1649] [1650] [1651] [1652] [1653] [1654]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1664] [1665] [1666] [1667]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1668] [1669] [1670] [1671] [1672] [1673] [1674]
Underfull \hbox (badness 2503) in paragraph at lines 20381--20384
[]\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 ,

Underfull \hbox (badness 3919) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
[1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685]
[1686] [1687] [1688] [1689] [1690] [1691] [1692]
Underfull \hbox (badness 10000) in paragraph at lines 21485--21491
[]\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 ,
[1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703]
[1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714]
[1715]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723]
Overfull \hbox (27.74408pt too wide) in paragraph at lines 23399--23399
 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1724] [1725] [1726] [1727] [1728]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 4205) in paragraph at lines 23650--23653
\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
[1729] [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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 \T1/zi4/m/n/10 y[j] =
[1738]
Underfull \hbox (badness 3690) in paragraph at lines 24287--24291
[][][]\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
[1739] [1740] [1741] [1742] [1743] [1744] [1745]
Underfull \vbox (badness 10000) has occurred while \output is active [1746]
[1747]
Underfull \hbox (badness 2165) in paragraph at lines 24777--24782
[]\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 ,
[1748] [1749] [1750]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
[1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761]
[1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772]
[1773] [1774]
Underfull \vbox (badness 10000) has occurred while \output is active [1775]
Underfull \hbox (badness 3514) in paragraph at lines 26556--26561
[]\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
[1776] [1777] [1778] [1779]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26790--26790
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1780]
Underfull \hbox (badness 3514) in paragraph at lines 26826--26832
[]\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
[1781] [1782] [1783] [1784]
Underfull \hbox (badness 3514) in paragraph at lines 27040--27045
[]\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
[1785] [1786]
Underfull \hbox (badness 3514) in paragraph at lines 27127--27132
[]\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
[1787]
Underfull \hbox (badness 3514) in paragraph at lines 27192--27197
[]\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
[1788] [1789]
Underfull \hbox (badness 3514) in paragraph at lines 27286--27291
[]\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
[1790]
Underfull \hbox (badness 6691) in paragraph at lines 27378--27383
[]\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
[1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799]
Underfull \hbox (badness 4024) in paragraph at lines 27908--27911
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
[1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809]
Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\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
[1810] [1811] [1812]
Underfull \hbox (badness 5431) in paragraph at lines 28724--28727
[]\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
[1813] [1814] [1815] [1816] [1817] [1818]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1819] [1820] [1821] [1822] [1823]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834]
[1835] [1836] [1837] [1838] [1839] [1840] [1841] [1842]
Underfull \hbox (badness 3557) in paragraph at lines 30470--30474
[]\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 \T1/zi4
/m/n/10 interval =
[1843] [1844] [1845]
Underfull \vbox (badness 10000) has occurred while \output is active [1846]
[1847] [1848]
Underfull \hbox (badness 1337) in paragraph at lines 30834--30838
[]\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
[1849] [1850] [1851] [1852] [1853] [1854] [1855] [1856] [1857]
Underfull \hbox (badness 1337) in paragraph at lines 31361--31365
[]\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
[1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867])
(./stats4-pkg.tex [1868]
Chapter 11.
[1869] [1870] [1871] [1872] [1873] [1874]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1875] [1876] [1877])
(./tcltk-pkg.tex [1878]
Chapter 12.
[1879] [1880] [1881] [1882] [1883] [1884] [1885]
Underfull \vbox (badness 10000) has occurred while \output is active [1886]
Underfull \vbox (badness 10000) has occurred while \output is active [1887]
Underfull \hbox (badness 1546) in paragraph at lines 664--671
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898]
[1899]) (./tools-pkg.tex [1900]
Chapter 13.
[1901]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 72.

[1902]
Underfull \hbox (badness 3039) in paragraph at lines 164--167
[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1903] [1904]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

Underfull \hbox (badness 4967) in paragraph at lines 285--298
\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1905] [1906]
Underfull \hbox (badness 3039) in paragraph at lines 389--391
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917]
[1918]
Underfull \hbox (badness 4441) in paragraph at lines 1139--1149
\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-
[1919]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
[1920]
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209
\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 ,
[1921] [1922] [1923] [1924] [1925]
Underfull \hbox (badness 2293) in paragraph at lines 1558--1560
[]\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
[1926] [1927]
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Underfull \hbox (badness 1082) in paragraph at lines 1703--1705
[]\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
[1928] [1929] [1930] [1931]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1932] [1933] [1934]
[1935] [1936]
Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202
 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1937] [1938] [1939]
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1940] [1941] [1942] [1943] [1944] [1945] [1946]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
(Font)              using `T1/zi4/m/n' instead on input line 2846.

[1947] [1948] [1949] [1950] [1951]
Underfull \hbox (badness 1424) in paragraph at lines 3128--3130
[]\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
[1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962]
Underfull \hbox (badness 10000) in paragraph at lines 3832--3834
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1963] [1964]
Underfull \hbox (badness 10000) in paragraph at lines 3971--3974
[]\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
[1965] [1966]
Underfull \hbox (badness 1137) in paragraph at lines 4073--4075
[]\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
[1967] [1968] [1969] [1970] [1971]
Underfull \hbox (badness 1796) in paragraph at lines 4381--4386
[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1972]
Underfull \hbox (badness 1838) in paragraph at lines 4455--4461
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

Underfull \hbox (badness 10000) in paragraph at lines 4455--4461
\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
[1973] [1974] [1975]
Underfull \hbox (badness 2197) in paragraph at lines 4671--4681
[]\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 :
[1976]
Underfull \hbox (badness 1571) in paragraph at lines 4734--4738
[]\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
[1977] [1978] [1979]) (./utils-pkg.tex [1980]
Chapter 14.
[1981]
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 ',
[1982] [1983] [1984] [1985] [1986]
Underfull \hbox (badness 10000) in paragraph at lines 376--381
\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
[1987] [1988] [1989] [1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\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 717--723
\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
[1992] [1993]
Underfull \hbox (badness 5847) in paragraph at lines 850--856
[]\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 850--856
\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
[1994]
Underfull \hbox (badness 3861) in paragraph at lines 918--923
[]\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 ,
[1995] [1996]
Underfull \hbox (badness 3323) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

Underfull \hbox (badness 3919) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 3735) in paragraph at lines 1089--1097
\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 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
[1997]
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1998] [1999]
Underfull \vbox (badness 3803) has occurred while \output is active [2000]
[2001] [2002] [2003] [2004]
Underfull \hbox (badness 1371) in paragraph at lines 1606--1608
[]\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
[2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Underfull \hbox (badness 2057) in paragraph at lines 2215--2217
[]\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
[2015] [2016] [2017] [2018] [2019] [2020]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [2021] [2022]
Underfull \hbox (badness 1748) in paragraph at lines 2733--2736
[]\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
[2023] [2024] [2025] [2026] [2027] [2028] [2029]
Underfull \hbox (badness 5388) in paragraph at lines 3142--3146
[]\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 [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

Underfull \hbox (badness 2285) in paragraph at lines 3147--3150
[]\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 =
[2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040]
Underfull \hbox (badness 1430) in paragraph at lines 3906--3914
[]\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
[2041]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\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
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [2056] [2057] [2058]
[2059] [2060] [2061] [2062] [2063]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073]
Underfull \hbox (badness 1371) in paragraph at lines 5996--5998
[]\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
[2074]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2075] [2076] [2077]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2078]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2079] [2080]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[2081] [2082] [2083]
Underfull \hbox (badness 1325) in paragraph at lines 6632--6636
[]\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

Underfull \hbox (badness 4726) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of
[2084]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[2085]
Underfull \hbox (badness 3219) in paragraph at lines 6792--6799
[]\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 6792--6799
\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 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

Underfull \hbox (badness 1596) in paragraph at lines 6792--6799
[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently

Underfull \hbox (badness 2932) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[2086]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,
[2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097]
[2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108]
[2109] [2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 8436--8438
[]\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 2310) in paragraph at lines 8458--8463
[]\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,
[2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119]
Underfull \hbox (badness 1248) in paragraph at lines 8982--8986
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[2120]
Underfull \hbox (badness 1789) in paragraph at lines 9060--9062
[]\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
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130]
Underfull \vbox (badness 10000) has occurred while \output is active [2131]
[2132] [2133]
Underfull \hbox (badness 1097) in paragraph at lines 9897--9900
[]\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
[2134] [2135]
Underfull \hbox (badness 3000) in paragraph at lines 10033--10038
[][][]\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 ;
[2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144]
Underfull \hbox (badness 2134) in paragraph at lines 10616--10621
[][][]\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 ;

Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 2469) in paragraph at lines 11165--11169
[]\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 11165--11169
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2154] [2155] [2156] [2157] [2158]
Underfull \hbox (badness 4060) in paragraph at lines 11496--11499
[]\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 11519--11519
 []\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 '[] 
[2159] [2160] [2161] [2162]
Underfull \hbox (badness 2150) in paragraph at lines 11758--11760
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2163] [2164] [2165] [2166]
Underfull \hbox (badness 10000) in paragraph at lines 11977--11981
[]\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 12008--12014
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2167] [2168] [2169]
Underfull \hbox (badness 1009) in paragraph at lines 12202--12214
[]\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

Underfull \hbox (badness 4779) in paragraph at lines 12239--12241
[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd
[2170]
Underfull \hbox (badness 1077) in paragraph at lines 12269--12276
\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2171] [2172] [2173] [2174] [2175] [2176]
Underfull \hbox (badness 3780) in paragraph at lines 12670--12674
[]\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 12686--12689
[]\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
[2177] [2178] [2179] [2180]
Underfull \hbox (badness 2302) in paragraph at lines 12891--12893
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2181] [2182] [2183] [2184]
Underfull \hbox (badness 10000) in paragraph at lines 13187--13192
[]\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 13196--13199
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2185] [2186]
Underfull \vbox (badness 10000) has occurred while \output is active [2187]
[2188] [2189] [2190] [2191]
Underfull \hbox (badness 2932) in paragraph at lines 13616--13623
[]\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,

Underfull \hbox (badness 1688) in paragraph at lines 13616--13623
\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2192] [2193] [2194] [2195] [2196]
Underfull \hbox (badness 6510) in paragraph at lines 13925--13929
[]\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 13932--13935
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 13932--13935
\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
[2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 10000) in paragraph at lines 14596--14601
[]\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 14596--14601
[][]\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 14602--14604
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2207]
Underfull \hbox (badness 10000) in paragraph at lines 14661--14664
[][][]\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 ,
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219]
Underfull \hbox (badness 10000) in paragraph at lines 15434--15436
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2220] [2221] [2222] [2223]) [2224] (./refman.ind [2225] [2226] [2227] [2228]
[2229] [2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239]
[2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249] [2250]
[2251] [2252] [2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260] [2261]
[2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272]
[2273] [2274]
Overfull \hbox (33.3567pt too wide) in paragraph at lines 8854--8856
[]\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , 

[2275] [2276] [2277] [2278] [2279] [2280]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 10177--10179
[]\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE 
[2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288]
Overfull \hbox (5.8567pt too wide) in paragraph at lines 11923--11925
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 11925--11927
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_results 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 11927--11929
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings 
[2289] [2290] [2291] [2292] [2293] [2294] [2295] [2296] [2297]) (./refman.aux)

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


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

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed 
one

pdfTeX warning (dest): name{Rfn.lmList} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparse.model.matrix} has been referenced but do
es not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nlsList} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/
texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4b.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr5.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/
fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on refman.pdf (2328 pages, 6262075 bytes).
Transcript written on refman.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./refman.tex
LaTeX2e <2018-12-01>
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2018/09/03 v1.4i Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file refman.idx
(./refman.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./refman.out) (./refman.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] (./refman.toc
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] [3]
[4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]
[20] [21] [22] [23] [24] [25] [26] [27] [28] [29]) [30] (./base-pkg.tex
Chapter 1.
[1] [2]
Underfull \hbox (badness 6995) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
/ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It

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

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

Underfull \hbox (badness 10000) in paragraph at lines 141--149
\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As

Underfull \hbox (badness 4995) in paragraph at lines 141--149
\T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi
4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 ,
[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] [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 1178--1181
[]\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 1953--1953
 []\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] [34] [35] [36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via

Underfull \hbox (badness 1102) in paragraph at lines 2392--2397
\T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim
-ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit

[38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52]
[53] [54] [55] [56] [57] [58] [59]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[60] [61] [62]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77]
[78]
Underfull \hbox (badness 2521) in paragraph at lines 5033--5035
[]\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
[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93]
[94] [95] [96]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6189--6189
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[97] [98] [99] [100] [101] [102]
Overfull \hbox (46.35893pt too wide) in paragraph at lines 6598--6600
[]\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 : 
[103] [104]
Underfull \hbox (badness 10000) in paragraph at lines 6746--6749
[]\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
[105] [106]
Underfull \hbox (badness 6063) in paragraph at lines 6928--6934
[]\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-


Underfull \hbox (badness 2343) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1708) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
s not rec-om-mended) when

Underfull \hbox (badness 1831) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
/10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
[107]
Underfull \hbox (badness 3568) in paragraph at lines 6990--6997
\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
[108] [109]
Underfull \vbox (badness 10000) has occurred while \output is active [110]
Underfull \vbox (badness 10000) has occurred while \output is active [111]
[112]
Underfull \hbox (badness 1077) in paragraph at lines 7307--7313
[]\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 7307--7313
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[113] [114] [115] [116] [117] [118]
Underfull \hbox (badness 2096) in paragraph at lines 7648--7652
\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 .
[119] [120]
Underfull \hbox (badness 2351) in paragraph at lines 7766--7769
[][][]\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 ,
[121] [122] [123] [124] [125]
Underfull \hbox (badness 4479) in paragraph at lines 8092--8102
[][][]\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),
[126] [127] [128] [129] [130] [131]
Underfull \hbox (badness 1629) in paragraph at lines 8539--8551
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

Underfull \hbox (badness 1609) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which

Underfull \hbox (badness 2426) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that 
value is on those OSes also used as an er-ror code.
[132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
Underfull \hbox (badness 1178) in paragraph at lines 9275--9279
[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154]
[155] [156] [157] [158] [159] [160]
Underfull \hbox (badness 1735) in paragraph at lines 10423--10427
\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 .
[161] [162] [163] [164] [165] [166] [167]
Underfull \hbox (badness 6396) in paragraph at lines 10862--10870
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 1946) in paragraph at lines 10862--10870
\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
[168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181] [182] [183] [184]
Underfull \hbox (badness 4569) in paragraph at lines 11978--11982
[]\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 11978--11982
\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
[185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196]
[197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208]
[209]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[210]
Underfull \hbox (badness 1565) in paragraph at lines 13712--13716
[][][]\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
[211]
Underfull \hbox (badness 4927) in paragraph at lines 13756--13758
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
[212]
Underfull \hbox (badness 3148) in paragraph at lines 13849--13854
[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
[213]
Underfull \hbox (badness 1466) in paragraph at lines 13896--13899
[]\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
[214] [215]
Underfull \hbox (badness 10000) in paragraph at lines 14015--14019
[][][]\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 14026--14029
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[216] [217] [218] [219]
Underfull \hbox (badness 3965) in paragraph at lines 14316--14320
[]\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,
[220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
[232]
Underfull \hbox (badness 4429) in paragraph at lines 15092--15095
[]\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
[233] [234]
Underfull \hbox (badness 10000) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

Underfull \hbox (badness 1215) in paragraph at lines 15198--15200
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

Underfull \hbox (badness 10000) in paragraph at lines 15220--15225
[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

Underfull \hbox (badness 1558) in paragraph at lines 15220--15225
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

Underfull \hbox (badness 10000) in paragraph at lines 15232--15236
[]\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

Underfull \hbox (badness 2426) in paragraph at lines 15232--15236
\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[235]
Underfull \hbox (badness 2035) in paragraph at lines 15271--15275
[]\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 within
[236]
Underfull \vbox (badness 10000) has occurred while \output is active [237]
[238] [239] [240] [241] [242] [243] [244]
Underfull \hbox (badness 2452) in paragraph at lines 15870--15874
[]\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 15870--15874
\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
[245] [246] [247]
Underfull \hbox (badness 1092) in paragraph at lines 16043--16048
[][]\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
[248] [249] [250]
Underfull \hbox (badness 6741) in paragraph at lines 16293--16297
\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
 ,
[251] [252] [253] [254] [255] [256] [257] [258] [259]
Underfull \vbox (badness 3803) has occurred while \output is active [260]
Underfull \vbox (badness 10000) has occurred while \output is active [261]
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1478) in paragraph at lines 17582--17585
[]\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
[271] [272] [273] [274]
Underfull \hbox (badness 10000) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[275] [276] [277] [278] [279] [280] [281] [282] [283]
Underfull \hbox (badness 1442) in paragraph at lines 18437--18439
[]\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
[284]
Underfull \hbox (badness 2452) in paragraph at lines 18529--18545
[][][]\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 ,
[285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 1248) in paragraph at lines 18948--18951
[]\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 ,
[292] [293] [294] [295]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[296] [297] [298] [299] [300] [301]
Underfull \hbox (badness 1596) in paragraph at lines 19625--19630
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 2469) in paragraph at lines 20229--20234
[]\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 20243--20250
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[313]
Underfull \hbox (badness 10000) in paragraph at lines 20317--20321
[]\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 20317--20321
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[314] [315]
Underfull \hbox (badness 1014) in paragraph at lines 20487--20492
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
Underfull \hbox (badness 1264) in paragraph at lines 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[328]
Underfull \hbox (badness 4441) in paragraph at lines 21305--21308
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 6047) in paragraph at lines 22052--22054
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351]
[352] [353] [354] [355] [356]
Underfull \hbox (badness 1077) in paragraph at lines 23093--23099
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\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 .
[357] [358] [359] [360] [361] [362] [363] [364] [365]
Underfull \hbox (badness 2790) in paragraph at lines 23589--23592
[]\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 23589--23592
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[366] [367] [368] [369]
Underfull \hbox (badness 1194) in paragraph at lines 23871--23874
[]\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
[370] [371] [372]
Underfull \hbox (badness 2368) in paragraph at lines 24077--24083
[]\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 list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24077--24083
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[373] [374] [375] [376] [377] [378]
Underfull \hbox (badness 10000) in paragraph at lines 24459--24462
[]\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
[379] [380] [381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 25064--25066
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
[400]
Underfull \hbox (badness 1038) in paragraph at lines 25904--25912
[]\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 1735) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25913--25916
[]\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 25932--25934
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[401] [402]
Underfull \hbox (badness 2142) in paragraph at lines 26073--26077
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 26123--26128
[]\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
[403] [404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 26411--26417
[]\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 26411--26417
\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 26411--26417
\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 26424--26427
[]\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 26450--26452
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 26485--26490
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and
[407]
Underfull \hbox (badness 7203) in paragraph at lines 26503--26506
[]\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 10000) in paragraph at lines 26527--26532
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26527--26532
\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).
[408] [409] [410] [411] [412] [413] [414] [415]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[416]
Underfull \hbox (badness 7925) in paragraph at lines 27124--27128
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

Underfull \hbox (badness 1622) in paragraph at lines 27124--27128
[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

Underfull \hbox (badness 6125) in paragraph at lines 27129--27138
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427]
Underfull \hbox (badness 2726) in paragraph at lines 27850--27853
[]\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
[428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439]
[440] [441] [442] [443] [444] [445]
Underfull \vbox (badness 3803) has occurred while \output is active [446]
[447] [448] [449] [450] [451] [452] [453]
Underfull \hbox (badness 1533) in paragraph at lines 29541--29544
[]\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
[454] [455] [456]
Underfull \hbox (badness 1163) in paragraph at lines 29704--29715
[]\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
[457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468]
[469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 31250--31254
[]\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 31250--31254
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 31272--31274
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[481] [482] [483] [484] [485] [486] [487] [488] [489]
Underfull \hbox (badness 1655) in paragraph at lines 31828--31830
[]\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
[490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501]
[502] [503] [504] [505] [506]
Underfull \hbox (badness 2261) in paragraph at lines 32947--32952
[]\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
[507]
Underfull \hbox (badness 10000) in paragraph at lines 32974--32980
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1484) in paragraph at lines 32974--32980
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519]
[520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
[532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543]
[544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555]
Underfull \hbox (badness 1072) in paragraph at lines 36116--36120
[]\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 36121--36125
[]\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 36149--36155
[]\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 36149--36155
\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 36149--36155
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in

Underfull \hbox (badness 3009) in paragraph at lines 36161--36168
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 36161--36168
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 36161--36168
\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 36161--36168
\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
[556] [557] [558] [559] [560] [561]
Underfull \hbox (badness 1142) in paragraph at lines 36514--36520
[]\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 \T1/zi4/m/n/10 "%Y-%m-%d
[562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573]
[574] [575] [576] [577] [578] [579] [580] [581]
Underfull \hbox (badness 1565) in paragraph at lines 37787--37789
[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[582] [583] [584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 4967) in paragraph at lines 38386--38391
[]\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
[592] [593]
Underfull \hbox (badness 1616) in paragraph at lines 38499--38504
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
[594] [595] [596] [597]
Underfull \vbox (badness 10000) has occurred while \output is active [598]
[599] [600] [601] [602]
Underfull \hbox (badness 1472) in paragraph at lines 39025--39028
[]\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
[603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614]
[615]
Underfull \vbox (badness 3803) has occurred while \output is active [616]
Underfull \hbox (badness 10000) in paragraph at lines 39939--39943
[]\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., \T1/zi4/m/n/10
 length(bin) >
[617] [618] [619] [620]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[621] [622] [623]
Underfull \hbox (badness 10000) in paragraph at lines 40374--40378
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[624] [625] [626] [627] [628] [629] [630] [631] [632]
Underfull \hbox (badness 10000) in paragraph at lines 40987--40990
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
[633] [634] [635] [636] [637] [638]
Underfull \vbox (badness 10000) has occurred while \output is active [639]
[640] [641] [642] [643] [644] [645] [646]
Underfull \hbox (badness 1990) in paragraph at lines 41890--41898
[]\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 41890--41898
\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
[647] [648] [649] [650] [651] [652] [653] [654]
Underfull \hbox (badness 1917) in paragraph at lines 42396--42403
[]\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
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665]
Underfull \hbox (badness 3668) in paragraph at lines 43125--43127
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[666] [667]
Underfull \hbox (badness 2401) in paragraph at lines 43253--43257
[]\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
[668] [669] [670]
Underfull \hbox (badness 2111) in paragraph at lines 43442--43447
\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 10000) in paragraph at lines 43463--43468
[]\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
[671] [672] [673] [674] [675] [676] [677] [678] [679]
Underfull \hbox (badness 5417) in paragraph at lines 44045--44049
[]\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
[680]
Underfull \hbox (badness 10000) in paragraph at lines 44106--44110
[]\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
[681] [682]) (./compiler-pkg.tex
Chapter 2.
[683] [684] [685] [686]) (./datasets-pkg.tex
Chapter 3.
[687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698]
[699] [700] [701] [702] [703]
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.
[704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715]
[716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726]
Underfull \vbox (badness 1448) has occurred while \output is active [727]
[728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738]
Overfull \vbox (19.74611pt too high) has occurred while \output is active
[739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
[751] [752] [753] [754]
Underfull \vbox (badness 10000) has occurred while \output is active [755]
[756] [757] [758]
Underfull \vbox (badness 10000) has occurred while \output is active [759]
[760] [761] [762] [763] [764]
Overfull \vbox (18.9959pt too high) has occurred while \output is active
[765] [766] [767]) (./grDevices-pkg.tex [768]
Chapter 4.
[769] [770] [771] [772] [773]
Underfull \hbox (badness 3158) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

Underfull \hbox (badness 10000) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

Underfull \hbox (badness 1852) in paragraph at lines 298--303
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
[774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785]
[786]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\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
[787] [788] [789] [790]
Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
[]\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
[791] [792] [793]
Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
\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
[794] [795] [796] [797] [798] [799]
Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
\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 ,
[800] [801]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[802] [803] [804]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[805] [806] [807] [808] [809] [810] [811] [812] [813] [814]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829

[815] [816] [817] [818] [819] [820] [821] [822] [823]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[824] [825] [826] [827] [828]
Underfull \vbox (badness 10000) has occurred while \output is active [829]
Underfull \hbox (badness 10000) in paragraph at lines 3785--3788
[]\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
[830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

Underfull \hbox (badness 4181) in paragraph at lines 4514--4519
\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
[841]
Underfull \vbox (badness 10000) has occurred while \output is active [842]
[843]
Underfull \hbox (badness 1067) in paragraph at lines 4668--4675
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[844] [845] [846] [847]
Underfull \hbox (badness 1377) in paragraph at lines 4971--4976
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[848]
Underfull \hbox (badness 1418) in paragraph at lines 5047--5054
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[849] [850]
Underfull \hbox (badness 1377) in paragraph at lines 5176--5181
[]\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
[851]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\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
[852] [853]
Underfull \hbox (badness 2035) in paragraph at lines 5380--5389
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\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 ,
[854]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5448--5455
\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 .
[855] [856] [857]
Underfull \hbox (badness 1546) in paragraph at lines 5590--5598
[]\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 ,
[858] [859] [860] [861] [862] [863] [864] [865]
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877]
[878]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[879]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[880] [881] [882] [883] [884]
Underfull \hbox (badness 3780) in paragraph at lines 7345--7351
[]\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 ,
[885] [886] [887]
Underfull \hbox (badness 2680) in paragraph at lines 7546--7548
[]\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
[888] [889] [890]) (./graphics-pkg.tex
Chapter 5.
[891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902]
[903] [904] [905] [906] [907] [908] [909] [910] [911] [912]
Underfull \hbox (badness 4634) in paragraph at lines 1351--1354
[][][]\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 ,
[913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924]
[925] [926] [927] [928] [929]
Underfull \hbox (badness 1009) in paragraph at lines 2390--2397
\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
[930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941]
[942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952]
Underfull \vbox (badness 10000) has occurred while \output is active [953]
[954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965]
Underfull \hbox (badness 3229) in paragraph at lines 4534--4539
[]\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
[966] [967] [968] [969] [970]
Underfull \hbox (badness 10000) in paragraph at lines 4891--4897
[]\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 4891--4897
\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
[971]
Underfull \hbox (badness 10000) in paragraph at lines 5022--5025

[972]
Underfull \hbox (badness 10000) in paragraph at lines 5083--5085

[973 </build/r-base-3.6.1/library/graphics/help/figures/mai.pdf>] [974 </build/
r-base-3.6.1/library/graphics/help/figures/oma.pdf>] [975]
Underfull \hbox (badness 10000) in paragraph at lines 5273--5275
[]\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
[976]
Underfull \vbox (badness 3803) has occurred while \output is active [977]
[978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989]
[990] [991] [992] [993] [994] [995] [996] [997] [998]
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6751--6752
[][] 
[999] [1000 </build/r-base-3.6.1/library/graphics/help/figures/pch.pdf>]
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011]
[1012]
Underfull \hbox (badness 2012) in paragraph at lines 7576--7579
[]\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 poi
nt
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
[1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033]
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

Underfull \hbox (badness 10000) in paragraph at lines 8838--8840
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
[1034]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [1035] [1036] [1037] [1038])
(./grid-pkg.tex
Chapter 6.

Underfull \vbox (badness 10000) has occurred while \output is active [1039]
[1040] [1041] [1042] [1043] [1044] [1045] [1046]
Underfull \hbox (badness 2680) in paragraph at lines 483--486
[]\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
[1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056]
Underfull \hbox (badness 4279) in paragraph at lines 1064--1073
[][][]\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 ,
[1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067]
[1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078]
[1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089]
[1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100]
Underfull \vbox (badness 10000) has occurred while \output is active [1101]
[1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
[1113] [1114]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\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
[1115] [1116] [1117] [1118]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129]
[1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140]
[1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149]
Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
[]\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 \T1/zi4/m/n/10 depth
[1150] [1151] [1152] [1153]) (./methods-pkg.tex [1154]
Chapter 7.
[1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162]
Underfull \vbox (badness 3803) has occurred while \output is active [1163]
Underfull \vbox (badness 10000) has occurred while \output is active [1164]
[1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173]
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
[1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181]
Underfull \hbox (badness 2181) 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
[1182]
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
[1183] [1184] [1185]
Underfull \hbox (badness 2213) 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 =
[1186] [1187] [1188] [1189] [1190]
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
[1191] [1192]
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
[1193]
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
[1194] [1195] [1196] [1197] [1198] [1199] [1200]
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
[1201] [1202] [1203] [1204] [1205]
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
[1206]
Underfull \hbox (badness 10000) in paragraph at lines 3642--3651
[]\T1/ptm/m/n/10 The
[1207]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
[1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218]
Underfull \hbox (badness 1769) in paragraph at lines 4472--4478
[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228]
Underfull \vbox (badness 10000) has occurred while \output is active [1229]
[1230] [1231]
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
[1232]
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
[1233] [1234] [1235] [1236]
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
[1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244]
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
[1245] [1246] [1247] [1248]
Underfull \vbox (badness 10000) has occurred while \output is active [1249]
[1250] [1251] [1252]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}
                               [1253] [1254] [1255]pdfTeX warning (ext4): desti
nation with the same identifier (name{Rfn.Complex}) has been already used, dupl
icate ignored
<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}
                                                 [1256]
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
[1257] [1258] [1259]
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
[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281]
[1282] [1283] [1284] [1285] [1286]
Underfull \vbox (badness 10000) has occurred while \output is active [1287]
[1288] [1289] [1290] [1291] [1292] [1293] [1294]
Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1295] [1296] [1297] [1298] [1299] [1300] [1301]
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.,
[1302] [1303] [1304] [1305]) (./parallel-pkg.tex [1306]
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
[1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317]
[1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327]
Underfull \hbox (badness 3386) in paragraph at lines 1365--1368
[]\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
[1328] [1329] [1330]) (./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
[1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341]
[1342] [1343] [1344] [1345] [1346]) (./stats-pkg.tex
Chapter 10.
[1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
[1358] [1359] [1360]
Underfull \hbox (badness 1412) in paragraph at lines 875--877
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368]
Underfull \hbox (badness 2503) in paragraph at lines 1356--1359
[]\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 ,
[1369] [1370] [1371]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
[1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382]
[1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
[1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401]
Underfull \hbox (badness 2503) in paragraph at lines 3437--3440
[]\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 ,
[1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
[1413] [1414] [1415] [1416]
Underfull \hbox (badness 1127) in paragraph at lines 4351--4354
[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1417] [1418] [1419] [1420] [1421]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431]
Underfull \hbox (badness 2556) in paragraph at lines 5317--5320
[]\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 5334--5336
[]\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
[1432] [1433] [1434] [1435] [1436] [1437] [1438]
Underfull \hbox (badness 2503) in paragraph at lines 5726--5730
[]\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 ,
[1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
[1450] [1451]
Underfull \hbox (badness 7081) in paragraph at lines 6520--6523
[]\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 6524--6526
[]\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
[1452] [1453] [1454] [1455] [1456]
Underfull \vbox (badness 3803) has occurred while \output is active [1457]
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 7369--7372
[]\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
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
Underfull \vbox (badness 10000) has occurred while \output is active [1487]
[1488] [1489] [1490] [1491]
Underfull \hbox (badness 2626) in paragraph at lines 9048--9051
[]\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
[1492] [1493]
Underfull \hbox (badness 2503) in paragraph at lines 9155--9159
[]\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 ,
[1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504]
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516] [1517] [1518]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 10844--10847
[]\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,
[1519]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1526] [1527] [1528] [1529] [1530] [1531]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\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

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1532] [1533]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1534] [1535]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\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
[1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 \T1/zi4/m/n/10 SSinit =
[1546] [1547] [1548] [1549] [1550] [1551]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562]
[1563]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1574] [1575]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\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
[1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586]
[1587] [1588] [1589] [1590] [1591] [1592] [1593]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\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 ,
[1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\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
[1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612]
[1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623]
[1624] [1625] [1626] [1627] [1628] [1629]
Underfull \vbox (badness 10000) has occurred while \output is active [1630]
Underfull \vbox (badness 10000) has occurred while \output is active [1631]
[1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642]
[1643]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

Underfull \hbox (badness 1735) in paragraph at lines 18581--18584
[]\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
[1644]
Underfull \hbox (badness 2343) in paragraph at lines 18594--18598
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

Underfull \hbox (badness 3471) in paragraph at lines 18594--18598
\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18602--18606
[]\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
[1645] [1646] [1647]
Overfull \hbox (15.73795pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1648]
[1649] [1650] [1651] [1652] [1653] [1654]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1664] [1665] [1666] [1667]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1668] [1669] [1670] [1671] [1672] [1673] [1674]
Underfull \hbox (badness 2503) in paragraph at lines 20381--20384
[]\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 ,

Underfull \hbox (badness 3919) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
[1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685]
[1686] [1687] [1688] [1689] [1690] [1691] [1692]
Underfull \hbox (badness 10000) in paragraph at lines 21485--21491
[]\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 ,
[1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703]
[1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714]
[1715]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723]
Overfull \hbox (27.74408pt too wide) in paragraph at lines 23399--23399
 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1724] [1725] [1726] [1727] [1728]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 4205) in paragraph at lines 23650--23653
\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
[1729] [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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 \T1/zi4/m/n/10 y[j] =
[1738]
Underfull \hbox (badness 3690) in paragraph at lines 24287--24291
[][][]\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
[1739] [1740] [1741] [1742] [1743] [1744] [1745]
Underfull \vbox (badness 10000) has occurred while \output is active [1746]
[1747]
Underfull \hbox (badness 2165) in paragraph at lines 24777--24782
[]\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 ,
[1748] [1749] [1750]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
[1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761]
[1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772]
[1773] [1774]
Underfull \vbox (badness 10000) has occurred while \output is active [1775]
Underfull \hbox (badness 3514) in paragraph at lines 26556--26561
[]\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
[1776] [1777] [1778] [1779]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26790--26790
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1780]
Underfull \hbox (badness 3514) in paragraph at lines 26826--26832
[]\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
[1781] [1782] [1783] [1784]
Underfull \hbox (badness 3514) in paragraph at lines 27040--27045
[]\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
[1785] [1786]
Underfull \hbox (badness 3514) in paragraph at lines 27127--27132
[]\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
[1787]
Underfull \hbox (badness 3514) in paragraph at lines 27192--27197
[]\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
[1788] [1789]
Underfull \hbox (badness 3514) in paragraph at lines 27286--27291
[]\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
[1790]
Underfull \hbox (badness 6691) in paragraph at lines 27378--27383
[]\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
[1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799]
Underfull \hbox (badness 4024) in paragraph at lines 27908--27911
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
[1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809]
Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\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
[1810] [1811] [1812]
Underfull \hbox (badness 5431) in paragraph at lines 28724--28727
[]\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
[1813] [1814] [1815] [1816] [1817] [1818]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1819] [1820] [1821] [1822] [1823]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834]
[1835] [1836] [1837] [1838] [1839] [1840] [1841] [1842]
Underfull \hbox (badness 3557) in paragraph at lines 30470--30474
[]\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 \T1/zi4
/m/n/10 interval =
[1843] [1844] [1845]
Underfull \vbox (badness 10000) has occurred while \output is active [1846]
[1847] [1848]
Underfull \hbox (badness 1337) in paragraph at lines 30834--30838
[]\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
[1849] [1850] [1851] [1852] [1853] [1854] [1855] [1856] [1857]
Underfull \hbox (badness 1337) in paragraph at lines 31361--31365
[]\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
[1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867])
(./stats4-pkg.tex [1868]
Chapter 11.
[1869] [1870] [1871] [1872] [1873] [1874]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1875] [1876] [1877])
(./tcltk-pkg.tex [1878]
Chapter 12.
[1879] [1880] [1881] [1882] [1883] [1884] [1885]
Underfull \vbox (badness 10000) has occurred while \output is active [1886]
Underfull \vbox (badness 10000) has occurred while \output is active [1887]
Underfull \hbox (badness 1546) in paragraph at lines 664--671
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898]
[1899]) (./tools-pkg.tex [1900]
Chapter 13.
[1901]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 72.

[1902]
Underfull \hbox (badness 3039) in paragraph at lines 164--167
[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1903] [1904]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

Underfull \hbox (badness 4967) in paragraph at lines 285--298
\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1905] [1906]
Underfull \hbox (badness 3039) in paragraph at lines 389--391
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917]
[1918]
Underfull \hbox (badness 4441) in paragraph at lines 1139--1149
\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-
[1919]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
[1920]
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209
\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 ,
[1921] [1922] [1923] [1924] [1925]
Underfull \hbox (badness 2293) in paragraph at lines 1558--1560
[]\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
[1926] [1927]
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Underfull \hbox (badness 1082) in paragraph at lines 1703--1705
[]\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
[1928] [1929] [1930] [1931]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1932] [1933] [1934]
[1935] [1936]
Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202
 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1937] [1938] [1939]
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1940] [1941] [1942] [1943] [1944] [1945] [1946]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
(Font)              using `T1/zi4/m/n' instead on input line 2846.

[1947] [1948] [1949] [1950] [1951]
Underfull \hbox (badness 1424) in paragraph at lines 3128--3130
[]\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
[1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962]
Underfull \hbox (badness 10000) in paragraph at lines 3832--3834
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1963] [1964]
Underfull \hbox (badness 10000) in paragraph at lines 3971--3974
[]\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
[1965] [1966]
Underfull \hbox (badness 1137) in paragraph at lines 4073--4075
[]\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
[1967] [1968] [1969] [1970] [1971]
Underfull \hbox (badness 1796) in paragraph at lines 4381--4386
[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1972]
Underfull \hbox (badness 1838) in paragraph at lines 4455--4461
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

Underfull \hbox (badness 10000) in paragraph at lines 4455--4461
\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
[1973] [1974] [1975]
Underfull \hbox (badness 2197) in paragraph at lines 4671--4681
[]\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 :
[1976]
Underfull \hbox (badness 1571) in paragraph at lines 4734--4738
[]\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
[1977] [1978] [1979]) (./utils-pkg.tex [1980]
Chapter 14.
[1981]
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 ',
[1982] [1983] [1984] [1985] [1986]
Underfull \hbox (badness 10000) in paragraph at lines 376--381
\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
[1987] [1988] [1989] [1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\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 717--723
\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
[1992] [1993]
Underfull \hbox (badness 5847) in paragraph at lines 850--856
[]\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 850--856
\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
[1994]
Underfull \hbox (badness 3861) in paragraph at lines 918--923
[]\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 ,
[1995] [1996]
Underfull \hbox (badness 3323) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

Underfull \hbox (badness 3919) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 3735) in paragraph at lines 1089--1097
\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 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
[1997]
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1998] [1999]
Underfull \vbox (badness 3803) has occurred while \output is active [2000]
[2001] [2002] [2003] [2004]
Underfull \hbox (badness 1371) in paragraph at lines 1606--1608
[]\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
[2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Underfull \hbox (badness 2057) in paragraph at lines 2215--2217
[]\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
[2015] [2016] [2017] [2018] [2019] [2020]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [2021] [2022]
Underfull \hbox (badness 1748) in paragraph at lines 2733--2736
[]\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
[2023] [2024] [2025] [2026] [2027] [2028] [2029]
Underfull \hbox (badness 5388) in paragraph at lines 3142--3146
[]\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 [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

Underfull \hbox (badness 2285) in paragraph at lines 3147--3150
[]\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 =
[2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040]
Underfull \hbox (badness 1430) in paragraph at lines 3906--3914
[]\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
[2041]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\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
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [2056] [2057] [2058]
[2059] [2060] [2061] [2062] [2063]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073]
Underfull \hbox (badness 1371) in paragraph at lines 5996--5998
[]\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
[2074]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2075] [2076] [2077]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2078]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2079] [2080]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[2081] [2082] [2083]
Underfull \hbox (badness 1325) in paragraph at lines 6632--6636
[]\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

Underfull \hbox (badness 4726) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of
[2084]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[2085]
Underfull \hbox (badness 3219) in paragraph at lines 6792--6799
[]\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 6792--6799
\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 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

Underfull \hbox (badness 1596) in paragraph at lines 6792--6799
[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently

Underfull \hbox (badness 2932) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[2086]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,
[2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097]
[2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108]
[2109] [2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 8436--8438
[]\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 2310) in paragraph at lines 8458--8463
[]\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,
[2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119]
Underfull \hbox (badness 1248) in paragraph at lines 8982--8986
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[2120]
Underfull \hbox (badness 1789) in paragraph at lines 9060--9062
[]\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
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130]
Underfull \vbox (badness 10000) has occurred while \output is active [2131]
[2132] [2133]
Underfull \hbox (badness 1097) in paragraph at lines 9897--9900
[]\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
[2134] [2135]
Underfull \hbox (badness 3000) in paragraph at lines 10033--10038
[][][]\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 ;
[2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144]
Underfull \hbox (badness 2134) in paragraph at lines 10616--10621
[][][]\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 ;

Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 2469) in paragraph at lines 11165--11169
[]\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 11165--11169
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2154] [2155] [2156] [2157] [2158]
Underfull \hbox (badness 4060) in paragraph at lines 11496--11499
[]\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 11519--11519
 []\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 '[] 
[2159] [2160] [2161] [2162]
Underfull \hbox (badness 2150) in paragraph at lines 11758--11760
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2163] [2164] [2165] [2166]
Underfull \hbox (badness 10000) in paragraph at lines 11977--11981
[]\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 12008--12014
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2167] [2168] [2169]
Underfull \hbox (badness 1009) in paragraph at lines 12202--12214
[]\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

Underfull \hbox (badness 4779) in paragraph at lines 12239--12241
[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd
[2170]
Underfull \hbox (badness 1077) in paragraph at lines 12269--12276
\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2171] [2172] [2173] [2174] [2175] [2176]
Underfull \hbox (badness 3780) in paragraph at lines 12670--12674
[]\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 12686--12689
[]\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
[2177] [2178] [2179] [2180]
Underfull \hbox (badness 2302) in paragraph at lines 12891--12893
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2181] [2182] [2183] [2184]
Underfull \hbox (badness 10000) in paragraph at lines 13187--13192
[]\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 13196--13199
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2185] [2186]
Underfull \vbox (badness 10000) has occurred while \output is active [2187]
[2188] [2189] [2190] [2191]
Underfull \hbox (badness 2932) in paragraph at lines 13616--13623
[]\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,

Underfull \hbox (badness 1688) in paragraph at lines 13616--13623
\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2192] [2193] [2194] [2195] [2196]
Underfull \hbox (badness 6510) in paragraph at lines 13925--13929
[]\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 13932--13935
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 13932--13935
\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
[2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 10000) in paragraph at lines 14596--14601
[]\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 14596--14601
[][]\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 14602--14604
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2207]
Underfull \hbox (badness 10000) in paragraph at lines 14661--14664
[][][]\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 ,
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219]
Underfull \hbox (badness 10000) in paragraph at lines 15434--15436
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2220] [2221] [2222] [2223]) [2224] (./refman.ind [2225] [2226] [2227] [2228]
[2229] [2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239]
[2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249] [2250]
[2251] [2252] [2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260] [2261]
[2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272]
[2273] [2274]
Overfull \hbox (33.3567pt too wide) in paragraph at lines 8854--8856
[]\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , 

[2275] [2276] [2277] [2278] [2279] [2280]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 10177--10179
[]\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE 
[2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288]
Overfull \hbox (5.8567pt too wide) in paragraph at lines 11923--11925
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 11925--11927
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_results 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 11927--11929
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings 
[2289] [2290] [2291] [2292] [2293] [2294] [2295] [2296] [2297]) (./refman.aux)

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

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed 
one

pdfTeX warning (dest): name{Rfn.lmList} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparse.model.matrix} has been referenced but do
es not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nlsList} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/
texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4b.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr5.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/
fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on refman.pdf (2328 pages, 6262394 bytes).
Transcript written on refman.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-admin.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] [-1] Chapter 1
Writing index file R-admin.cp
Writing index file R-admin.en
[1] Chapter 2 [2] Cross reference values unknown; you must run TeX again.
[3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16]
[17] [18] [19] [20] [21] Chapter 4 [22] [23]
Underfull \hbox (badness 10000) in paragraph at lines 1962--1974
@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[24] Chapter 5 [25] Chapter 6 [26]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 2113--2113
 []@texttt [1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "met
hods"[] 
[27] [28]
Underfull \hbox (badness 6842) in paragraph at lines 2307--2318
[]@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age
s. No ad-di-
[29] [30] [31] [32] [33] [34]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 2767--2767
 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text
tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] 

Overfull \hbox (20.69044pt too wide) in paragraph at lines 2787--2787
 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --
install=check:@textttsl pkg@texttt .log @textttsl pkg[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 2788--2788
 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i
nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] 
[35] Chapter 7 [36] [37] [38] Chapter 8 [39] Chapter 9 [40] [41] [42] [43]
Appendix A [44] [45]
Overfull \hbox (49.43388pt too wide) in paragraph at lines 3421--3421
 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
disable-cpp[] 
[46] [47] [48] [49]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 3692--3692
 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6
4/jre[] 
[50] [51] [52] [53] [54] [55] Appendix B [56] [57] [58] [59] [60] [61]
Appendix C [62] [63] [64] [65] [66] [67]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036
 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m
acOS_10.14.pkg \[] 

Overfull \hbox (78.17732pt too wide) in paragraph at lines 5044--5044
 []@texttt CPPFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.
sdk/usr/include"[] 
[68]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 5146--5146
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig \[] 
[69]
Overfull \hbox (106.92076pt too wide) in paragraph at lines 5183--5183
 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 5217--5217
 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1
1/lib[] 
[70]
Underfull \hbox (badness 10000) in paragraph at lines 5322--5327
[]@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled
, run
[71]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 5346--5346
 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content
s/Home[] 
[72] [73]
Overfull \hbox (32.18782pt too wide) in paragraph at lines 5515--5515
 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/
csw/lib"[] 
[74]
Underfull \hbox (badness 10000) in paragraph at lines 5620--5626
@texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca
l/lib/sparcv9[] @textrm as

Overfull \hbox (141.41289pt too wide) in paragraph at lines 5628--5628
 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc
onfig:/usr/lib/64/pkgconfig[] 

Overfull \hbox (26.43913pt too wide) in paragraph at lines 5635--5635
 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s
olaris"[] 
[75]
Underfull \hbox (badness 10000) in paragraph at lines 5685--5689
[]@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/
local/lib/amd64[] @textrm and
[76] Appendix D [77] [78] [79] (Function and variable index) [80]
No file R-admin.vrs.
(Concept index) [81]
No file R-admin.cps.
(Environment variable index) [82]
No file R-admin.ens.
[83] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.p
fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-admin.pdf (86 pages, 477131 bytes).
Transcript written on R-admin.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-admin.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-admin.toc [-1]
[-2]) [-3] (/build/r-base-3.6.1/doc/manual/R-admin.toc)
(/build/r-base-3.6.1/doc/manual/R-admin.toc) Chapter 1
(/build/r-base-3.6.1/doc/manual/R-admin.aux)
Writing index file R-admin.cp
Writing index file R-admin.en
[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14]
Chapter 3 [15] [16] [17] [18] [19] [20] [21] Chapter 4 [22] [23]
Underfull \hbox (badness 10000) in paragraph at lines 1962--1974
@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[24] Chapter 5 [25] Chapter 6 [26]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 2113--2113
 []@texttt [1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "met
hods"[] 
[27] [28]
Underfull \hbox (badness 6842) in paragraph at lines 2307--2318
[]@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age
s. No ad-di-
[29] [30] [31] [32] [33] [34]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 2767--2767
 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text
tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] 

Overfull \hbox (20.69044pt too wide) in paragraph at lines 2787--2787
 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --
install=check:@textttsl pkg@texttt .log @textttsl pkg[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 2788--2788
 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i
nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] 
[35] Chapter 7 [36] [37] [38] Chapter 8 [39] Chapter 9 [40] [41] [42] [43]
Appendix A [44] [45]
Overfull \hbox (49.43388pt too wide) in paragraph at lines 3421--3421
 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
disable-cpp[] 
[46] [47] [48] [49]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 3692--3692
 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6
4/jre[] 
[50] [51] [52] [53] [54] [55] Appendix B [56] [57] [58] [59] [60] [61]
Appendix C [62] [63] [64] [65] [66] [67]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036
 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m
acOS_10.14.pkg \[] 

Overfull \hbox (78.17732pt too wide) in paragraph at lines 5044--5044
 []@texttt CPPFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.
sdk/usr/include"[] 
[68]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 5146--5146
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig \[] 
[69]
Overfull \hbox (106.92076pt too wide) in paragraph at lines 5183--5183
 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 5217--5217
 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1
1/lib[] 
[70]
Underfull \hbox (badness 10000) in paragraph at lines 5322--5327
[]@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled
, run
[71]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 5346--5346
 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content
s/Home[] 
[72] [73]
Overfull \hbox (32.18782pt too wide) in paragraph at lines 5515--5515
 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/
csw/lib"[] 
[74]
Underfull \hbox (badness 10000) in paragraph at lines 5620--5626
@texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca
l/lib/sparcv9[] @textrm as

Overfull \hbox (141.41289pt too wide) in paragraph at lines 5628--5628
 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc
onfig:/usr/lib/64/pkgconfig[] 

Overfull \hbox (26.43913pt too wide) in paragraph at lines 5635--5635
 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s
olaris"[] 
[75]
Underfull \hbox (badness 10000) in paragraph at lines 5685--5689
[]@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/
local/lib/amd64[] @textrm and
[76] Appendix D [77] [78] [79] (Function and variable index) [80]
(Concept index) [81] (Environment variable index) [82] [83] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmtt9.pfb>
Output written on R-admin.pdf (88 pages, 522005 bytes).
Transcript written on R-admin.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-admin.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-admin.toc [-1]
[-2]) [-3] (/build/r-base-3.6.1/doc/manual/R-admin.toc)
(/build/r-base-3.6.1/doc/manual/R-admin.toc) Chapter 1
(/build/r-base-3.6.1/doc/manual/R-admin.aux)
Writing index file R-admin.cp
Writing index file R-admin.en
[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14]
Chapter 3 [15] [16] [17] [18] [19] [20] [21] Chapter 4 [22] [23]
Underfull \hbox (badness 10000) in paragraph at lines 1962--1974
@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
textrm , @texttt org.r-project.x86_
[24] Chapter 5 [25] Chapter 6 [26]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 2113--2113
 []@texttt [1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "met
hods"[] 
[27] [28]
Underfull \hbox (badness 6842) in paragraph at lines 2307--2318
[]@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age
s. No ad-di-
[29] [30] [31] [32] [33] [34]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 2767--2767
 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text
tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] 

Overfull \hbox (20.69044pt too wide) in paragraph at lines 2787--2787
 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --
install=check:@textttsl pkg@texttt .log @textttsl pkg[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 2788--2788
 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i
nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] 
[35] Chapter 7 [36] [37] [38] Chapter 8 [39] Chapter 9 [40] [41] [42] [43]
Appendix A [44] [45]
Overfull \hbox (49.43388pt too wide) in paragraph at lines 3421--3421
 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit --
disable-cpp[] 
[46] [47] [48] [49]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 3692--3692
 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6
4/jre[] 
[50] [51] [52] [53] [54] [55] Appendix B [56] [57] [58] [59] [60] [61]
Appendix C [62] [63] [64] [65] [66] [67]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036
 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m
acOS_10.14.pkg \[] 

Overfull \hbox (78.17732pt too wide) in paragraph at lines 5044--5044
 []@texttt CPPFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.
sdk/usr/include"[] 
[68]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 5146--5146
 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr
/lib/pkgconfig \[] 
[69]
Overfull \hbox (106.92076pt too wide) in paragraph at lines 5183--5183
 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf
ig:/usr/lib/pkgconfig[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 5217--5217
 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1
1/lib[] 
[70]
Underfull \hbox (badness 10000) in paragraph at lines 5322--5327
[]@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled
, run
[71]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 5346--5346
 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content
s/Home[] 
[72] [73]
Overfull \hbox (32.18782pt too wide) in paragraph at lines 5515--5515
 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/
csw/lib"[] 
[74]
Underfull \hbox (badness 10000) in paragraph at lines 5620--5626
@texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca
l/lib/sparcv9[] @textrm as

Overfull \hbox (141.41289pt too wide) in paragraph at lines 5628--5628
 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc
onfig:/usr/lib/64/pkgconfig[] 

Overfull \hbox (26.43913pt too wide) in paragraph at lines 5635--5635
 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s
olaris"[] 
[75]
Underfull \hbox (badness 10000) in paragraph at lines 5685--5689
[]@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/
local/lib/amd64[] @textrm and
[76] Appendix D [77] [78] [79] (Function and variable index) [80]
(Concept index) [81] (Environment variable index) [82] [83] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
r10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmtt9.pfb>
Output written on R-admin.pdf (88 pages, 522057 bytes).
Transcript written on R-admin.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-data.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] [-1] (Acknowledgements)
Underfull \hbox (badness 10000) in paragraph at lines 87--87
 [][]@textbf DBI

Underfull \hbox (badness 10000) in paragraph at lines 87--87
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 87--87
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87
 @texttt package=DBI[]@textrm )[][]| 

Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88
 [][]@textbf dataframes2xls

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt org /

Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88
 @texttt package=dataframes2xls[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 [][]@textbf foreign

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89
 @texttt package=foreign[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 [][]@textbf gdata

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90
 @texttt package=gdata[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 [][]@textbf ncdf4

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91
 @texttt package=ncdf4[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 [][]@textbf rJava

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92
 @texttt package=rJava[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf RJDBC

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93
 @texttt package=RJDBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 [][]@textbf RMySQL

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt org /

Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94
 @texttt package=RMySQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 [][]@textbf RNetCDF

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95
 @texttt package=RNetCDF[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 [][]@textbf RODBC

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96
 @texttt package=RODBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 [][]@textbf ROracle

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97
 @texttt package=ROracle[]@textrm )[][]| 

Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98
 [][]@textbf RPostgreSQL

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt org /

Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98
 @texttt package=RPostgreSQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 [][]@textbf RSQLite

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101
 @texttt package=RSQLite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 [][]@textbf WriteXLS

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt org /

Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103
 @texttt package=WriteXLS[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 [][]@textbf XLConnect

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 @texttt org /

Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104
 @texttt package=XLConnect[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 [][]@textbf XML

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105
 @texttt package=XML[]@textrm )[][]| 
[1] [2] Chapter 1 [3]
Writing index file R-data.cp
Cross reference values unknown; you must run TeX again. [4] [5] [6] [7]
Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4
[17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7
[26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33]
(Function and variable index) [34]
No file R-data.vrs.
(Concept index) [35]
No file R-data.cps.
[36] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm
/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-data.pdf (39 pages, 272428 bytes).
Transcript written on R-data.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-data.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-data.toc [-1])
[-2] (/build/r-base-3.6.1/doc/manual/R-data.toc)
(/build/r-base-3.6.1/doc/manual/R-data.toc) (Acknowledgements)
(/build/r-base-3.6.1/doc/manual/R-data.aux)
Underfull \hbox (badness 10000) in paragraph at lines 87--87
 [][]@textbf DBI

Underfull \hbox (badness 10000) in paragraph at lines 87--87
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 87--87
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87
 @texttt package=DBI[]@textrm )[][]| 

Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88
 [][]@textbf dataframes2xls

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt org /

Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88
 @texttt package=dataframes2xls[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 [][]@textbf foreign

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89
 @texttt package=foreign[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 [][]@textbf gdata

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90
 @texttt package=gdata[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 [][]@textbf ncdf4

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91
 @texttt package=ncdf4[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 [][]@textbf rJava

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92
 @texttt package=rJava[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf RJDBC

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93
 @texttt package=RJDBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 [][]@textbf RMySQL

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt org /

Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94
 @texttt package=RMySQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 [][]@textbf RNetCDF

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95
 @texttt package=RNetCDF[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 [][]@textbf RODBC

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96
 @texttt package=RODBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 [][]@textbf ROracle

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97
 @texttt package=ROracle[]@textrm )[][]| 

Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98
 [][]@textbf RPostgreSQL

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt org /

Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98
 @texttt package=RPostgreSQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 [][]@textbf RSQLite

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101
 @texttt package=RSQLite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 [][]@textbf WriteXLS

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt org /

Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103
 @texttt package=WriteXLS[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 [][]@textbf XLConnect

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 @texttt org /

Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104
 @texttt package=XLConnect[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 [][]@textbf XML

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105
 @texttt package=XML[]@textrm )[][]| 
[1] [2] Chapter 1 [3]
Writing index file R-data.cp
[4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15]
[16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6
[25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32]
Appendix A [33] (Function and variable index) [34] [35] (Concept index)
[36] [37]
Overfull \vbox (1.73251pt too high) has occurred while \output is active
[38] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-data.pdf (42 pages, 312466 bytes).
Transcript written on R-data.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-data.t2d/pdf/xtr/R-data.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-data.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-data.toc [-1])
[-2] (/build/r-base-3.6.1/doc/manual/R-data.toc)
(/build/r-base-3.6.1/doc/manual/R-data.toc) (Acknowledgements)
(/build/r-base-3.6.1/doc/manual/R-data.aux)
Underfull \hbox (badness 10000) in paragraph at lines 87--87
 [][]@textbf DBI

Underfull \hbox (badness 10000) in paragraph at lines 87--87
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 87--87
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87
 @texttt package=DBI[]@textrm )[][]| 

Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88
 [][]@textbf dataframes2xls

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 88--88
 @texttt org /

Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88
 @texttt package=dataframes2xls[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 [][]@textbf foreign

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 89--89
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89
 @texttt package=foreign[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 [][]@textbf gdata

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 90--90
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90
 @texttt package=gdata[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 [][]@textbf ncdf4

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 91--91
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91
 @texttt package=ncdf4[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 [][]@textbf rJava

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 92--92
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92
 @texttt package=rJava[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 [][]@textbf RJDBC

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 93--93
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93
 @texttt package=RJDBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 [][]@textbf RMySQL

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 94--94
 @texttt org /

Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94
 @texttt package=RMySQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 [][]@textbf RNetCDF

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 95--95
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95
 @texttt package=RNetCDF[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 [][]@textbf RODBC

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 96--96
 @texttt org /

Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96
 @texttt package=RODBC[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 [][]@textbf ROracle

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 97--97
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97
 @texttt package=ROracle[]@textrm )[][]| 

Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98
 [][]@textbf RPostgreSQL

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 98--98
 @texttt org /

Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98
 @texttt package=RPostgreSQL[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 [][]@textbf RSQLite

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 101--101
 @texttt org /

Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101
 @texttt package=RSQLite[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 [][]@textbf WriteXLS

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 103--103
 @texttt org /

Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103
 @texttt package=WriteXLS[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 [][]@textbf XLConnect

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 104--104
 @texttt org /

Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104
 @texttt package=XLConnect[]@textrm )[][]| 

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 [][]@textbf XML

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt CRAN .

Underfull \hbox (badness 10000) in paragraph at lines 105--105
 @texttt org /

Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105
 @texttt package=XML[]@textrm )[][]| 
[1] [2] Chapter 1 [3]
Writing index file R-data.cp
[4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15]
[16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6
[25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32]
Appendix A [33] (Function and variable index) [34] [35] (Concept index)
[36] [37]
Overfull \vbox (1.73251pt too high) has occurred while \output is active
[38] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-data.pdf (42 pages, 312468 bytes).
Transcript written on R-data.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-exts.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1]
Writing index file R-exts.cp
Cross reference values unknown; you must run TeX again. [2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 493--496
[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 1965--1965
 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF
LAGS)[] 
[25] [26] [27] [28] [29]
Overfull \hbox (67.78206pt too wide) in paragraph at lines 2335--2335
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 

Overfull \hbox (53.60722pt too wide) in paragraph at lines 2337--2337
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[30] [31]
Overfull \hbox (16.92342pt too wide) in paragraph at lines 2479--2479
 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar
e defined.[]  
[32] [33]
Underfull \hbox (badness 10000) in paragraph at lines 2586--2588
[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[34] [35]
Overfull \hbox (60.93126pt too wide) in paragraph at lines 2719--2719
 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[36]
Overfull \hbox (2.98494pt too wide) in paragraph at lines 2862--2864
[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51]
[52] [53] [54] [55] [56] [57] [58] [59] [60]
Overfull \hbox (53.86903pt too wide) in paragraph at lines 4729--4729
 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 

Overfull \hbox (48.12035pt too wide) in paragraph at lines 4731--4731
 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 

Overfull \hbox (65.36641pt too wide) in paragraph at lines 4732--4732
 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 

Overfull \hbox (76.86378pt too wide) in paragraph at lines 4747--4747
 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[61] [62] [63] [64] [65]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 5055--5055
 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@
euro"[] 
[66] [67]
Overfull \hbox (30.87428pt too wide) in paragraph at lines 5271--5271
 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me
mcpy[] 
[68]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5272--5272
 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro
r[] 
[69]
Overfull \hbox (25.1256pt too wide) in paragraph at lines 5369--5369
 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr
unc[] 

Overfull \hbox (53.86903pt too wide) in paragraph at lines 5401--5401
 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[70]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5435--5435
 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__)
)[] 
[71] [72]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5663--5663
 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String
)[] 
[73] [74] [75] Chapter 2 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85]
[86] [87] [88] [89]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6930
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[90] [91] [92] [93]
Underfull \hbox (badness 10000) in paragraph at lines 7244--7248
[]@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file
[94] [95] [96] Chapter 3 [97] [98] [99] [100] [101] [102]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 7845--7845
 []                 @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1,
 28)))[] 
[103] [104] [105] Chapter 4 [106] [107] [108]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 8223--8223
 []@texttt evaluation nested too deeply: infinite recursion / options(expressio
ns=)?[] 
[109]
Overfull \hbox (25.25755pt too wide) in paragraph at lines 8264--8264
 []@smalltt Message:  Error: no valid set of coefficients has been found: pleas
e supply starting values[] 
[110]
Overfull \hbox (20.53261pt too wide) in paragraph at lines 8368--8368
 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star
t, etastart = etastart,[] 
[111]
Overfull \hbox (38.96663pt too wide) in paragraph at lines 8398--8407
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g. @texttt debug(stats:::predict.Arima)[]@textrm .
[112] [113] [114]
Overfull \hbox (44.18301pt too wide) in paragraph at lines 8675--8676
[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[115] [116]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 8807--8807
 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 

Overfull \hbox (29.50735pt too wide) in paragraph at lines 8835--8837
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -fsanitize=undefined,address[]

Overfull \hbox (32.18782pt too wide) in paragraph at lines 8849--8849
 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo
und,vptr[] 
[117] [118]
Overfull \hbox (72.42863pt too wide) in paragraph at lines 8967--8967
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[119]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 9014--9014
 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl
assi,[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 9017--9017
 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t(
cu)),[] 
[120]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 9096--9096
 []@texttt #5  0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9
698f98,[] 
[121] [122]
Overfull \hbox (124.16682pt too wide) in paragraph at lines 9301--9301
 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati
on [-Wlto-type-mismatch][] 
[123]
Overfull \hbox (147.16158pt too wide) in paragraph at lines 9317--9317
 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla
ration [-Wlto-type-mismatch][] 
Chapter 5 [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134]
Overfull \hbox (30.87428pt too wide) in paragraph at lines 10103--10103
 []                      @texttt double *w, int *iper, double *span, double *al
pha,[] 

Overfull \hbox (51.66371pt too wide) in paragraph at lines 10159--10159
 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[135] [136] [137] [138] [139] [140] [141] [142]
Overfull \hbox (37.93651pt too wide) in paragraph at lines 10739--10739
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 11521--11521
 []    @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL
SE");[] 
[153]
Underfull \hbox (badness 10000) in paragraph at lines 11582--11584
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[154] [155] [156] [157] [158] [159] [160]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12109--12109
 []    @texttt // a version with (too) much PROTECT()ion .. "better safe than s
orry"[] 
[161] [162]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12232--12232
 []    @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet
a)));[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 12237--12237
 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 12292--12292
 []    @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet
a)));[] 
[163]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12304--12304
 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 
[164]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 12403--12403
 []        @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV
alue));[] 
[165] [166]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12539--12539
 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one
xit);[] 
[167]
Overfull \hbox (43.6852pt too wide) in paragraph at lines 12620--12620
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[168]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12716--12716
 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety
pe_t;[] 
Chapter 6 [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181]
Underfull \hbox (badness 10000) in paragraph at lines 13895--13899
 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na
.last, decreasing)[]@textrm .
[182] [183] Warning: unbalanced parentheses in @def... [184] [185]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 14106--14106
 []                     @texttt void (*clean)(void *data, Rboolean jump), void 
*cdata,[] 
[186] [187] [188] [189] Chapter 7 [190] [191] Chapter 8 [192] [193] [194]
Overfull \hbox (43.6852pt too wide) in paragraph at lines 14862--14862
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[195]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 14905--14905
 []@texttt extern int  (*ptr_R_ReadConsole)(const char *, unsigned char *, int,
 int);[] 

Overfull \hbox (55.18257pt too wide) in paragraph at lines 14921--14921
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[196] [197] [198] [199]
Underfull \hbox (badness 10000) in paragraph at lines 15164--15171
 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan
ohttp.c[] @textrm and @texttt src/
[200] [201] [202] [203] [204]
Underfull \hbox (badness 10000) in paragraph at lines 15547--15551
 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [205]
No file R-exts.vrs.
(Concept index) [206]
No file R-exts.cps.
[207] )
(see the transcript file for additional information)pdfTeX warning (\pdffontatt
r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att
ributes assigned to @textsl

</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type
1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public
/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
msltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/latxfont/lcircle1.pfb>
Output written on R-exts.pdf (210 pages, 910929 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-exts.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-exts.toc [-1]
[-2] [-3] [-4]) [-5] (/build/r-base-3.6.1/doc/manual/R-exts.toc)
(/build/r-base-3.6.1/doc/manual/R-exts.toc) (Acknowledgements)
(/build/r-base-3.6.1/doc/manual/R-exts.aux) Chapter 1 [1]
Writing index file R-exts.cp
[2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 493--496
[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 1965--1965
 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF
LAGS)[] 
[25] [26] [27] [28] [29]
Overfull \hbox (67.78206pt too wide) in paragraph at lines 2335--2335
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 

Overfull \hbox (53.60722pt too wide) in paragraph at lines 2337--2337
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[30] [31]
Overfull \hbox (16.92342pt too wide) in paragraph at lines 2479--2479
 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar
e defined.[]  
[32] [33]
Underfull \hbox (badness 10000) in paragraph at lines 2586--2588
[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[34] [35]
Overfull \hbox (60.93126pt too wide) in paragraph at lines 2719--2719
 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[36]
Overfull \hbox (2.98494pt too wide) in paragraph at lines 2862--2864
[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51]
[52] [53] [54] [55] [56] [57] [58] [59] [60]
Overfull \hbox (53.86903pt too wide) in paragraph at lines 4729--4729
 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 

Overfull \hbox (48.12035pt too wide) in paragraph at lines 4731--4731
 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 

Overfull \hbox (65.36641pt too wide) in paragraph at lines 4732--4732
 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 

Overfull \hbox (76.86378pt too wide) in paragraph at lines 4747--4747
 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[61] [62] [63] [64] [65]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 5055--5055
 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@
euro"[] 
[66] [67]
Overfull \hbox (30.87428pt too wide) in paragraph at lines 5271--5271
 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me
mcpy[] 
[68]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5272--5272
 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro
r[] 
[69]
Overfull \hbox (25.1256pt too wide) in paragraph at lines 5369--5369
 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr
unc[] 

Overfull \hbox (53.86903pt too wide) in paragraph at lines 5401--5401
 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[70]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5435--5435
 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__)
)[] 
[71] [72]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5663--5663
 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String
)[] 
[73] [74] [75] Chapter 2 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85]
[86] [87] [88] [89]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6930
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[90] [91] [92] [93]
Underfull \hbox (badness 10000) in paragraph at lines 7244--7248
[]@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file
[94] [95] [96] Chapter 3 [97] [98] [99] [100] [101] [102]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 7845--7845
 []                 @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1,
 28)))[] 
[103] [104] [105] Chapter 4 [106] [107] [108]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 8223--8223
 []@texttt evaluation nested too deeply: infinite recursion / options(expressio
ns=)?[] 
[109]
Overfull \hbox (25.25755pt too wide) in paragraph at lines 8264--8264
 []@smalltt Message:  Error: no valid set of coefficients has been found: pleas
e supply starting values[] 
[110]
Overfull \hbox (20.53261pt too wide) in paragraph at lines 8368--8368
 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star
t, etastart = etastart,[] 
[111]
Overfull \hbox (38.96663pt too wide) in paragraph at lines 8398--8407
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g. @texttt debug(stats:::predict.Arima)[]@textrm .
[112] [113] [114]
Overfull \hbox (44.18301pt too wide) in paragraph at lines 8675--8676
[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[115] [116]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 8807--8807
 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 

Overfull \hbox (29.50735pt too wide) in paragraph at lines 8835--8837
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -fsanitize=undefined,address[]

Overfull \hbox (32.18782pt too wide) in paragraph at lines 8849--8849
 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo
und,vptr[] 
[117] [118]
Overfull \hbox (72.42863pt too wide) in paragraph at lines 8967--8967
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[119]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 9014--9014
 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl
assi,[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 9017--9017
 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t(
cu)),[] 
[120]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 9096--9096
 []@texttt #5  0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9
698f98,[] 
[121] [122]
Overfull \hbox (124.16682pt too wide) in paragraph at lines 9301--9301
 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati
on [-Wlto-type-mismatch][] 
[123]
Overfull \hbox (147.16158pt too wide) in paragraph at lines 9317--9317
 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla
ration [-Wlto-type-mismatch][] 
Chapter 5 [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134]
Overfull \hbox (30.87428pt too wide) in paragraph at lines 10103--10103
 []                      @texttt double *w, int *iper, double *span, double *al
pha,[] 

Overfull \hbox (51.66371pt too wide) in paragraph at lines 10159--10159
 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[135] [136] [137] [138] [139] [140] [141] [142]
Overfull \hbox (37.93651pt too wide) in paragraph at lines 10739--10739
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 11521--11521
 []    @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL
SE");[] 
[153]
Underfull \hbox (badness 10000) in paragraph at lines 11582--11584
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[154] [155] [156] [157] [158] [159] [160]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12109--12109
 []    @texttt // a version with (too) much PROTECT()ion .. "better safe than s
orry"[] 
[161] [162]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12232--12232
 []    @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet
a)));[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 12237--12237
 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 12292--12292
 []    @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet
a)));[] 
[163]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12304--12304
 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 
[164]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 12403--12403
 []        @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV
alue));[] 
[165] [166]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12539--12539
 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one
xit);[] 
[167]
Overfull \hbox (43.6852pt too wide) in paragraph at lines 12620--12620
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[168]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12716--12716
 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety
pe_t;[] 
Chapter 6 [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181]
Underfull \hbox (badness 10000) in paragraph at lines 13895--13899
 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na
.last, decreasing)[]@textrm .
[182] [183] Warning: unbalanced parentheses in @def... [184] [185]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 14106--14106
 []                     @texttt void (*clean)(void *data, Rboolean jump), void 
*cdata,[] 
[186] [187] [188] [189] Chapter 7 [190] [191] Chapter 8 [192] [193] [194]
Overfull \hbox (43.6852pt too wide) in paragraph at lines 14862--14862
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[195]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 14905--14905
 []@texttt extern int  (*ptr_R_ReadConsole)(const char *, unsigned char *, int,
 int);[] 

Overfull \hbox (55.18257pt too wide) in paragraph at lines 14921--14921
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[196] [197] [198] [199]
Underfull \hbox (badness 10000) in paragraph at lines 15164--15171
 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan
ohttp.c[] @textrm and @texttt src/
[200] [201] [202] [203] [204]
Underfull \hbox (badness 10000) in paragraph at lines 15547--15551
 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [205] [206] [207] [208] (Concept index) [209]
[210] [211] )
(see the transcript file for additional information)pdfTeX warning (\pdffontatt
r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att
ributes assigned to @textsl

</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.p
fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/latxfont/lcircle1.pfb>
Output written on R-exts.pdf (218 pages, 974815 bytes).
Transcript written on R-exts.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-exts.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-exts.toc [-1]
[-2] [-3] [-4]) [-5] (/build/r-base-3.6.1/doc/manual/R-exts.toc)
(/build/r-base-3.6.1/doc/manual/R-exts.toc) (Acknowledgements)
(/build/r-base-3.6.1/doc/manual/R-exts.aux) Chapter 1 [1]
Writing index file R-exts.cp
[2] [3] [4] [5]
Underfull \hbox (badness 10000) in paragraph at lines 493--496
[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo
[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 1965--1965
 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF
LAGS)[] 
[25] [26] [27] [28] [29]
Overfull \hbox (67.78206pt too wide) in paragraph at lines 2335--2335
 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c
pp model/*/*.cpp model/*/*/*.cpp)[] 

Overfull \hbox (53.60722pt too wide) in paragraph at lines 2337--2337
 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien
a07models.o $(SOURCES:.cpp=.o)[] 
[30] [31]
Overfull \hbox (16.92342pt too wide) in paragraph at lines 2479--2479
 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar
e defined.[]  
[32] [33]
Underfull \hbox (badness 10000) in paragraph at lines 2586--2588
[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[34] [35]
Overfull \hbox (60.93126pt too wide) in paragraph at lines 2719--2719
 []            @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX
11PICFLAGS)")[] 
[36]
Overfull \hbox (2.98494pt too wide) in paragraph at lines 2862--2864
[][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v
er-sions such as @smalltt ~/.R/check.Renviron.i386[]
[37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51]
[52] [53] [54] [55] [56] [57] [58] [59] [60]
Overfull \hbox (53.86903pt too wide) in paragraph at lines 4729--4729
 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v
ersion")[] 

Overfull \hbox (48.12035pt too wide) in paragraph at lines 4731--4731
 []  @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse 
= "."))[] 

Overfull \hbox (65.36641pt too wide) in paragraph at lines 4732--4732
 []  @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a
vailable")[] 

Overfull \hbox (76.86378pt too wide) in paragraph at lines 4747--4747
 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor 
version 52.0[] 
[61] [62] [63] [64] [65]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 5055--5055
 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@
euro"[] 
[66] [67]
Overfull \hbox (30.87428pt too wide) in paragraph at lines 5271--5271
 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me
mcpy[] 
[68]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5272--5272
 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro
r[] 
[69]
Overfull \hbox (25.1256pt too wide) in paragraph at lines 5369--5369
 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr
unc[] 

Overfull \hbox (53.86903pt too wide) in paragraph at lines 5401--5401
 []@texttt 'register' storage class specifier is deprecated and incompatible wi
th C++17[] 
[70]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5435--5435
 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__)
)[] 
[71] [72]
Overfull \hbox (13.62822pt too wide) in paragraph at lines 5663--5663
 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String
)[] 
[73] [74] [75] Chapter 2 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85]
[86] [87] [88] [89]
Underfull \hbox (badness 10000) in paragraph at lines 6923--6930
[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[90] [91] [92] [93]
Underfull \hbox (badness 10000) in paragraph at lines 7244--7248
[]@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file
[94] [95] [96] Chapter 3 [97] [98] [99] [100] [101] [102]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 7845--7845
 []                 @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1,
 28)))[] 
[103] [104] [105] Chapter 4 [106] [107] [108]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 8223--8223
 []@texttt evaluation nested too deeply: infinite recursion / options(expressio
ns=)?[] 
[109]
Overfull \hbox (25.25755pt too wide) in paragraph at lines 8264--8264
 []@smalltt Message:  Error: no valid set of coefficients has been found: pleas
e supply starting values[] 
[110]
Overfull \hbox (20.53261pt too wide) in paragraph at lines 8368--8368
 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star
t, etastart = etastart,[] 
[111]
Overfull \hbox (38.96663pt too wide) in paragraph at lines 8398--8407
[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
 e.g. @texttt debug(stats:::predict.Arima)[]@textrm .
[112] [113] [114]
Overfull \hbox (44.18301pt too wide) in paragraph at lines 8675--8676
[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[115] [116]
Overfull \hbox (78.17732pt too wide) in paragraph at lines 8807--8807
 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_
odr_violation=0'[] 

Overfull \hbox (29.50735pt too wide) in paragraph at lines 8835--8837
[]@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t
exttt -fsanitize=undefined,address[]

Overfull \hbox (32.18782pt too wide) in paragraph at lines 8849--8849
 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo
und,vptr[] 
[117] [118]
Overfull \hbox (72.42863pt too wide) in paragraph at lines 8967--8967
 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u
pper bound of 0[] 
[119]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 9014--9014
 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl
assi,[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 9017--9017
 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t(
cu)),[] 
[120]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 9096--9096
 []@texttt #5  0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9
698f98,[] 
[121] [122]
Overfull \hbox (124.16682pt too wide) in paragraph at lines 9301--9301
 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati
on [-Wlto-type-mismatch][] 
[123]
Overfull \hbox (147.16158pt too wide) in paragraph at lines 9317--9317
 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla
ration [-Wlto-type-mismatch][] 
Chapter 5 [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134]
Overfull \hbox (30.87428pt too wide) in paragraph at lines 10103--10103
 []                      @texttt double *w, int *iper, double *span, double *al
pha,[] 

Overfull \hbox (51.66371pt too wide) in paragraph at lines 10159--10159
 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
riv, PACKAGE = "splines")[] 
[135] [136] [137] [138] [139] [140] [141] [142]
Overfull \hbox (37.93651pt too wide) in paragraph at lines 10739--10739
 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)
" -lpackB[] 
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 11521--11521
 []    @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL
SE");[] 
[153]
Underfull \hbox (badness 10000) in paragraph at lines 11582--11584
[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[154] [155] [156] [157] [158] [159] [160]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12109--12109
 []    @texttt // a version with (too) much PROTECT()ion .. "better safe than s
orry"[] 
[161] [162]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12232--12232
 []    @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet
a)));[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 12237--12237
 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 

Overfull \hbox (14.94176pt too wide) in paragraph at lines 12292--12292
 []    @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet
a)));[] 
[163]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12304--12304
 []    @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an
s)) {[] 
[164]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 12403--12403
 []        @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV
alue));[] 
[165] [166]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12539--12539
 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one
xit);[] 
[167]
Overfull \hbox (43.6852pt too wide) in paragraph at lines 12620--12620
 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[168]
Overfull \hbox (14.94176pt too wide) in paragraph at lines 12716--12716
 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety
pe_t;[] 
Chapter 6 [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181]
Underfull \hbox (badness 10000) in paragraph at lines 13895--13899
 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na
.last, decreasing)[]@textrm .
[182] [183] Warning: unbalanced parentheses in @def... [184] [185]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 14106--14106
 []                     @texttt void (*clean)(void *data, Rboolean jump), void 
*cdata,[] 
[186] [187] [188] [189] Chapter 7 [190] [191] Chapter 8 [192] [193] [194]
Overfull \hbox (43.6852pt too wide) in paragraph at lines 14862--14862
 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s
tatic libR[] 
[195]
Overfull \hbox (20.69044pt too wide) in paragraph at lines 14905--14905
 []@texttt extern int  (*ptr_R_ReadConsole)(const char *, unsigned char *, int,
 int);[] 

Overfull \hbox (55.18257pt too wide) in paragraph at lines 14921--14921
 []@texttt extern int  (*ptr_R_EditFiles)(int, const char **, const char **, co
nst char *);[] 
[196] [197] [198] [199]
Underfull \hbox (badness 10000) in paragraph at lines 15164--15171
 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan
ohttp.c[] @textrm and @texttt src/
[200] [201] [202] [203] [204]
Underfull \hbox (badness 10000) in paragraph at lines 15547--15551
 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R
-core\R32[] @textrm or
(Function and variable index) [205] [206] [207] [208] (Concept index) [209]
[210] [211] )
(see the transcript file for additional information)pdfTeX warning (\pdffontatt
r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att
ributes assigned to @textsl

</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.p
fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/latxfont/lcircle1.pfb>
Output written on R-exts.pdf (218 pages, 974896 bytes).
Transcript written on R-exts.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up
dmap/pdftex.map}] [-1] Chapter 1
Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2]
[3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16]
[17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25]
[26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
Writing index file R-FAQ.fn
[39] [40] [41]
Underfull \hbox (badness 10000) in paragraph at lines 3271--3279
@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
ed on the
[42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/latxfont/lcircle1.pfb>
Output written on R-FAQ.pdf (50 pages, 358555 bytes).
Transcript written on R-FAQ.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up
dmap/pdftex.map}] (/build/r-base-3.6.1/doc/manual/R-FAQ.toc [-1] [-2]) [-3]
(/build/r-base-3.6.1/doc/manual/R-FAQ.toc)
(/build/r-base-3.6.1/doc/manual/R-FAQ.toc) Chapter 1
(/build/r-base-3.6.1/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5]
[6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18]
Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26]
Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
Writing index file R-FAQ.fn
[39] [40] [41]
Underfull \hbox (badness 10000) in paragraph at lines 3271--3279
@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
ed on the
[42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/latxfont/lcircle1.pfb>
Output written on R-FAQ.pdf (52 pages, 374889 bytes).
Transcript written on R-FAQ.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
(/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up
dmap/pdftex.map}] (/build/r-base-3.6.1/doc/manual/R-FAQ.toc [-1] [-2]) [-3]
(/build/r-base-3.6.1/doc/manual/R-FAQ.toc)
(/build/r-base-3.6.1/doc/manual/R-FAQ.toc) Chapter 1
(/build/r-base-3.6.1/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5]
[6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18]
Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26]
Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38]
Writing index file R-FAQ.fn
[39] [40] [41]
Underfull \hbox (badness 10000) in paragraph at lines 3271--3279
@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
ed on the
[42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/latxfont/lcircle1.pfb>
Output written on R-FAQ.pdf (52 pages, 374887 bytes).
Transcript written on R-FAQ.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-intro.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] [-1] (Preface)
Cross reference values unknown; you must run TeX again. Chapter 1 [1]
Writing index file R-intro.cp
[2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13]
[14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24]
[25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34]
Chapter 8 [35] [36] [37] </build/r-base-3.6.1/doc/manual/images/hist.pdf> </bui
ld/r-base-3.6.1/doc/manual/images/ecdf.pdf> [38] </build/r-base-3.6.1/doc/manua
l/images/QQ.pdf> [39] </build/r-base-3.6.1/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]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741
 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{
n-x})))[] 
[72] [73] [74] [75] [76] </build/r-base-3.6.1/doc/manual/images/fig11.pdf>
[77] </build/r-base-3.6.1/doc/manual/images/fig12.pdf> [78] [79] [80] [81]
Chapter 13 [82]
Underfull \hbox (badness 10000) in paragraph at lines 6447--6452
[]@textrm Users con-nected to the In-ter-net can use the @texttt install.packag
es()[] @textrm and
[83] Chapter 14 [84] [85]
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and
[86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95]
[96] [97] [98] Appendix C [99] [100] Appendix D [101]
No file R-intro.vrs.
Appendix E [102]
No file R-intro.cps.
Appendix F [103] [104] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm
mi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/tex
live/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmsy9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb>
Output written on R-intro.pdf (107 pages, 575876 bytes).
Transcript written on R-intro.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-intro.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-intro.toc [-1]
[-2] [-3]) [-4] (/build/r-base-3.6.1/doc/manual/R-intro.toc)
(/build/r-base-3.6.1/doc/manual/R-intro.toc) (Preface)
(/build/r-base-3.6.1/doc/manual/R-intro.aux) Chapter 1 [1]
Writing index file R-intro.cp
[2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13]
[14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24]
[25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34]
Chapter 8 [35] [36] [37] </build/r-base-3.6.1/doc/manual/images/hist.pdf> </bui
ld/r-base-3.6.1/doc/manual/images/ecdf.pdf> [38] </build/r-base-3.6.1/doc/manua
l/images/QQ.pdf> [39] </build/r-base-3.6.1/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]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741
 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{
n-x})))[] 
[72] [73] [74] [75] [76] </build/r-base-3.6.1/doc/manual/images/fig11.pdf>
[77] </build/r-base-3.6.1/doc/manual/images/fig12.pdf> [78] [79] [80] [81]
Chapter 13 [82]
Underfull \hbox (badness 10000) in paragraph at lines 6447--6452
[]@textrm Users con-nected to the In-ter-net can use the @texttt install.packag
es()[] @textrm and
[83] Chapter 14 [84] [85]
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and
[86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95]
[96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E
[104] [105] Appendix F [106] [107] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi9.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmt
i9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb>
Output written on R-intro.pdf (113 pages, 625538 bytes).
Transcript written on R-intro.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-intro.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-intro.toc [-1]
[-2] [-3]) [-4] (/build/r-base-3.6.1/doc/manual/R-intro.toc)
(/build/r-base-3.6.1/doc/manual/R-intro.toc) (Preface)
(/build/r-base-3.6.1/doc/manual/R-intro.aux) Chapter 1 [1]
Writing index file R-intro.cp
[2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13]
[14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24]
[25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34]
Chapter 8 [35] [36] [37] </build/r-base-3.6.1/doc/manual/images/hist.pdf> </bui
ld/r-base-3.6.1/doc/manual/images/ecdf.pdf> [38] </build/r-base-3.6.1/doc/manua
l/images/QQ.pdf> [39] </build/r-base-3.6.1/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]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741
 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{
n-x})))[] 
[72] [73] [74] [75] [76] </build/r-base-3.6.1/doc/manual/images/fig11.pdf>
[77] </build/r-base-3.6.1/doc/manual/images/fig12.pdf> [78] [79] [80] [81]
Chapter 13 [82]
Underfull \hbox (badness 10000) in paragraph at lines 6447--6452
[]@textrm Users con-nected to the In-ter-net can use the @texttt install.packag
es()[] @textrm and
[83] Chapter 14 [84] [85]
Underfull \hbox (badness 10000) in paragraph at lines 6647--6652
 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t
extrm and
[86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95]
[96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E
[104] [105] Appendix F [106] [107] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi9.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmt
i9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb
></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb>
Output written on R-intro.pdf (113 pages, 625607 bytes).
Transcript written on R-intro.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-ints.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] [-1] Chapter 1
Writing index file R-ints.cp
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
[18]
Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455
 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 

Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456
 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 

Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457
 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 

Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[] 
[19] [20] [21] [22] [23] [24] Chapter 2 [25]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983
 []    @texttt if (!is.character(x)) x <- structure(as.character(x), names = na
mes(x))[] 
[26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34]
Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
Chapter 7 [48]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link,

Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl
ib[]@textrm ,
[49] Chapter 8 [50] [51] [52] [53] [54] [55]
Underfull \hbox (badness 10000) in paragraph at lines 4036--4044
 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u
sed for

Underfull \hbox (badness 7869) in paragraph at lines 4036--4044
 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI
LE_

Underfull \hbox (badness 10000) in paragraph at lines 4036--4044
 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa
tchArgs = FALSE[] @textrm and
[56] [57] [58] [59] [60] Chapter 9 [61] [62] Chapter 10 [63] Chapter 11
[64] Chapter 12 [65] [66] (Function and variable index) [67] [68]
No file R-ints.vrs.
(Concept index) [69]
No file R-ints.cps.
[70] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c
mr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-ints.pdf (73 pages, 401171 bytes).
Transcript written on R-ints.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-ints.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-ints.toc [-1]
[-2]) [-3] (/build/r-base-3.6.1/doc/manual/R-ints.toc)
(/build/r-base-3.6.1/doc/manual/R-ints.toc) Chapter 1
(/build/r-base-3.6.1/doc/manual/R-ints.aux)
Writing index file R-ints.cp
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
[18]
Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455
 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 

Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456
 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 

Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457
 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 

Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[] 
[19] [20] [21] [22] [23] [24] Chapter 2 [25]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983
 []    @texttt if (!is.character(x)) x <- structure(as.character(x), names = na
mes(x))[] 
[26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34]
Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
Chapter 7 [48]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link,

Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl
ib[]@textrm ,
[49] Chapter 8 [50] [51] [52] [53] [54] [55]
Underfull \hbox (badness 10000) in paragraph at lines 4036--4044
 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u
sed for

Underfull \hbox (badness 7869) in paragraph at lines 4036--4044
 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI
LE_

Underfull \hbox (badness 10000) in paragraph at lines 4036--4044
 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa
tchArgs = FALSE[] @textrm and
[56] [57] [58] [59] [60] Chapter 9 [61] [62] Chapter 10 [63] Chapter 11
[64] Chapter 12 [65] [66] (Function and variable index) [67] [68] [69]
(Concept index) [70] [71] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmtt9.pfb>
Output written on R-ints.pdf (76 pages, 451709 bytes).
Transcript written on R-ints.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-ints.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-ints.toc [-1]
[-2]) [-3] (/build/r-base-3.6.1/doc/manual/R-ints.toc)
(/build/r-base-3.6.1/doc/manual/R-ints.toc) Chapter 1
(/build/r-base-3.6.1/doc/manual/R-ints.aux)
Writing index file R-ints.cp
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
[18]
Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455
 [] @texttt length(nM <- asNamespace("Matrix") )                    # 941 for M
atrix 1.2-6[] 

Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456
 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener
ics with methods[] 

Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457
 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' 
(group)generic[] 

Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458
 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix
" "ANY#ldiMatrix" "ANY#Matrix"[] 
[19] [20] [21] [22] [23] [24] Chapter 2 [25]
Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983
 []    @texttt if (!is.character(x)) x <- structure(as.character(x), names = na
mes(x))[] 
[26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34]
Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47]
Chapter 7 [48]
Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a 
sym-bolic link,

Underfull \hbox (badness 10000) in paragraph at lines 3631--3640
@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl
ib[]@textrm ,
[49] Chapter 8 [50] [51] [52] [53] [54] [55]
Underfull \hbox (badness 10000) in paragraph at lines 4036--4044
 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u
sed for

Underfull \hbox (badness 7869) in paragraph at lines 4036--4044
 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI
LE_

Underfull \hbox (badness 10000) in paragraph at lines 4036--4044
 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa
tchArgs = FALSE[] @textrm and
[56] [57] [58] [59] [60] Chapter 9 [61] [62] Chapter 10 [63] Chapter 11
[64] Chapter 12 [65] [66] (Function and variable index) [67] [68] [69]
(Concept index) [70] [71] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmtt9.pfb>
Output written on R-ints.pdf (76 pages, 451713 bytes).
Transcript written on R-ints.log.
TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-lang.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] [-1] Chapter 1
Writing index file R-lang.cp
Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again.
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28]
Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39]
[40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48]
[49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58]
(Function and Variable Index) [59]
No file R-lang.vrs.
(Concept Index) [60]
No file R-lang.cps.
Appendix A [61] [62] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm
/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-lang.pdf (65 pages, 329929 bytes).
Transcript written on R-lang.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-lang.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-lang.toc [-1]
[-2]) [-3] (/build/r-base-3.6.1/doc/manual/R-lang.toc)
(/build/r-base-3.6.1/doc/manual/R-lang.toc) Chapter 1
(/build/r-base-3.6.1/doc/manual/R-lang.aux)
Writing index file R-lang.cp
Chapter 2 [1] [2]
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28]
Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39]
[40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48]
[49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58]
(Function and Variable Index) [59] [60] (Concept Index) [61] [62]
Overfull \vbox (1.73251pt too high) has occurred while \output is active
Overfull \vbox (1.73251pt too high) has occurred while \output is active
Appendix A [63] [64] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-lang.pdf (69 pages, 379003 bytes).
Transcript written on R-lang.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdfetex)
 restricted \write18 enabled.
entering extended mode
(/build/r-base-3.6.1/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi
(/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2018-01-09.11]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions,
(/build/r-base-3.6.1/doc/manual/epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
) localization, formatting, and turning on texinfo input format.)
Writing index file R-lang.vr
(/build/r-base-3.6.1/doc/manual/R-defs.texi
(/usr/share/texmf/tex/texinfo/txi-en.tex))
(/build/r-base-3.6.1/doc/manual/version.texi) [1{/var/lib/texmf/fonts/map/pdfte
x/updmap/pdftex.map}] [2] (/build/r-base-3.6.1/doc/manual/R-lang.toc [-1]
[-2]) [-3] (/build/r-base-3.6.1/doc/manual/R-lang.toc)
(/build/r-base-3.6.1/doc/manual/R-lang.toc) Chapter 1
(/build/r-base-3.6.1/doc/manual/R-lang.aux)
Writing index file R-lang.cp
Chapter 2 [1] [2]
Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294
 @textbf storage.mode| 
[3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28]
Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39]
[40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48]
[49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58]
(Function and Variable Index) [59] [60] (Concept Index) [61] [62]
Overfull \vbox (1.73251pt too high) has occurred while \output is active
Overfull \vbox (1.73251pt too high) has occurred while \output is active
Appendix A [63] [64] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf
-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/
fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on R-lang.pdf (69 pages, 378997 bytes).
Transcript written on R-lang.log.
make[1]: Leaving directory '/build/r-base-3.6.1/doc/manual'
/usr/bin/make -k pdf
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
PDF/LaTeX documentation: full reference index ...
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./fullrefman.tex
LaTeX2e <2018-12-01>
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2018/09/03 v1.4i Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
No file fullrefman.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex
Chapter 1.
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2]
Underfull \hbox (badness 6995) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
/ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It

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

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

Underfull \hbox (badness 10000) in paragraph at lines 141--149
\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As

Underfull \hbox (badness 4995) in paragraph at lines 141--149
\T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi
4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 ,
[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] [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 1178--1181
[]\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 1953--1953
 []\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] [34] [35] [36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via

Underfull \hbox (badness 1102) in paragraph at lines 2392--2397
\T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim
-ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit

[38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52]
[53] [54] [55] [56] [57] [58] [59]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[60] [61] [62]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77]
[78]
Underfull \hbox (badness 2521) in paragraph at lines 5033--5035
[]\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
[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93]
[94] [95] [96]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6189--6189
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[97] [98] [99] [100] [101] [102]
Overfull \hbox (46.35893pt too wide) in paragraph at lines 6598--6600
[]\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 : 
[103] [104]
Underfull \hbox (badness 10000) in paragraph at lines 6746--6749
[]\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
[105] [106]
Underfull \hbox (badness 6063) in paragraph at lines 6928--6934
[]\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-


Underfull \hbox (badness 2343) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1708) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
s not rec-om-mended) when

Underfull \hbox (badness 1831) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
/10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
[107]
Underfull \hbox (badness 3568) in paragraph at lines 6990--6997
\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
[108] [109]
Underfull \vbox (badness 10000) has occurred while \output is active [110]
Underfull \vbox (badness 10000) has occurred while \output is active [111]
[112]
Underfull \hbox (badness 1077) in paragraph at lines 7307--7313
[]\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 7307--7313
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[113] [114] [115] [116] [117] [118]
Underfull \hbox (badness 2096) in paragraph at lines 7648--7652
\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 .
[119] [120]
Underfull \hbox (badness 2351) in paragraph at lines 7766--7769
[][][]\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 ,
[121] [122] [123] [124] [125]
Underfull \hbox (badness 4479) in paragraph at lines 8092--8102
[][][]\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),
[126] [127] [128] [129] [130] [131]
Underfull \hbox (badness 1629) in paragraph at lines 8539--8551
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

Underfull \hbox (badness 1609) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which

Underfull \hbox (badness 2426) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that 
value is on those OSes also used as an er-ror code.
[132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
Underfull \hbox (badness 1178) in paragraph at lines 9275--9279
[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154]
[155] [156] [157] [158] [159] [160]
Underfull \hbox (badness 1735) in paragraph at lines 10423--10427
\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 .
[161] [162] [163] [164] [165] [166] [167]
Underfull \hbox (badness 6396) in paragraph at lines 10862--10870
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 1946) in paragraph at lines 10862--10870
\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
[168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181] [182] [183] [184]
Underfull \hbox (badness 4569) in paragraph at lines 11978--11982
[]\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 11978--11982
\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
[185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196]
[197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208]
[209]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[210]
Underfull \hbox (badness 1565) in paragraph at lines 13712--13716
[][][]\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
[211]
Underfull \hbox (badness 4927) in paragraph at lines 13756--13758
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
[212]
Underfull \hbox (badness 3148) in paragraph at lines 13849--13854
[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
[213]
Underfull \hbox (badness 1466) in paragraph at lines 13896--13899
[]\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
[214] [215]
Underfull \hbox (badness 10000) in paragraph at lines 14015--14019
[][][]\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 14026--14029
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[216] [217] [218] [219]
Underfull \hbox (badness 3965) in paragraph at lines 14316--14320
[]\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,
[220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
[232]
Underfull \hbox (badness 4429) in paragraph at lines 15092--15095
[]\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
[233] [234]
Underfull \hbox (badness 10000) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

Underfull \hbox (badness 1215) in paragraph at lines 15198--15200
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

Underfull \hbox (badness 10000) in paragraph at lines 15220--15225
[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

Underfull \hbox (badness 1558) in paragraph at lines 15220--15225
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

Underfull \hbox (badness 10000) in paragraph at lines 15232--15236
[]\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

Underfull \hbox (badness 2426) in paragraph at lines 15232--15236
\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[235]
Underfull \hbox (badness 2035) in paragraph at lines 15271--15275
[]\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 within
[236]
Underfull \vbox (badness 10000) has occurred while \output is active [237]
[238] [239] [240] [241] [242] [243] [244]
Underfull \hbox (badness 2452) in paragraph at lines 15870--15874
[]\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 15870--15874
\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
[245] [246] [247]
Underfull \hbox (badness 1092) in paragraph at lines 16043--16048
[][]\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
[248] [249] [250]
Underfull \hbox (badness 6741) in paragraph at lines 16293--16297
\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
 ,
[251] [252] [253] [254] [255] [256] [257] [258] [259]
Underfull \vbox (badness 3803) has occurred while \output is active [260]
Underfull \vbox (badness 10000) has occurred while \output is active [261]
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1478) in paragraph at lines 17582--17585
[]\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
[271] [272] [273] [274]
Underfull \hbox (badness 10000) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[275] [276] [277] [278] [279] [280] [281] [282] [283]
Underfull \hbox (badness 1442) in paragraph at lines 18437--18439
[]\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
[284]
Underfull \hbox (badness 2452) in paragraph at lines 18529--18545
[][][]\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 ,
[285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 1248) in paragraph at lines 18948--18951
[]\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 ,
[292] [293] [294] [295]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[296] [297] [298] [299] [300] [301]
Underfull \hbox (badness 1596) in paragraph at lines 19625--19630
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 2469) in paragraph at lines 20229--20234
[]\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 20243--20250
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[313]
Underfull \hbox (badness 10000) in paragraph at lines 20317--20321
[]\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 20317--20321
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[314] [315]
Underfull \hbox (badness 1014) in paragraph at lines 20487--20492
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
Underfull \hbox (badness 1264) in paragraph at lines 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[328]
Underfull \hbox (badness 4441) in paragraph at lines 21305--21308
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 6047) in paragraph at lines 22052--22054
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351]
[352] [353] [354] [355] [356]
Underfull \hbox (badness 1077) in paragraph at lines 23093--23099
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\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 .
[357] [358] [359] [360] [361] [362] [363] [364] [365]
Underfull \hbox (badness 2790) in paragraph at lines 23589--23592
[]\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 23589--23592
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[366] [367] [368] [369]
Underfull \hbox (badness 1194) in paragraph at lines 23871--23874
[]\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
[370] [371] [372]
Underfull \hbox (badness 2368) in paragraph at lines 24077--24083
[]\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 list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24077--24083
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[373] [374] [375] [376] [377] [378]
Underfull \hbox (badness 10000) in paragraph at lines 24459--24462
[]\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
[379] [380] [381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 25064--25066
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
[400]
Underfull \hbox (badness 1038) in paragraph at lines 25904--25912
[]\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 1735) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25913--25916
[]\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 25932--25934
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[401] [402]
Underfull \hbox (badness 2142) in paragraph at lines 26073--26077
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 26123--26128
[]\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
[403] [404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 26411--26417
[]\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 26411--26417
\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 26411--26417
\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 26424--26427
[]\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 26450--26452
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 26485--26490
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and
[407]
Underfull \hbox (badness 7203) in paragraph at lines 26503--26506
[]\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 10000) in paragraph at lines 26527--26532
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26527--26532
\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).
[408] [409] [410] [411] [412] [413] [414] [415]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[416]
Underfull \hbox (badness 7925) in paragraph at lines 27124--27128
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

Underfull \hbox (badness 1622) in paragraph at lines 27124--27128
[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

Underfull \hbox (badness 6125) in paragraph at lines 27129--27138
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427]
Underfull \hbox (badness 2726) in paragraph at lines 27850--27853
[]\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
[428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439]
[440] [441] [442] [443] [444] [445]
Underfull \vbox (badness 3803) has occurred while \output is active [446]
[447] [448] [449] [450] [451] [452] [453]
Underfull \hbox (badness 1533) in paragraph at lines 29541--29544
[]\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
[454] [455] [456]
Underfull \hbox (badness 1163) in paragraph at lines 29704--29715
[]\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
[457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468]
[469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 31250--31254
[]\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 31250--31254
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 31272--31274
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[481] [482] [483] [484] [485] [486] [487] [488] [489]
Underfull \hbox (badness 1655) in paragraph at lines 31828--31830
[]\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
[490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501]
[502] [503] [504] [505] [506]
Underfull \hbox (badness 2261) in paragraph at lines 32947--32952
[]\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
[507]
Underfull \hbox (badness 10000) in paragraph at lines 32974--32980
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1484) in paragraph at lines 32974--32980
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519]
[520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
[532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543]
[544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555]
Underfull \hbox (badness 1072) in paragraph at lines 36116--36120
[]\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 36121--36125
[]\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 36149--36155
[]\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 36149--36155
\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 36149--36155
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in

Underfull \hbox (badness 3009) in paragraph at lines 36161--36168
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 36161--36168
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 36161--36168
\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 36161--36168
\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
[556] [557] [558] [559] [560] [561]
Underfull \hbox (badness 1142) in paragraph at lines 36514--36520
[]\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 \T1/zi4/m/n/10 "%Y-%m-%d
[562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573]
[574] [575] [576] [577] [578] [579] [580] [581]
Underfull \hbox (badness 1565) in paragraph at lines 37787--37789
[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[582] [583] [584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 4967) in paragraph at lines 38386--38391
[]\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
[592] [593]
Underfull \hbox (badness 1616) in paragraph at lines 38499--38504
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
[594] [595] [596] [597]
Underfull \vbox (badness 10000) has occurred while \output is active [598]
[599] [600] [601] [602]
Underfull \hbox (badness 1472) in paragraph at lines 39025--39028
[]\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
[603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614]
[615]
Underfull \vbox (badness 3803) has occurred while \output is active [616]
Underfull \hbox (badness 10000) in paragraph at lines 39939--39943
[]\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., \T1/zi4/m/n/10
 length(bin) >
[617] [618] [619] [620]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[621] [622] [623]
Underfull \hbox (badness 10000) in paragraph at lines 40374--40378
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[624] [625] [626] [627] [628] [629] [630] [631] [632]
Underfull \hbox (badness 10000) in paragraph at lines 40987--40990
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
[633] [634] [635] [636] [637] [638]
Underfull \vbox (badness 10000) has occurred while \output is active [639]
[640] [641] [642] [643] [644] [645] [646]
Underfull \hbox (badness 1990) in paragraph at lines 41890--41898
[]\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 41890--41898
\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
[647] [648] [649] [650] [651] [652] [653] [654]
Underfull \hbox (badness 1917) in paragraph at lines 42396--42403
[]\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
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665]
Underfull \hbox (badness 3668) in paragraph at lines 43125--43127
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[666] [667]
Underfull \hbox (badness 2401) in paragraph at lines 43253--43257
[]\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
[668] [669] [670]
Underfull \hbox (badness 2111) in paragraph at lines 43442--43447
\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 10000) in paragraph at lines 43463--43468
[]\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
[671] [672] [673] [674] [675] [676] [677] [678] [679]
Underfull \hbox (badness 5417) in paragraph at lines 44045--44049
[]\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
[680]
Underfull \hbox (badness 10000) in paragraph at lines 44106--44110
[]\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
[681] [682]) (./compiler-pkg.tex
Chapter 2.
[683] [684] [685] [686]) (./datasets-pkg.tex
Chapter 3.
[687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698]
[699] [700] [701] [702] [703]
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.
[704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715]
[716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726]
Underfull \vbox (badness 1448) has occurred while \output is active [727]
[728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738]
Overfull \vbox (19.74611pt too high) has occurred while \output is active
[739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
[751] [752] [753] [754]
Underfull \vbox (badness 10000) has occurred while \output is active [755]
[756] [757] [758]
Underfull \vbox (badness 10000) has occurred while \output is active [759]
[760] [761] [762] [763] [764]
Overfull \vbox (18.9959pt too high) has occurred while \output is active
[765] [766] [767]) (./grDevices-pkg.tex [768]
Chapter 4.
[769] [770] [771] [772] [773]
Underfull \hbox (badness 3158) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

Underfull \hbox (badness 10000) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

Underfull \hbox (badness 1852) in paragraph at lines 298--303
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
[774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785]
[786]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\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
[787] [788] [789] [790]
Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
[]\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
[791] [792] [793]
Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
\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
[794] [795] [796] [797] [798] [799]
Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
\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 ,
[800] [801]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[802] [803] [804]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[805] [806] [807] [808] [809] [810] [811] [812] [813] [814]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829

[815] [816] [817] [818] [819] [820] [821] [822] [823]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[824] [825] [826] [827] [828]
Underfull \vbox (badness 10000) has occurred while \output is active [829]
Underfull \hbox (badness 10000) in paragraph at lines 3785--3788
[]\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
[830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

Underfull \hbox (badness 4181) in paragraph at lines 4514--4519
\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
[841]
Underfull \vbox (badness 10000) has occurred while \output is active [842]
[843]
Underfull \hbox (badness 1067) in paragraph at lines 4668--4675
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[844] [845] [846] [847]
Underfull \hbox (badness 1377) in paragraph at lines 4971--4976
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[848]
Underfull \hbox (badness 1418) in paragraph at lines 5047--5054
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[849] [850]
Underfull \hbox (badness 1377) in paragraph at lines 5176--5181
[]\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
[851]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\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
[852] [853]
Underfull \hbox (badness 2035) in paragraph at lines 5380--5389
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\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 ,
[854]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5448--5455
\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 .
[855] [856] [857]
Underfull \hbox (badness 1546) in paragraph at lines 5590--5598
[]\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 ,
[858] [859] [860] [861] [862] [863] [864] [865]
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877]
[878]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[879]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[880] [881] [882] [883] [884]
Underfull \hbox (badness 3780) in paragraph at lines 7345--7351
[]\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 ,
[885] [886] [887]
Underfull \hbox (badness 2680) in paragraph at lines 7546--7548
[]\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
[888] [889] [890]) (./graphics-pkg.tex
Chapter 5.
[891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902]
[903] [904] [905] [906] [907] [908] [909] [910] [911] [912]
Underfull \hbox (badness 4634) in paragraph at lines 1351--1354
[][][]\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 ,
[913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924]
[925] [926] [927] [928] [929]
Underfull \hbox (badness 1009) in paragraph at lines 2390--2397
\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
[930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941]
[942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952]
Underfull \vbox (badness 10000) has occurred while \output is active [953]
[954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965]
Underfull \hbox (badness 3229) in paragraph at lines 4534--4539
[]\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
[966] [967] [968] [969] [970]
Underfull \hbox (badness 10000) in paragraph at lines 4891--4897
[]\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 4891--4897
\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
[971]
Underfull \hbox (badness 10000) in paragraph at lines 5022--5025

[972]
Underfull \hbox (badness 10000) in paragraph at lines 5083--5085

[973 </build/r-base-3.6.1/library/graphics/help/figures/mai.pdf>] [974 </build/
r-base-3.6.1/library/graphics/help/figures/oma.pdf>] [975]
Underfull \hbox (badness 10000) in paragraph at lines 5273--5275
[]\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
[976]
Underfull \vbox (badness 3803) has occurred while \output is active [977]
[978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989]
[990] [991] [992] [993] [994] [995] [996] [997] [998]
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6751--6752
[][] 
[999] [1000 </build/r-base-3.6.1/library/graphics/help/figures/pch.pdf>]
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011]
[1012]
Underfull \hbox (badness 2012) in paragraph at lines 7576--7579
[]\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 poi
nt
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
[1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033]
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

Underfull \hbox (badness 10000) in paragraph at lines 8838--8840
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
[1034]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [1035] [1036] [1037] [1038])
(./grid-pkg.tex
Chapter 6.

Underfull \vbox (badness 10000) has occurred while \output is active [1039]
[1040] [1041] [1042] [1043] [1044] [1045] [1046]
Underfull \hbox (badness 2680) in paragraph at lines 483--486
[]\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
[1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056]
Underfull \hbox (badness 4279) in paragraph at lines 1064--1073
[][][]\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 ,
[1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067]
[1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078]
[1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089]
[1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100]
Underfull \vbox (badness 10000) has occurred while \output is active [1101]
[1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
[1113] [1114]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\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
[1115] [1116] [1117] [1118]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129]
[1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140]
[1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149]
Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
[]\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 \T1/zi4/m/n/10 depth
[1150] [1151] [1152] [1153]) (./methods-pkg.tex [1154]
Chapter 7.
[1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162]
Underfull \vbox (badness 3803) has occurred while \output is active [1163]
Underfull \vbox (badness 10000) has occurred while \output is active [1164]
[1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173]
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
[1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181]
Underfull \hbox (badness 2181) 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
[1182]
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
[1183] [1184] [1185]
Underfull \hbox (badness 2213) 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 =
[1186] [1187] [1188] [1189] [1190]
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
[1191] [1192]
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
[1193]
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
[1194] [1195] [1196] [1197] [1198] [1199] [1200]
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
[1201] [1202] [1203] [1204] [1205]
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
[1206]
Underfull \hbox (badness 10000) in paragraph at lines 3642--3651
[]\T1/ptm/m/n/10 The
[1207]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
[1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218]
Underfull \hbox (badness 1769) in paragraph at lines 4472--4478
[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228]
Underfull \vbox (badness 10000) has occurred while \output is active [1229]
[1230] [1231]
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
[1232]
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
[1233] [1234] [1235] [1236]
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
[1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244]
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
[1245] [1246] [1247] [1248]
Underfull \vbox (badness 10000) has occurred while \output is active [1249]
[1250] [1251] [1252]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}
                               [1253] [1254] [1255]pdfTeX warning (ext4): desti
nation with the same identifier (name{Rfn.Complex}) has been already used, dupl
icate ignored
<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}
                                                 [1256]
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
[1257] [1258] [1259]
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
[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281]
[1282] [1283] [1284] [1285] [1286]
Underfull \vbox (badness 10000) has occurred while \output is active [1287]
[1288] [1289] [1290] [1291] [1292] [1293] [1294]
Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1295] [1296] [1297] [1298] [1299] [1300] [1301]
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.,
[1302] [1303] [1304] [1305]) (./parallel-pkg.tex [1306]
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
[1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317]
[1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327]
Underfull \hbox (badness 3386) in paragraph at lines 1365--1368
[]\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
[1328] [1329] [1330]) (./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
[1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341]
[1342] [1343] [1344] [1345] [1346]) (./stats-pkg.tex
Chapter 10.
[1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
[1358] [1359] [1360]
Underfull \hbox (badness 1412) in paragraph at lines 875--877
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368]
Underfull \hbox (badness 2503) in paragraph at lines 1356--1359
[]\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 ,
[1369] [1370] [1371]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
[1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382]
[1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
[1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401]
Underfull \hbox (badness 2503) in paragraph at lines 3437--3440
[]\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 ,
[1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
[1413] [1414] [1415] [1416]
Underfull \hbox (badness 1127) in paragraph at lines 4351--4354
[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1417] [1418] [1419] [1420] [1421]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431]
Underfull \hbox (badness 2556) in paragraph at lines 5317--5320
[]\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 5334--5336
[]\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
[1432] [1433] [1434] [1435] [1436] [1437] [1438]
Underfull \hbox (badness 2503) in paragraph at lines 5726--5730
[]\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 ,
[1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
[1450] [1451]
Underfull \hbox (badness 7081) in paragraph at lines 6520--6523
[]\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 6524--6526
[]\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
[1452] [1453] [1454] [1455] [1456]
Underfull \vbox (badness 3803) has occurred while \output is active [1457]
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 7369--7372
[]\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
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
Underfull \vbox (badness 10000) has occurred while \output is active [1487]
[1488] [1489] [1490] [1491]
Underfull \hbox (badness 2626) in paragraph at lines 9048--9051
[]\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
[1492] [1493]
Underfull \hbox (badness 2503) in paragraph at lines 9155--9159
[]\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 ,
[1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504]
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516] [1517] [1518]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 10844--10847
[]\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,
[1519]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1526] [1527] [1528] [1529] [1530] [1531]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\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

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1532] [1533]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1534] [1535]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\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
[1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 \T1/zi4/m/n/10 SSinit =
[1546] [1547] [1548] [1549] [1550] [1551]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562]
[1563]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1574] [1575]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\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
[1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586]
[1587] [1588] [1589] [1590] [1591] [1592] [1593]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\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 ,
[1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\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
[1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612]
[1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623]
[1624] [1625] [1626] [1627] [1628] [1629]
Underfull \vbox (badness 10000) has occurred while \output is active [1630]
Underfull \vbox (badness 10000) has occurred while \output is active [1631]
[1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642]
[1643]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

Underfull \hbox (badness 1735) in paragraph at lines 18581--18584
[]\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
[1644]
Underfull \hbox (badness 2343) in paragraph at lines 18594--18598
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

Underfull \hbox (badness 3471) in paragraph at lines 18594--18598
\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18602--18606
[]\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
[1645] [1646] [1647]
Overfull \hbox (15.73795pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1648]
[1649] [1650] [1651] [1652] [1653] [1654]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1664] [1665] [1666] [1667]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1668] [1669] [1670] [1671] [1672] [1673] [1674]
Underfull \hbox (badness 2503) in paragraph at lines 20381--20384
[]\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 ,

Underfull \hbox (badness 3919) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
[1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685]
[1686] [1687] [1688] [1689] [1690] [1691] [1692]
Underfull \hbox (badness 10000) in paragraph at lines 21485--21491
[]\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 ,
[1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703]
[1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714]
[1715]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723]
Overfull \hbox (27.74408pt too wide) in paragraph at lines 23399--23399
 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1724] [1725] [1726] [1727] [1728]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 4205) in paragraph at lines 23650--23653
\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
[1729] [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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 \T1/zi4/m/n/10 y[j] =
[1738]
Underfull \hbox (badness 3690) in paragraph at lines 24287--24291
[][][]\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
[1739] [1740] [1741] [1742] [1743] [1744] [1745]
Underfull \vbox (badness 10000) has occurred while \output is active [1746]
[1747]
Underfull \hbox (badness 2165) in paragraph at lines 24777--24782
[]\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 ,
[1748] [1749] [1750]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
[1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761]
[1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772]
[1773] [1774]
Underfull \vbox (badness 10000) has occurred while \output is active [1775]
Underfull \hbox (badness 3514) in paragraph at lines 26556--26561
[]\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
[1776] [1777] [1778] [1779]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26790--26790
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1780]
Underfull \hbox (badness 3514) in paragraph at lines 26826--26832
[]\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
[1781] [1782] [1783] [1784]
Underfull \hbox (badness 3514) in paragraph at lines 27040--27045
[]\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
[1785] [1786]
Underfull \hbox (badness 3514) in paragraph at lines 27127--27132
[]\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
[1787]
Underfull \hbox (badness 3514) in paragraph at lines 27192--27197
[]\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
[1788] [1789]
Underfull \hbox (badness 3514) in paragraph at lines 27286--27291
[]\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
[1790]
Underfull \hbox (badness 6691) in paragraph at lines 27378--27383
[]\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
[1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799]
Underfull \hbox (badness 4024) in paragraph at lines 27908--27911
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
[1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809]
Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\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
[1810] [1811] [1812]
Underfull \hbox (badness 5431) in paragraph at lines 28724--28727
[]\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
[1813] [1814] [1815] [1816] [1817] [1818]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1819] [1820] [1821] [1822] [1823]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834]
[1835] [1836] [1837] [1838] [1839] [1840] [1841] [1842]
Underfull \hbox (badness 3557) in paragraph at lines 30470--30474
[]\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 \T1/zi4
/m/n/10 interval =
[1843] [1844] [1845]
Underfull \vbox (badness 10000) has occurred while \output is active [1846]
[1847] [1848]
Underfull \hbox (badness 1337) in paragraph at lines 30834--30838
[]\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
[1849] [1850] [1851] [1852] [1853] [1854] [1855] [1856] [1857]
Underfull \hbox (badness 1337) in paragraph at lines 31361--31365
[]\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
[1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867])
(./stats4-pkg.tex [1868]
Chapter 11.
[1869] [1870] [1871] [1872] [1873] [1874]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1875] [1876] [1877])
(./tcltk-pkg.tex [1878]
Chapter 12.
[1879] [1880] [1881] [1882] [1883] [1884] [1885]
Underfull \vbox (badness 10000) has occurred while \output is active [1886]
Underfull \vbox (badness 10000) has occurred while \output is active [1887]
Underfull \hbox (badness 1546) in paragraph at lines 664--671
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898]
[1899]) (./tools-pkg.tex [1900]
Chapter 13.
[1901]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 72.

[1902]
Underfull \hbox (badness 3039) in paragraph at lines 164--167
[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1903] [1904]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

Underfull \hbox (badness 4967) in paragraph at lines 285--298
\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1905] [1906]
Underfull \hbox (badness 3039) in paragraph at lines 389--391
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917]
[1918]
Underfull \hbox (badness 4441) in paragraph at lines 1139--1149
\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-
[1919]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
[1920]
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209
\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 ,
[1921] [1922] [1923] [1924] [1925]
Underfull \hbox (badness 2293) in paragraph at lines 1558--1560
[]\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
[1926] [1927]
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Underfull \hbox (badness 1082) in paragraph at lines 1703--1705
[]\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
[1928] [1929] [1930] [1931]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1932] [1933] [1934]
[1935] [1936]
Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202
 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1937] [1938] [1939]
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1940] [1941] [1942] [1943] [1944] [1945] [1946]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
(Font)              using `T1/zi4/m/n' instead on input line 2846.

[1947] [1948] [1949] [1950] [1951]
Underfull \hbox (badness 1424) in paragraph at lines 3128--3130
[]\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
[1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962]
Underfull \hbox (badness 10000) in paragraph at lines 3832--3834
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1963] [1964]
Underfull \hbox (badness 10000) in paragraph at lines 3971--3974
[]\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
[1965] [1966]
Underfull \hbox (badness 1137) in paragraph at lines 4073--4075
[]\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
[1967] [1968] [1969] [1970] [1971]
Underfull \hbox (badness 1796) in paragraph at lines 4381--4386
[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1972]
Underfull \hbox (badness 1838) in paragraph at lines 4455--4461
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

Underfull \hbox (badness 10000) in paragraph at lines 4455--4461
\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
[1973] [1974] [1975]
Underfull \hbox (badness 2197) in paragraph at lines 4671--4681
[]\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 :
[1976]
Underfull \hbox (badness 1571) in paragraph at lines 4734--4738
[]\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
[1977] [1978] [1979]) (./utils-pkg.tex [1980]
Chapter 14.
[1981]
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 ',
[1982] [1983] [1984] [1985] [1986]
Underfull \hbox (badness 10000) in paragraph at lines 376--381
\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
[1987] [1988] [1989] [1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\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 717--723
\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
[1992] [1993]
Underfull \hbox (badness 5847) in paragraph at lines 850--856
[]\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 850--856
\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
[1994]
Underfull \hbox (badness 3861) in paragraph at lines 918--923
[]\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 ,
[1995] [1996]
Underfull \hbox (badness 3323) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

Underfull \hbox (badness 3919) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 3735) in paragraph at lines 1089--1097
\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 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
[1997]
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1998] [1999]
Underfull \vbox (badness 3803) has occurred while \output is active [2000]
[2001] [2002] [2003] [2004]
Underfull \hbox (badness 1371) in paragraph at lines 1606--1608
[]\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
[2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Underfull \hbox (badness 2057) in paragraph at lines 2215--2217
[]\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
[2015] [2016] [2017] [2018] [2019] [2020]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [2021] [2022]
Underfull \hbox (badness 1748) in paragraph at lines 2733--2736
[]\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
[2023] [2024] [2025] [2026] [2027] [2028] [2029]
Underfull \hbox (badness 5388) in paragraph at lines 3142--3146
[]\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 [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

Underfull \hbox (badness 2285) in paragraph at lines 3147--3150
[]\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 =
[2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040]
Underfull \hbox (badness 1430) in paragraph at lines 3906--3914
[]\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
[2041]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\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
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [2056] [2057] [2058]
[2059] [2060] [2061] [2062] [2063]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073]
Underfull \hbox (badness 1371) in paragraph at lines 5996--5998
[]\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
[2074]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2075] [2076] [2077]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2078]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2079] [2080]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[2081] [2082] [2083]
Underfull \hbox (badness 1325) in paragraph at lines 6632--6636
[]\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

Underfull \hbox (badness 4726) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of
[2084]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[2085]
Underfull \hbox (badness 3219) in paragraph at lines 6792--6799
[]\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 6792--6799
\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 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

Underfull \hbox (badness 1596) in paragraph at lines 6792--6799
[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently

Underfull \hbox (badness 2932) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[2086]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,
[2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097]
[2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108]
[2109] [2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 8436--8438
[]\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 2310) in paragraph at lines 8458--8463
[]\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,
[2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119]
Underfull \hbox (badness 1248) in paragraph at lines 8982--8986
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[2120]
Underfull \hbox (badness 1789) in paragraph at lines 9060--9062
[]\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
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130]
Underfull \vbox (badness 10000) has occurred while \output is active [2131]
[2132] [2133]
Underfull \hbox (badness 1097) in paragraph at lines 9897--9900
[]\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
[2134] [2135]
Underfull \hbox (badness 3000) in paragraph at lines 10033--10038
[][][]\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 ;
[2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144]
Underfull \hbox (badness 2134) in paragraph at lines 10616--10621
[][][]\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 ;

Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 2469) in paragraph at lines 11165--11169
[]\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 11165--11169
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2154] [2155] [2156] [2157] [2158]
Underfull \hbox (badness 4060) in paragraph at lines 11496--11499
[]\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 11519--11519
 []\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 '[] 
[2159] [2160] [2161] [2162]
Underfull \hbox (badness 2150) in paragraph at lines 11758--11760
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2163] [2164] [2165] [2166]
Underfull \hbox (badness 10000) in paragraph at lines 11977--11981
[]\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 12008--12014
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2167] [2168] [2169]
Underfull \hbox (badness 1009) in paragraph at lines 12202--12214
[]\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

Underfull \hbox (badness 4779) in paragraph at lines 12239--12241
[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd
[2170]
Underfull \hbox (badness 1077) in paragraph at lines 12269--12276
\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2171] [2172] [2173] [2174] [2175] [2176]
Underfull \hbox (badness 3780) in paragraph at lines 12670--12674
[]\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 12686--12689
[]\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
[2177] [2178] [2179] [2180]
Underfull \hbox (badness 2302) in paragraph at lines 12891--12893
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2181] [2182] [2183] [2184]
Underfull \hbox (badness 10000) in paragraph at lines 13187--13192
[]\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 13196--13199
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2185] [2186]
Underfull \vbox (badness 10000) has occurred while \output is active [2187]
[2188] [2189] [2190] [2191]
Underfull \hbox (badness 2932) in paragraph at lines 13616--13623
[]\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,

Underfull \hbox (badness 1688) in paragraph at lines 13616--13623
\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2192] [2193] [2194] [2195] [2196]
Underfull \hbox (badness 6510) in paragraph at lines 13925--13929
[]\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 13932--13935
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 13932--13935
\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
[2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 10000) in paragraph at lines 14596--14601
[]\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 14596--14601
[][]\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 14602--14604
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2207]
Underfull \hbox (badness 10000) in paragraph at lines 14661--14664
[][][]\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 ,
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219]
Underfull \hbox (badness 10000) in paragraph at lines 15434--15436
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2220] [2221] [2222] [2223]) [2224]
No file fullrefman.ind.
(./fullrefman.aux)

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


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

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed 
one

pdfTeX warning (dest): name{Rfn.lmList} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparse.model.matrix} has been referenced but do
es not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nlsList} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/
texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4b.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr5.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/
fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on fullrefman.pdf (2227 pages, 5567528 bytes).
Transcript written on fullrefman.log.
This is makeindex, version 2.15 [TeX Live 2019/dev] (kpathsea + Thai support).
Scanning input file fullrefman.idx.................done (13921 entries accepted, 34 rejected).
Sorting entries..................................................................................................................................................done (213790 comparisons).
Generating output file fullrefman.ind................done (13715 lines written, 56 warnings).
Output written in fullrefman.ind.
Transcript written in fullrefman.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./fullrefman.tex
LaTeX2e <2018-12-01>
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2018/09/03 v1.4i Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
(./fullrefman.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./fullrefman.out) (./fullrefman.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] [3]
[4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]
[20] [21] [22] [23] [24] [25] [26] [27] [28] [29]) [30] (./base-pkg.tex
Chapter 1.
[1] [2]
Underfull \hbox (badness 6995) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
/ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It

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

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

Underfull \hbox (badness 10000) in paragraph at lines 141--149
\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As

Underfull \hbox (badness 4995) in paragraph at lines 141--149
\T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi
4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 ,
[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] [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 1178--1181
[]\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 1953--1953
 []\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] [34] [35] [36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via

Underfull \hbox (badness 1102) in paragraph at lines 2392--2397
\T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim
-ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit

[38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52]
[53] [54] [55] [56] [57] [58] [59]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[60] [61] [62]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77]
[78]
Underfull \hbox (badness 2521) in paragraph at lines 5033--5035
[]\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
[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93]
[94] [95] [96]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6189--6189
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[97] [98] [99] [100] [101] [102]
Overfull \hbox (46.35893pt too wide) in paragraph at lines 6598--6600
[]\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 : 
[103] [104]
Underfull \hbox (badness 10000) in paragraph at lines 6746--6749
[]\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
[105] [106]
Underfull \hbox (badness 6063) in paragraph at lines 6928--6934
[]\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-


Underfull \hbox (badness 2343) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1708) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
s not rec-om-mended) when

Underfull \hbox (badness 1831) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
/10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
[107]
Underfull \hbox (badness 3568) in paragraph at lines 6990--6997
\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
[108] [109]
Underfull \vbox (badness 10000) has occurred while \output is active [110]
Underfull \vbox (badness 10000) has occurred while \output is active [111]
[112]
Underfull \hbox (badness 1077) in paragraph at lines 7307--7313
[]\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 7307--7313
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[113] [114] [115] [116] [117] [118]
Underfull \hbox (badness 2096) in paragraph at lines 7648--7652
\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 .
[119] [120]
Underfull \hbox (badness 2351) in paragraph at lines 7766--7769
[][][]\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 ,
[121] [122] [123] [124] [125]
Underfull \hbox (badness 4479) in paragraph at lines 8092--8102
[][][]\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),
[126] [127] [128] [129] [130] [131]
Underfull \hbox (badness 1629) in paragraph at lines 8539--8551
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

Underfull \hbox (badness 1609) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which

Underfull \hbox (badness 2426) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that 
value is on those OSes also used as an er-ror code.
[132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
Underfull \hbox (badness 1178) in paragraph at lines 9275--9279
[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154]
[155] [156] [157] [158] [159] [160]
Underfull \hbox (badness 1735) in paragraph at lines 10423--10427
\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 .
[161] [162] [163] [164] [165] [166] [167]
Underfull \hbox (badness 6396) in paragraph at lines 10862--10870
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 1946) in paragraph at lines 10862--10870
\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
[168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181] [182] [183] [184]
Underfull \hbox (badness 4569) in paragraph at lines 11978--11982
[]\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 11978--11982
\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
[185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196]
[197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208]
[209]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[210]
Underfull \hbox (badness 1565) in paragraph at lines 13712--13716
[][][]\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
[211]
Underfull \hbox (badness 4927) in paragraph at lines 13756--13758
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
[212]
Underfull \hbox (badness 3148) in paragraph at lines 13849--13854
[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
[213]
Underfull \hbox (badness 1466) in paragraph at lines 13896--13899
[]\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
[214] [215]
Underfull \hbox (badness 10000) in paragraph at lines 14015--14019
[][][]\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 14026--14029
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[216] [217] [218] [219]
Underfull \hbox (badness 3965) in paragraph at lines 14316--14320
[]\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,
[220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
[232]
Underfull \hbox (badness 4429) in paragraph at lines 15092--15095
[]\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
[233] [234]
Underfull \hbox (badness 10000) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

Underfull \hbox (badness 1215) in paragraph at lines 15198--15200
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

Underfull \hbox (badness 10000) in paragraph at lines 15220--15225
[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

Underfull \hbox (badness 1558) in paragraph at lines 15220--15225
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

Underfull \hbox (badness 10000) in paragraph at lines 15232--15236
[]\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

Underfull \hbox (badness 2426) in paragraph at lines 15232--15236
\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[235]
Underfull \hbox (badness 2035) in paragraph at lines 15271--15275
[]\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 within
[236]
Underfull \vbox (badness 10000) has occurred while \output is active [237]
[238] [239] [240] [241] [242] [243] [244]
Underfull \hbox (badness 2452) in paragraph at lines 15870--15874
[]\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 15870--15874
\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
[245] [246] [247]
Underfull \hbox (badness 1092) in paragraph at lines 16043--16048
[][]\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
[248] [249] [250]
Underfull \hbox (badness 6741) in paragraph at lines 16293--16297
\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
 ,
[251] [252] [253] [254] [255] [256] [257] [258] [259]
Underfull \vbox (badness 3803) has occurred while \output is active [260]
Underfull \vbox (badness 10000) has occurred while \output is active [261]
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1478) in paragraph at lines 17582--17585
[]\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
[271] [272] [273] [274]
Underfull \hbox (badness 10000) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[275] [276] [277] [278] [279] [280] [281] [282] [283]
Underfull \hbox (badness 1442) in paragraph at lines 18437--18439
[]\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
[284]
Underfull \hbox (badness 2452) in paragraph at lines 18529--18545
[][][]\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 ,
[285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 1248) in paragraph at lines 18948--18951
[]\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 ,
[292] [293] [294] [295]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[296] [297] [298] [299] [300] [301]
Underfull \hbox (badness 1596) in paragraph at lines 19625--19630
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 2469) in paragraph at lines 20229--20234
[]\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 20243--20250
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[313]
Underfull \hbox (badness 10000) in paragraph at lines 20317--20321
[]\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 20317--20321
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[314] [315]
Underfull \hbox (badness 1014) in paragraph at lines 20487--20492
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
Underfull \hbox (badness 1264) in paragraph at lines 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[328]
Underfull \hbox (badness 4441) in paragraph at lines 21305--21308
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 6047) in paragraph at lines 22052--22054
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351]
[352] [353] [354] [355] [356]
Underfull \hbox (badness 1077) in paragraph at lines 23093--23099
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\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 .
[357] [358] [359] [360] [361] [362] [363] [364] [365]
Underfull \hbox (badness 2790) in paragraph at lines 23589--23592
[]\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 23589--23592
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[366] [367] [368] [369]
Underfull \hbox (badness 1194) in paragraph at lines 23871--23874
[]\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
[370] [371] [372]
Underfull \hbox (badness 2368) in paragraph at lines 24077--24083
[]\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 list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24077--24083
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[373] [374] [375] [376] [377] [378]
Underfull \hbox (badness 10000) in paragraph at lines 24459--24462
[]\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
[379] [380] [381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 25064--25066
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
[400]
Underfull \hbox (badness 1038) in paragraph at lines 25904--25912
[]\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 1735) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25913--25916
[]\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 25932--25934
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[401] [402]
Underfull \hbox (badness 2142) in paragraph at lines 26073--26077
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 26123--26128
[]\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
[403] [404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 26411--26417
[]\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 26411--26417
\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 26411--26417
\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 26424--26427
[]\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 26450--26452
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 26485--26490
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and
[407]
Underfull \hbox (badness 7203) in paragraph at lines 26503--26506
[]\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 10000) in paragraph at lines 26527--26532
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26527--26532
\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).
[408] [409] [410] [411] [412] [413] [414] [415]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[416]
Underfull \hbox (badness 7925) in paragraph at lines 27124--27128
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

Underfull \hbox (badness 1622) in paragraph at lines 27124--27128
[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

Underfull \hbox (badness 6125) in paragraph at lines 27129--27138
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427]
Underfull \hbox (badness 2726) in paragraph at lines 27850--27853
[]\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
[428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439]
[440] [441] [442] [443] [444] [445]
Underfull \vbox (badness 3803) has occurred while \output is active [446]
[447] [448] [449] [450] [451] [452] [453]
Underfull \hbox (badness 1533) in paragraph at lines 29541--29544
[]\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
[454] [455] [456]
Underfull \hbox (badness 1163) in paragraph at lines 29704--29715
[]\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
[457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468]
[469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 31250--31254
[]\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 31250--31254
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 31272--31274
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[481] [482] [483] [484] [485] [486] [487] [488] [489]
Underfull \hbox (badness 1655) in paragraph at lines 31828--31830
[]\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
[490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501]
[502] [503] [504] [505] [506]
Underfull \hbox (badness 2261) in paragraph at lines 32947--32952
[]\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
[507]
Underfull \hbox (badness 10000) in paragraph at lines 32974--32980
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1484) in paragraph at lines 32974--32980
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519]
[520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
[532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543]
[544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555]
Underfull \hbox (badness 1072) in paragraph at lines 36116--36120
[]\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 36121--36125
[]\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 36149--36155
[]\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 36149--36155
\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 36149--36155
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in

Underfull \hbox (badness 3009) in paragraph at lines 36161--36168
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 36161--36168
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 36161--36168
\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 36161--36168
\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
[556] [557] [558] [559] [560] [561]
Underfull \hbox (badness 1142) in paragraph at lines 36514--36520
[]\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 \T1/zi4/m/n/10 "%Y-%m-%d
[562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573]
[574] [575] [576] [577] [578] [579] [580] [581]
Underfull \hbox (badness 1565) in paragraph at lines 37787--37789
[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[582] [583] [584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 4967) in paragraph at lines 38386--38391
[]\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
[592] [593]
Underfull \hbox (badness 1616) in paragraph at lines 38499--38504
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
[594] [595] [596] [597]
Underfull \vbox (badness 10000) has occurred while \output is active [598]
[599] [600] [601] [602]
Underfull \hbox (badness 1472) in paragraph at lines 39025--39028
[]\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
[603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614]
[615]
Underfull \vbox (badness 3803) has occurred while \output is active [616]
Underfull \hbox (badness 10000) in paragraph at lines 39939--39943
[]\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., \T1/zi4/m/n/10
 length(bin) >
[617] [618] [619] [620]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[621] [622] [623]
Underfull \hbox (badness 10000) in paragraph at lines 40374--40378
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[624] [625] [626] [627] [628] [629] [630] [631] [632]
Underfull \hbox (badness 10000) in paragraph at lines 40987--40990
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
[633] [634] [635] [636] [637] [638]
Underfull \vbox (badness 10000) has occurred while \output is active [639]
[640] [641] [642] [643] [644] [645] [646]
Underfull \hbox (badness 1990) in paragraph at lines 41890--41898
[]\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 41890--41898
\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
[647] [648] [649] [650] [651] [652] [653] [654]
Underfull \hbox (badness 1917) in paragraph at lines 42396--42403
[]\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
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665]
Underfull \hbox (badness 3668) in paragraph at lines 43125--43127
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[666] [667]
Underfull \hbox (badness 2401) in paragraph at lines 43253--43257
[]\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
[668] [669] [670]
Underfull \hbox (badness 2111) in paragraph at lines 43442--43447
\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 10000) in paragraph at lines 43463--43468
[]\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
[671] [672] [673] [674] [675] [676] [677] [678] [679]
Underfull \hbox (badness 5417) in paragraph at lines 44045--44049
[]\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
[680]
Underfull \hbox (badness 10000) in paragraph at lines 44106--44110
[]\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
[681] [682]) (./compiler-pkg.tex
Chapter 2.
[683] [684] [685] [686]) (./datasets-pkg.tex
Chapter 3.
[687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698]
[699] [700] [701] [702] [703]
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.
[704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715]
[716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726]
Underfull \vbox (badness 1448) has occurred while \output is active [727]
[728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738]
Overfull \vbox (19.74611pt too high) has occurred while \output is active
[739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
[751] [752] [753] [754]
Underfull \vbox (badness 10000) has occurred while \output is active [755]
[756] [757] [758]
Underfull \vbox (badness 10000) has occurred while \output is active [759]
[760] [761] [762] [763] [764]
Overfull \vbox (18.9959pt too high) has occurred while \output is active
[765] [766] [767]) (./grDevices-pkg.tex [768]
Chapter 4.
[769] [770] [771] [772] [773]
Underfull \hbox (badness 3158) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

Underfull \hbox (badness 10000) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

Underfull \hbox (badness 1852) in paragraph at lines 298--303
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
[774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785]
[786]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\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
[787] [788] [789] [790]
Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
[]\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
[791] [792] [793]
Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
\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
[794] [795] [796] [797] [798] [799]
Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
\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 ,
[800] [801]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[802] [803] [804]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[805] [806] [807] [808] [809] [810] [811] [812] [813] [814]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829

[815] [816] [817] [818] [819] [820] [821] [822] [823]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[824] [825] [826] [827] [828]
Underfull \vbox (badness 10000) has occurred while \output is active [829]
Underfull \hbox (badness 10000) in paragraph at lines 3785--3788
[]\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
[830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

Underfull \hbox (badness 4181) in paragraph at lines 4514--4519
\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
[841]
Underfull \vbox (badness 10000) has occurred while \output is active [842]
[843]
Underfull \hbox (badness 1067) in paragraph at lines 4668--4675
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[844] [845] [846] [847]
Underfull \hbox (badness 1377) in paragraph at lines 4971--4976
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[848]
Underfull \hbox (badness 1418) in paragraph at lines 5047--5054
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[849] [850]
Underfull \hbox (badness 1377) in paragraph at lines 5176--5181
[]\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
[851]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\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
[852] [853]
Underfull \hbox (badness 2035) in paragraph at lines 5380--5389
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\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 ,
[854]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5448--5455
\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 .
[855] [856] [857]
Underfull \hbox (badness 1546) in paragraph at lines 5590--5598
[]\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 ,
[858] [859] [860] [861] [862] [863] [864] [865]
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877]
[878]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[879]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[880] [881] [882] [883] [884]
Underfull \hbox (badness 3780) in paragraph at lines 7345--7351
[]\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 ,
[885] [886] [887]
Underfull \hbox (badness 2680) in paragraph at lines 7546--7548
[]\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
[888] [889] [890]) (./graphics-pkg.tex
Chapter 5.
[891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902]
[903] [904] [905] [906] [907] [908] [909] [910] [911] [912]
Underfull \hbox (badness 4634) in paragraph at lines 1351--1354
[][][]\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 ,
[913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924]
[925] [926] [927] [928] [929]
Underfull \hbox (badness 1009) in paragraph at lines 2390--2397
\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
[930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941]
[942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952]
Underfull \vbox (badness 10000) has occurred while \output is active [953]
[954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965]
Underfull \hbox (badness 3229) in paragraph at lines 4534--4539
[]\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
[966] [967] [968] [969] [970]
Underfull \hbox (badness 10000) in paragraph at lines 4891--4897
[]\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 4891--4897
\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
[971]
Underfull \hbox (badness 10000) in paragraph at lines 5022--5025

[972]
Underfull \hbox (badness 10000) in paragraph at lines 5083--5085

[973 </build/r-base-3.6.1/library/graphics/help/figures/mai.pdf>] [974 </build/
r-base-3.6.1/library/graphics/help/figures/oma.pdf>] [975]
Underfull \hbox (badness 10000) in paragraph at lines 5273--5275
[]\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
[976]
Underfull \vbox (badness 3803) has occurred while \output is active [977]
[978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989]
[990] [991] [992] [993] [994] [995] [996] [997] [998]
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6751--6752
[][] 
[999] [1000 </build/r-base-3.6.1/library/graphics/help/figures/pch.pdf>]
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011]
[1012]
Underfull \hbox (badness 2012) in paragraph at lines 7576--7579
[]\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 poi
nt
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
[1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033]
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

Underfull \hbox (badness 10000) in paragraph at lines 8838--8840
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
[1034]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [1035] [1036] [1037] [1038])
(./grid-pkg.tex
Chapter 6.

Underfull \vbox (badness 10000) has occurred while \output is active [1039]
[1040] [1041] [1042] [1043] [1044] [1045] [1046]
Underfull \hbox (badness 2680) in paragraph at lines 483--486
[]\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
[1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056]
Underfull \hbox (badness 4279) in paragraph at lines 1064--1073
[][][]\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 ,
[1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067]
[1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078]
[1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089]
[1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100]
Underfull \vbox (badness 10000) has occurred while \output is active [1101]
[1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
[1113] [1114]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\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
[1115] [1116] [1117] [1118]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129]
[1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140]
[1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149]
Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
[]\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 \T1/zi4/m/n/10 depth
[1150] [1151] [1152] [1153]) (./methods-pkg.tex [1154]
Chapter 7.
[1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162]
Underfull \vbox (badness 3803) has occurred while \output is active [1163]
Underfull \vbox (badness 10000) has occurred while \output is active [1164]
[1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173]
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
[1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181]
Underfull \hbox (badness 2181) 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
[1182]
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
[1183] [1184] [1185]
Underfull \hbox (badness 2213) 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 =
[1186] [1187] [1188] [1189] [1190]
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
[1191] [1192]
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
[1193]
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
[1194] [1195] [1196] [1197] [1198] [1199] [1200]
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
[1201] [1202] [1203] [1204] [1205]
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
[1206]
Underfull \hbox (badness 10000) in paragraph at lines 3642--3651
[]\T1/ptm/m/n/10 The
[1207]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
[1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218]
Underfull \hbox (badness 1769) in paragraph at lines 4472--4478
[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228]
Underfull \vbox (badness 10000) has occurred while \output is active [1229]
[1230] [1231]
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
[1232]
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
[1233] [1234] [1235] [1236]
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
[1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244]
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
[1245] [1246] [1247] [1248]
Underfull \vbox (badness 10000) has occurred while \output is active [1249]
[1250] [1251] [1252]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}
                               [1253] [1254] [1255]pdfTeX warning (ext4): desti
nation with the same identifier (name{Rfn.Complex}) has been already used, dupl
icate ignored
<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}
                                                 [1256]
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
[1257] [1258] [1259]
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
[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281]
[1282] [1283] [1284] [1285] [1286]
Underfull \vbox (badness 10000) has occurred while \output is active [1287]
[1288] [1289] [1290] [1291] [1292] [1293] [1294]
Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1295] [1296] [1297] [1298] [1299] [1300] [1301]
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.,
[1302] [1303] [1304] [1305]) (./parallel-pkg.tex [1306]
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
[1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317]
[1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327]
Underfull \hbox (badness 3386) in paragraph at lines 1365--1368
[]\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
[1328] [1329] [1330]) (./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
[1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341]
[1342] [1343] [1344] [1345] [1346]) (./stats-pkg.tex
Chapter 10.
[1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
[1358] [1359] [1360]
Underfull \hbox (badness 1412) in paragraph at lines 875--877
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368]
Underfull \hbox (badness 2503) in paragraph at lines 1356--1359
[]\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 ,
[1369] [1370] [1371]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
[1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382]
[1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
[1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401]
Underfull \hbox (badness 2503) in paragraph at lines 3437--3440
[]\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 ,
[1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
[1413] [1414] [1415] [1416]
Underfull \hbox (badness 1127) in paragraph at lines 4351--4354
[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1417] [1418] [1419] [1420] [1421]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431]
Underfull \hbox (badness 2556) in paragraph at lines 5317--5320
[]\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 5334--5336
[]\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
[1432] [1433] [1434] [1435] [1436] [1437] [1438]
Underfull \hbox (badness 2503) in paragraph at lines 5726--5730
[]\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 ,
[1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
[1450] [1451]
Underfull \hbox (badness 7081) in paragraph at lines 6520--6523
[]\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 6524--6526
[]\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
[1452] [1453] [1454] [1455] [1456]
Underfull \vbox (badness 3803) has occurred while \output is active [1457]
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 7369--7372
[]\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
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
Underfull \vbox (badness 10000) has occurred while \output is active [1487]
[1488] [1489] [1490] [1491]
Underfull \hbox (badness 2626) in paragraph at lines 9048--9051
[]\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
[1492] [1493]
Underfull \hbox (badness 2503) in paragraph at lines 9155--9159
[]\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 ,
[1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504]
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516] [1517] [1518]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 10844--10847
[]\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,
[1519]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1526] [1527] [1528] [1529] [1530] [1531]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\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

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1532] [1533]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1534] [1535]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\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
[1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 \T1/zi4/m/n/10 SSinit =
[1546] [1547] [1548] [1549] [1550] [1551]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562]
[1563]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1574] [1575]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\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
[1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586]
[1587] [1588] [1589] [1590] [1591] [1592] [1593]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\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 ,
[1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\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
[1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612]
[1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623]
[1624] [1625] [1626] [1627] [1628] [1629]
Underfull \vbox (badness 10000) has occurred while \output is active [1630]
Underfull \vbox (badness 10000) has occurred while \output is active [1631]
[1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642]
[1643]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

Underfull \hbox (badness 1735) in paragraph at lines 18581--18584
[]\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
[1644]
Underfull \hbox (badness 2343) in paragraph at lines 18594--18598
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

Underfull \hbox (badness 3471) in paragraph at lines 18594--18598
\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18602--18606
[]\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
[1645] [1646] [1647]
Overfull \hbox (15.73795pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1648]
[1649] [1650] [1651] [1652] [1653] [1654]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1664] [1665] [1666] [1667]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1668] [1669] [1670] [1671] [1672] [1673] [1674]
Underfull \hbox (badness 2503) in paragraph at lines 20381--20384
[]\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 ,

Underfull \hbox (badness 3919) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
[1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685]
[1686] [1687] [1688] [1689] [1690] [1691] [1692]
Underfull \hbox (badness 10000) in paragraph at lines 21485--21491
[]\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 ,
[1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703]
[1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714]
[1715]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723]
Overfull \hbox (27.74408pt too wide) in paragraph at lines 23399--23399
 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1724] [1725] [1726] [1727] [1728]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 4205) in paragraph at lines 23650--23653
\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
[1729] [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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 \T1/zi4/m/n/10 y[j] =
[1738]
Underfull \hbox (badness 3690) in paragraph at lines 24287--24291
[][][]\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
[1739] [1740] [1741] [1742] [1743] [1744] [1745]
Underfull \vbox (badness 10000) has occurred while \output is active [1746]
[1747]
Underfull \hbox (badness 2165) in paragraph at lines 24777--24782
[]\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 ,
[1748] [1749] [1750]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
[1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761]
[1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772]
[1773] [1774]
Underfull \vbox (badness 10000) has occurred while \output is active [1775]
Underfull \hbox (badness 3514) in paragraph at lines 26556--26561
[]\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
[1776] [1777] [1778] [1779]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26790--26790
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1780]
Underfull \hbox (badness 3514) in paragraph at lines 26826--26832
[]\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
[1781] [1782] [1783] [1784]
Underfull \hbox (badness 3514) in paragraph at lines 27040--27045
[]\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
[1785] [1786]
Underfull \hbox (badness 3514) in paragraph at lines 27127--27132
[]\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
[1787]
Underfull \hbox (badness 3514) in paragraph at lines 27192--27197
[]\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
[1788] [1789]
Underfull \hbox (badness 3514) in paragraph at lines 27286--27291
[]\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
[1790]
Underfull \hbox (badness 6691) in paragraph at lines 27378--27383
[]\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
[1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799]
Underfull \hbox (badness 4024) in paragraph at lines 27908--27911
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
[1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809]
Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\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
[1810] [1811] [1812]
Underfull \hbox (badness 5431) in paragraph at lines 28724--28727
[]\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
[1813] [1814] [1815] [1816] [1817] [1818]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1819] [1820] [1821] [1822] [1823]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834]
[1835] [1836] [1837] [1838] [1839] [1840] [1841] [1842]
Underfull \hbox (badness 3557) in paragraph at lines 30470--30474
[]\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 \T1/zi4
/m/n/10 interval =
[1843] [1844] [1845]
Underfull \vbox (badness 10000) has occurred while \output is active [1846]
[1847] [1848]
Underfull \hbox (badness 1337) in paragraph at lines 30834--30838
[]\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
[1849] [1850] [1851] [1852] [1853] [1854] [1855] [1856] [1857]
Underfull \hbox (badness 1337) in paragraph at lines 31361--31365
[]\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
[1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867])
(./stats4-pkg.tex [1868]
Chapter 11.
[1869] [1870] [1871] [1872] [1873] [1874]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1875] [1876] [1877])
(./tcltk-pkg.tex [1878]
Chapter 12.
[1879] [1880] [1881] [1882] [1883] [1884] [1885]
Underfull \vbox (badness 10000) has occurred while \output is active [1886]
Underfull \vbox (badness 10000) has occurred while \output is active [1887]
Underfull \hbox (badness 1546) in paragraph at lines 664--671
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898]
[1899]) (./tools-pkg.tex [1900]
Chapter 13.
[1901]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 72.

[1902]
Underfull \hbox (badness 3039) in paragraph at lines 164--167
[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1903] [1904]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

Underfull \hbox (badness 4967) in paragraph at lines 285--298
\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1905] [1906]
Underfull \hbox (badness 3039) in paragraph at lines 389--391
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917]
[1918]
Underfull \hbox (badness 4441) in paragraph at lines 1139--1149
\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-
[1919]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
[1920]
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209
\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 ,
[1921] [1922] [1923] [1924] [1925]
Underfull \hbox (badness 2293) in paragraph at lines 1558--1560
[]\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
[1926] [1927]
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Underfull \hbox (badness 1082) in paragraph at lines 1703--1705
[]\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
[1928] [1929] [1930] [1931]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1932] [1933] [1934]
[1935] [1936]
Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202
 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1937] [1938] [1939]
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1940] [1941] [1942] [1943] [1944] [1945] [1946]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
(Font)              using `T1/zi4/m/n' instead on input line 2846.

[1947] [1948] [1949] [1950] [1951]
Underfull \hbox (badness 1424) in paragraph at lines 3128--3130
[]\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
[1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962]
Underfull \hbox (badness 10000) in paragraph at lines 3832--3834
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1963] [1964]
Underfull \hbox (badness 10000) in paragraph at lines 3971--3974
[]\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
[1965] [1966]
Underfull \hbox (badness 1137) in paragraph at lines 4073--4075
[]\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
[1967] [1968] [1969] [1970] [1971]
Underfull \hbox (badness 1796) in paragraph at lines 4381--4386
[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1972]
Underfull \hbox (badness 1838) in paragraph at lines 4455--4461
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

Underfull \hbox (badness 10000) in paragraph at lines 4455--4461
\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
[1973] [1974] [1975]
Underfull \hbox (badness 2197) in paragraph at lines 4671--4681
[]\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 :
[1976]
Underfull \hbox (badness 1571) in paragraph at lines 4734--4738
[]\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
[1977] [1978] [1979]) (./utils-pkg.tex [1980]
Chapter 14.
[1981]
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 ',
[1982] [1983] [1984] [1985] [1986]
Underfull \hbox (badness 10000) in paragraph at lines 376--381
\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
[1987] [1988] [1989] [1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\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 717--723
\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
[1992] [1993]
Underfull \hbox (badness 5847) in paragraph at lines 850--856
[]\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 850--856
\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
[1994]
Underfull \hbox (badness 3861) in paragraph at lines 918--923
[]\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 ,
[1995] [1996]
Underfull \hbox (badness 3323) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

Underfull \hbox (badness 3919) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 3735) in paragraph at lines 1089--1097
\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 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
[1997]
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1998] [1999]
Underfull \vbox (badness 3803) has occurred while \output is active [2000]
[2001] [2002] [2003] [2004]
Underfull \hbox (badness 1371) in paragraph at lines 1606--1608
[]\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
[2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Underfull \hbox (badness 2057) in paragraph at lines 2215--2217
[]\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
[2015] [2016] [2017] [2018] [2019] [2020]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [2021] [2022]
Underfull \hbox (badness 1748) in paragraph at lines 2733--2736
[]\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
[2023] [2024] [2025] [2026] [2027] [2028] [2029]
Underfull \hbox (badness 5388) in paragraph at lines 3142--3146
[]\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 [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

Underfull \hbox (badness 2285) in paragraph at lines 3147--3150
[]\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 =
[2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040]
Underfull \hbox (badness 1430) in paragraph at lines 3906--3914
[]\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
[2041]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\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
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [2056] [2057] [2058]
[2059] [2060] [2061] [2062] [2063]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073]
Underfull \hbox (badness 1371) in paragraph at lines 5996--5998
[]\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
[2074]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2075] [2076] [2077]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2078]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2079] [2080]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[2081] [2082] [2083]
Underfull \hbox (badness 1325) in paragraph at lines 6632--6636
[]\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

Underfull \hbox (badness 4726) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of
[2084]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[2085]
Underfull \hbox (badness 3219) in paragraph at lines 6792--6799
[]\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 6792--6799
\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 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

Underfull \hbox (badness 1596) in paragraph at lines 6792--6799
[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently

Underfull \hbox (badness 2932) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[2086]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,
[2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097]
[2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108]
[2109] [2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 8436--8438
[]\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 2310) in paragraph at lines 8458--8463
[]\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,
[2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119]
Underfull \hbox (badness 1248) in paragraph at lines 8982--8986
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[2120]
Underfull \hbox (badness 1789) in paragraph at lines 9060--9062
[]\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
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130]
Underfull \vbox (badness 10000) has occurred while \output is active [2131]
[2132] [2133]
Underfull \hbox (badness 1097) in paragraph at lines 9897--9900
[]\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
[2134] [2135]
Underfull \hbox (badness 3000) in paragraph at lines 10033--10038
[][][]\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 ;
[2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144]
Underfull \hbox (badness 2134) in paragraph at lines 10616--10621
[][][]\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 ;

Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 2469) in paragraph at lines 11165--11169
[]\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 11165--11169
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2154] [2155] [2156] [2157] [2158]
Underfull \hbox (badness 4060) in paragraph at lines 11496--11499
[]\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 11519--11519
 []\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 '[] 
[2159] [2160] [2161] [2162]
Underfull \hbox (badness 2150) in paragraph at lines 11758--11760
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2163] [2164] [2165] [2166]
Underfull \hbox (badness 10000) in paragraph at lines 11977--11981
[]\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 12008--12014
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2167] [2168] [2169]
Underfull \hbox (badness 1009) in paragraph at lines 12202--12214
[]\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

Underfull \hbox (badness 4779) in paragraph at lines 12239--12241
[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd
[2170]
Underfull \hbox (badness 1077) in paragraph at lines 12269--12276
\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2171] [2172] [2173] [2174] [2175] [2176]
Underfull \hbox (badness 3780) in paragraph at lines 12670--12674
[]\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 12686--12689
[]\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
[2177] [2178] [2179] [2180]
Underfull \hbox (badness 2302) in paragraph at lines 12891--12893
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2181] [2182] [2183] [2184]
Underfull \hbox (badness 10000) in paragraph at lines 13187--13192
[]\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 13196--13199
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2185] [2186]
Underfull \vbox (badness 10000) has occurred while \output is active [2187]
[2188] [2189] [2190] [2191]
Underfull \hbox (badness 2932) in paragraph at lines 13616--13623
[]\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,

Underfull \hbox (badness 1688) in paragraph at lines 13616--13623
\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2192] [2193] [2194] [2195] [2196]
Underfull \hbox (badness 6510) in paragraph at lines 13925--13929
[]\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 13932--13935
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 13932--13935
\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
[2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 10000) in paragraph at lines 14596--14601
[]\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 14596--14601
[][]\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 14602--14604
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2207]
Underfull \hbox (badness 10000) in paragraph at lines 14661--14664
[][][]\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 ,
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219]
Underfull \hbox (badness 10000) in paragraph at lines 15434--15436
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2220] [2221] [2222] [2223]) [2224] (./fullrefman.ind [2225] [2226] [2227]
[2228] [2229] [2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238]
[2239] [2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249]
[2250] [2251] [2252] [2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260]
[2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271]
[2272] [2273] [2274]
Overfull \hbox (33.3567pt too wide) in paragraph at lines 8854--8856
[]\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , 

[2275] [2276] [2277] [2278] [2279] [2280]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 10177--10179
[]\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE 
[2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288]
Overfull \hbox (5.8567pt too wide) in paragraph at lines 11923--11925
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 11925--11927
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_results 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 11927--11929
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings 
[2289] [2290] [2291] [2292] [2293] [2294] [2295] [2296] [2297])
(./fullrefman.aux)

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


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

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed 
one

pdfTeX warning (dest): name{Rfn.lmList} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparse.model.matrix} has been referenced but do
es not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nlsList} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/
texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4b.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr5.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/
fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on fullrefman.pdf (2328 pages, 6262075 bytes).
Transcript written on fullrefman.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./fullrefman.tex
LaTeX2e <2018-12-01>
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2018/09/03 v1.4i Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(../../share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
Writing index file fullrefman.idx
(./fullrefman.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./fullrefman.out) (./fullrefman.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] [3]
[4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19]
[20] [21] [22] [23] [24] [25] [26] [27] [28] [29]) [30] (./base-pkg.tex
Chapter 1.
[1] [2]
Underfull \hbox (badness 6995) in paragraph at lines 141--149
[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
/ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It

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

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

Underfull \hbox (badness 10000) in paragraph at lines 141--149
\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As

Underfull \hbox (badness 4995) in paragraph at lines 141--149
\T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi
4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 ,
[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] [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 1178--1181
[]\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 1953--1953
 []\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] [34] [35] [36] [37]
Underfull \hbox (badness 10000) in paragraph at lines 2389--2391
[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

Underfull \hbox (badness 10000) in paragraph at lines 2392--2397
[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via

Underfull \hbox (badness 1102) in paragraph at lines 2392--2397
\T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim
-ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit

[38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52]
[53] [54] [55] [56] [57] [58] [59]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[60] [61] [62]
Overfull \hbox (6.42029pt too wide) in paragraph at lines 4012--4012
 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77]
[78]
Underfull \hbox (badness 2521) in paragraph at lines 5033--5035
[]\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
[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93]
[94] [95] [96]
Overfull \hbox (5.27168pt too wide) in paragraph at lines 6189--6189
 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
[97] [98] [99] [100] [101] [102]
Overfull \hbox (46.35893pt too wide) in paragraph at lines 6598--6600
[]\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 : 
[103] [104]
Underfull \hbox (badness 10000) in paragraph at lines 6746--6749
[]\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
[105] [106]
Underfull \hbox (badness 6063) in paragraph at lines 6928--6934
[]\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-


Underfull \hbox (badness 2343) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

Underfull \hbox (badness 1708) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
s not rec-om-mended) when

Underfull \hbox (badness 1831) in paragraph at lines 6928--6934
\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
/10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
[107]
Underfull \hbox (badness 3568) in paragraph at lines 6990--6997
\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
[108] [109]
Underfull \vbox (badness 10000) has occurred while \output is active [110]
Underfull \vbox (badness 10000) has occurred while \output is active [111]
[112]
Underfull \hbox (badness 1077) in paragraph at lines 7307--7313
[]\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 7307--7313
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[113] [114] [115] [116] [117] [118]
Underfull \hbox (badness 2096) in paragraph at lines 7648--7652
\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 .
[119] [120]
Underfull \hbox (badness 2351) in paragraph at lines 7766--7769
[][][]\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 ,
[121] [122] [123] [124] [125]
Underfull \hbox (badness 4479) in paragraph at lines 8092--8102
[][][]\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),
[126] [127] [128] [129] [130] [131]
Underfull \hbox (badness 1629) in paragraph at lines 8539--8551
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

Underfull \hbox (badness 1609) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which

Underfull \hbox (badness 2426) in paragraph at lines 8539--8551
\T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that 
value is on those OSes also used as an er-ror code.
[132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142]
Underfull \hbox (badness 1178) in paragraph at lines 9275--9279
[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
[143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154]
[155] [156] [157] [158] [159] [160]
Underfull \hbox (badness 1735) in paragraph at lines 10423--10427
\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 .
[161] [162] [163] [164] [165] [166] [167]
Underfull \hbox (badness 6396) in paragraph at lines 10862--10870
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 1946) in paragraph at lines 10862--10870
\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
[168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179]
[180] [181] [182] [183] [184]
Underfull \hbox (badness 4569) in paragraph at lines 11978--11982
[]\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 11978--11982
\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
[185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196]
[197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208]
[209]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[210]
Underfull \hbox (badness 1565) in paragraph at lines 13712--13716
[][][]\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
[211]
Underfull \hbox (badness 4927) in paragraph at lines 13756--13758
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
[212]
Underfull \hbox (badness 3148) in paragraph at lines 13849--13854
[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
[213]
Underfull \hbox (badness 1466) in paragraph at lines 13896--13899
[]\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
[214] [215]
Underfull \hbox (badness 10000) in paragraph at lines 14015--14019
[][][]\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 14026--14029
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[216] [217] [218] [219]
Underfull \hbox (badness 3965) in paragraph at lines 14316--14320
[]\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,
[220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231]
[232]
Underfull \hbox (badness 4429) in paragraph at lines 15092--15095
[]\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
[233] [234]
Underfull \hbox (badness 10000) in paragraph at lines 15198--15200
[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

Underfull \hbox (badness 1215) in paragraph at lines 15198--15200
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

Underfull \hbox (badness 10000) in paragraph at lines 15220--15225
[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

Underfull \hbox (badness 1558) in paragraph at lines 15220--15225
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

Underfull \hbox (badness 10000) in paragraph at lines 15232--15236
[]\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

Underfull \hbox (badness 2426) in paragraph at lines 15232--15236
\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[235]
Underfull \hbox (badness 2035) in paragraph at lines 15271--15275
[]\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 within
[236]
Underfull \vbox (badness 10000) has occurred while \output is active [237]
[238] [239] [240] [241] [242] [243] [244]
Underfull \hbox (badness 2452) in paragraph at lines 15870--15874
[]\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 15870--15874
\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
[245] [246] [247]
Underfull \hbox (badness 1092) in paragraph at lines 16043--16048
[][]\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
[248] [249] [250]
Underfull \hbox (badness 6741) in paragraph at lines 16293--16297
\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
 ,
[251] [252] [253] [254] [255] [256] [257] [258] [259]
Underfull \vbox (badness 3803) has occurred while \output is active [260]
Underfull \vbox (badness 10000) has occurred while \output is active [261]
[262] [263] [264] [265] [266] [267] [268] [269] [270]
Underfull \hbox (badness 1478) in paragraph at lines 17582--17585
[]\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
[271] [272] [273] [274]
Underfull \hbox (badness 10000) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[275] [276] [277] [278] [279] [280] [281] [282] [283]
Underfull \hbox (badness 1442) in paragraph at lines 18437--18439
[]\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
[284]
Underfull \hbox (badness 2452) in paragraph at lines 18529--18545
[][][]\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 ,
[285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 1248) in paragraph at lines 18948--18951
[]\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 ,
[292] [293] [294] [295]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[296] [297] [298] [299] [300] [301]
Underfull \hbox (badness 1596) in paragraph at lines 19625--19630
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312]
Underfull \hbox (badness 2469) in paragraph at lines 20229--20234
[]\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 20243--20250
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[313]
Underfull \hbox (badness 10000) in paragraph at lines 20317--20321
[]\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 20317--20321
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/
10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T
1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10
 '
[314] [315]
Underfull \hbox (badness 1014) in paragraph at lines 20487--20492
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327]
Underfull \hbox (badness 1264) in paragraph at lines 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[328]
Underfull \hbox (badness 4441) in paragraph at lines 21305--21308
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 6047) in paragraph at lines 22052--22054
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351]
[352] [353] [354] [355] [356]
Underfull \hbox (badness 1077) in paragraph at lines 23093--23099
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\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 .
[357] [358] [359] [360] [361] [362] [363] [364] [365]
Underfull \hbox (badness 2790) in paragraph at lines 23589--23592
[]\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 23589--23592
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[366] [367] [368] [369]
Underfull \hbox (badness 1194) in paragraph at lines 23871--23874
[]\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
[370] [371] [372]
Underfull \hbox (badness 2368) in paragraph at lines 24077--24083
[]\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 list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24077--24083
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[373] [374] [375] [376] [377] [378]
Underfull \hbox (badness 10000) in paragraph at lines 24459--24462
[]\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
[379] [380] [381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 25064--25066
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
[400]
Underfull \hbox (badness 1038) in paragraph at lines 25904--25912
[]\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 1735) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25904--25912
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25913--25916
[]\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 25932--25934
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[401] [402]
Underfull \hbox (badness 2142) in paragraph at lines 26073--26077
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able

Underfull \hbox (badness 1968) in paragraph at lines 26123--26128
[]\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
[403] [404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 26411--26417
[]\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 26411--26417
\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 26411--26417
\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 26424--26427
[]\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 26450--26452
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

Underfull \hbox (badness 10000) in paragraph at lines 26485--26490
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26491--26502
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and
[407]
Underfull \hbox (badness 7203) in paragraph at lines 26503--26506
[]\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 10000) in paragraph at lines 26527--26532
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26527--26532
\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).
[408] [409] [410] [411] [412] [413] [414] [415]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[416]
Underfull \hbox (badness 7925) in paragraph at lines 27124--27128
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

Underfull \hbox (badness 1622) in paragraph at lines 27124--27128
[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

Underfull \hbox (badness 6125) in paragraph at lines 27129--27138
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427]
Underfull \hbox (badness 2726) in paragraph at lines 27850--27853
[]\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
[428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439]
[440] [441] [442] [443] [444] [445]
Underfull \vbox (badness 3803) has occurred while \output is active [446]
[447] [448] [449] [450] [451] [452] [453]
Underfull \hbox (badness 1533) in paragraph at lines 29541--29544
[]\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
[454] [455] [456]
Underfull \hbox (badness 1163) in paragraph at lines 29704--29715
[]\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
[457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468]
[469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480]
Underfull \hbox (badness 10000) in paragraph at lines 31250--31254
[]\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 31250--31254
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.

Underfull \hbox (badness 6188) in paragraph at lines 31272--31274
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[481] [482] [483] [484] [485] [486] [487] [488] [489]
Underfull \hbox (badness 1655) in paragraph at lines 31828--31830
[]\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
[490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501]
[502] [503] [504] [505] [506]
Underfull \hbox (badness 2261) in paragraph at lines 32947--32952
[]\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
[507]
Underfull \hbox (badness 10000) in paragraph at lines 32974--32980
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1484) in paragraph at lines 32974--32980
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
[508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519]
[520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531]
[532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543]
[544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555]
Underfull \hbox (badness 1072) in paragraph at lines 36116--36120
[]\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 36121--36125
[]\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 36149--36155
[]\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 36149--36155
\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 36149--36155
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in

Underfull \hbox (badness 3009) in paragraph at lines 36161--36168
[]\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is 
also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt
m/m/n/10 ' which is read

Underfull \hbox (badness 1038) in paragraph at lines 36161--36168
\T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron-
ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the

Underfull \hbox (badness 2573) in paragraph at lines 36161--36168
\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 36161--36168
\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
[556] [557] [558] [559] [560] [561]
Underfull \hbox (badness 1142) in paragraph at lines 36514--36520
[]\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 \T1/zi4/m/n/10 "%Y-%m-%d
[562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573]
[574] [575] [576] [577] [578] [579] [580] [581]
Underfull \hbox (badness 1565) in paragraph at lines 37787--37789
[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[582] [583] [584] [585] [586] [587] [588] [589] [590] [591]
Underfull \hbox (badness 4967) in paragraph at lines 38386--38391
[]\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
[592] [593]
Underfull \hbox (badness 1616) in paragraph at lines 38499--38504
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
[594] [595] [596] [597]
Underfull \vbox (badness 10000) has occurred while \output is active [598]
[599] [600] [601] [602]
Underfull \hbox (badness 1472) in paragraph at lines 39025--39028
[]\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
[603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614]
[615]
Underfull \vbox (badness 3803) has occurred while \output is active [616]
Underfull \hbox (badness 10000) in paragraph at lines 39939--39943
[]\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., \T1/zi4/m/n/10
 length(bin) >
[617] [618] [619] [620]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[621] [622] [623]
Underfull \hbox (badness 10000) in paragraph at lines 40374--40378
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[624] [625] [626] [627] [628] [629] [630] [631] [632]
Underfull \hbox (badness 10000) in paragraph at lines 40987--40990
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
[633] [634] [635] [636] [637] [638]
Underfull \vbox (badness 10000) has occurred while \output is active [639]
[640] [641] [642] [643] [644] [645] [646]
Underfull \hbox (badness 1990) in paragraph at lines 41890--41898
[]\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 41890--41898
\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
[647] [648] [649] [650] [651] [652] [653] [654]
Underfull \hbox (badness 1917) in paragraph at lines 42396--42403
[]\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
[655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665]
Underfull \hbox (badness 3668) in paragraph at lines 43125--43127
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[666] [667]
Underfull \hbox (badness 2401) in paragraph at lines 43253--43257
[]\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
[668] [669] [670]
Underfull \hbox (badness 2111) in paragraph at lines 43442--43447
\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 10000) in paragraph at lines 43463--43468
[]\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
[671] [672] [673] [674] [675] [676] [677] [678] [679]
Underfull \hbox (badness 5417) in paragraph at lines 44045--44049
[]\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
[680]
Underfull \hbox (badness 10000) in paragraph at lines 44106--44110
[]\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
[681] [682]) (./compiler-pkg.tex
Chapter 2.
[683] [684] [685] [686]) (./datasets-pkg.tex
Chapter 3.
[687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698]
[699] [700] [701] [702] [703]
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.
[704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715]
[716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726]
Underfull \vbox (badness 1448) has occurred while \output is active [727]
[728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738]
Overfull \vbox (19.74611pt too high) has occurred while \output is active
[739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]
[751] [752] [753] [754]
Underfull \vbox (badness 10000) has occurred while \output is active [755]
[756] [757] [758]
Underfull \vbox (badness 10000) has occurred while \output is active [759]
[760] [761] [762] [763] [764]
Overfull \vbox (18.9959pt too high) has occurred while \output is active
[765] [766] [767]) (./grDevices-pkg.tex [768]
Chapter 4.
[769] [770] [771] [772] [773]
Underfull \hbox (badness 3158) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

Underfull \hbox (badness 10000) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

Underfull \hbox (badness 1852) in paragraph at lines 298--303
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
[774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785]
[786]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\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
[787] [788] [789] [790]
Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
[]\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
[791] [792] [793]
Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
\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
[794] [795] [796] [797] [798] [799]
Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
\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 ,
[800] [801]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[802] [803] [804]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[805] [806] [807] [808] [809] [810] [811] [812] [813] [814]
Underfull \hbox (badness 10000) in paragraph at lines 2828--2829

[815] [816] [817] [818] [819] [820] [821] [822] [823]
Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[824] [825] [826] [827] [828]
Underfull \vbox (badness 10000) has occurred while \output is active [829]
Underfull \hbox (badness 10000) in paragraph at lines 3785--3788
[]\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
[830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

Underfull \hbox (badness 4181) in paragraph at lines 4514--4519
\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
[841]
Underfull \vbox (badness 10000) has occurred while \output is active [842]
[843]
Underfull \hbox (badness 1067) in paragraph at lines 4668--4675
\T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled
 with sup-
[844] [845] [846] [847]
Underfull \hbox (badness 1377) in paragraph at lines 4971--4976
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[848]
Underfull \hbox (badness 1418) in paragraph at lines 5047--5054
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 1755) in paragraph at lines 5065--5067
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[849] [850]
Underfull \hbox (badness 1377) in paragraph at lines 5176--5181
[]\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
[851]
Underfull \hbox (badness 7344) in paragraph at lines 5245--5247
[]\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
[852] [853]
Underfull \hbox (badness 2035) in paragraph at lines 5380--5389
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 5380--5389
\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 ,
[854]
Underfull \hbox (badness 10000) in paragraph at lines 5448--5455
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5448--5455
\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 .
[855] [856] [857]
Underfull \hbox (badness 1546) in paragraph at lines 5590--5598
[]\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 ,
[858] [859] [860] [861] [862] [863] [864] [865]
Underfull \hbox (badness 10000) in paragraph at lines 6125--6128
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877]
[878]
Underfull \hbox (badness 1189) in paragraph at lines 6947--6949
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[879]
Underfull \hbox (badness 10000) in paragraph at lines 7045--7047
[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[880] [881] [882] [883] [884]
Underfull \hbox (badness 3780) in paragraph at lines 7345--7351
[]\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 ,
[885] [886] [887]
Underfull \hbox (badness 2680) in paragraph at lines 7546--7548
[]\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
[888] [889] [890]) (./graphics-pkg.tex
Chapter 5.
[891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902]
[903] [904] [905] [906] [907] [908] [909] [910] [911] [912]
Underfull \hbox (badness 4634) in paragraph at lines 1351--1354
[][][]\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 ,
[913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924]
[925] [926] [927] [928] [929]
Underfull \hbox (badness 1009) in paragraph at lines 2390--2397
\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
[930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941]
[942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952]
Underfull \vbox (badness 10000) has occurred while \output is active [953]
[954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965]
Underfull \hbox (badness 3229) in paragraph at lines 4534--4539
[]\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
[966] [967] [968] [969] [970]
Underfull \hbox (badness 10000) in paragraph at lines 4891--4897
[]\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 4891--4897
\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
[971]
Underfull \hbox (badness 10000) in paragraph at lines 5022--5025

[972]
Underfull \hbox (badness 10000) in paragraph at lines 5083--5085

[973 </build/r-base-3.6.1/library/graphics/help/figures/mai.pdf>] [974 </build/
r-base-3.6.1/library/graphics/help/figures/oma.pdf>] [975]
Underfull \hbox (badness 10000) in paragraph at lines 5273--5275
[]\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
[976]
Underfull \vbox (badness 3803) has occurred while \output is active [977]
[978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989]
[990] [991] [992] [993] [994] [995] [996] [997] [998]
Overfull \hbox (31.57222pt too wide) in paragraph at lines 6751--6752
[][] 
[999] [1000 </build/r-base-3.6.1/library/graphics/help/figures/pch.pdf>]
[1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011]
[1012]
Underfull \hbox (badness 2012) in paragraph at lines 7576--7579
[]\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 poi
nt
[1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023]
[1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033]
Underfull \hbox (badness 10000) in paragraph at lines 8836--8838
[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

Underfull \hbox (badness 10000) in paragraph at lines 8838--8840
[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
[1034]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni
ts}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [1035] [1036] [1037] [1038])
(./grid-pkg.tex
Chapter 6.

Underfull \vbox (badness 10000) has occurred while \output is active [1039]
[1040] [1041] [1042] [1043] [1044] [1045] [1046]
Underfull \hbox (badness 2680) in paragraph at lines 483--486
[]\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
[1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056]
Underfull \hbox (badness 4279) in paragraph at lines 1064--1073
[][][]\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 ,
[1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067]
[1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078]
[1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089]
[1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100]
Underfull \vbox (badness 10000) has occurred while \output is active [1101]
[1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112]
[1113] [1114]
Underfull \hbox (badness 1067) in paragraph at lines 4486--4489
[]\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
[1115] [1116] [1117] [1118]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129]
[1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140]
[1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149]
Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
[]\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 \T1/zi4/m/n/10 depth
[1150] [1151] [1152] [1153]) (./methods-pkg.tex [1154]
Chapter 7.
[1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162]
Underfull \vbox (badness 3803) has occurred while \output is active [1163]
Underfull \vbox (badness 10000) has occurred while \output is active [1164]
[1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173]
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
[1174] [1175] [1176] [1177] [1178] [1179] [1180] [1181]
Underfull \hbox (badness 2181) 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
[1182]
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
[1183] [1184] [1185]
Underfull \hbox (badness 2213) 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 =
[1186] [1187] [1188] [1189] [1190]
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
[1191] [1192]
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
[1193]
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
[1194] [1195] [1196] [1197] [1198] [1199] [1200]
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
[1201] [1202] [1203] [1204] [1205]
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
[1206]
Underfull \hbox (badness 10000) in paragraph at lines 3642--3651
[]\T1/ptm/m/n/10 The
[1207]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
[1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218]
Underfull \hbox (badness 1769) in paragraph at lines 4472--4478
[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228]
Underfull \vbox (badness 10000) has occurred while \output is active [1229]
[1230] [1231]
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
[1232]
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
[1233] [1234] [1235] [1236]
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
[1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244]
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
[1245] [1246] [1247] [1248]
Underfull \vbox (badness 10000) has occurred while \output is active [1249]
[1250] [1251] [1252]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}
                               [1253] [1254] [1255]pdfTeX warning (ext4): desti
nation with the same identifier (name{Rfn.Complex}) has been already used, dupl
icate ignored
<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}
                                                 [1256]
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
[1257] [1258] [1259]
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
[1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270]
[1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281]
[1282] [1283] [1284] [1285] [1286]
Underfull \vbox (badness 10000) has occurred while \output is active [1287]
[1288] [1289] [1290] [1291] [1292] [1293] [1294]
Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1295] [1296] [1297] [1298] [1299] [1300] [1301]
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.,
[1302] [1303] [1304] [1305]) (./parallel-pkg.tex [1306]
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
[1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317]
[1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327]
Underfull \hbox (badness 3386) in paragraph at lines 1365--1368
[]\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
[1328] [1329] [1330]) (./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
[1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341]
[1342] [1343] [1344] [1345] [1346]) (./stats-pkg.tex
Chapter 10.
[1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357]
[1358] [1359] [1360]
Underfull \hbox (badness 1412) in paragraph at lines 875--877
[]\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
[1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368]
Underfull \hbox (badness 2503) in paragraph at lines 1356--1359
[]\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 ,
[1369] [1370] [1371]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
[1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382]
[1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
[1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401]
Underfull \hbox (badness 2503) in paragraph at lines 3437--3440
[]\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 ,
[1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]
[1413] [1414] [1415] [1416]
Underfull \hbox (badness 1127) in paragraph at lines 4351--4354
[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1417] [1418] [1419] [1420] [1421]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\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 =
[1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431]
Underfull \hbox (badness 2556) in paragraph at lines 5317--5320
[]\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 5334--5336
[]\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
[1432] [1433] [1434] [1435] [1436] [1437] [1438]
Underfull \hbox (badness 2503) in paragraph at lines 5726--5730
[]\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 ,
[1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
[1450] [1451]
Underfull \hbox (badness 7081) in paragraph at lines 6520--6523
[]\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 6524--6526
[]\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
[1452] [1453] [1454] [1455] [1456]
Underfull \vbox (badness 3803) has occurred while \output is active [1457]
[1458] [1459] [1460] [1461] [1462] [1463] [1464]
Underfull \hbox (badness 10000) in paragraph at lines 7369--7372
[]\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
[1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475]
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
Underfull \vbox (badness 10000) has occurred while \output is active [1487]
[1488] [1489] [1490] [1491]
Underfull \hbox (badness 2626) in paragraph at lines 9048--9051
[]\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
[1492] [1493]
Underfull \hbox (badness 2503) in paragraph at lines 9155--9159
[]\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 ,
[1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504]
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1514] [1515] [1516] [1517] [1518]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 10844--10847
[]\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,
[1519]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1526] [1527] [1528] [1529] [1530] [1531]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\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

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1532] [1533]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1534] [1535]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\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
[1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 \T1/zi4/m/n/10 SSinit =
[1546] [1547] [1548] [1549] [1550] [1551]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562]
[1563]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1574] [1575]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\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
[1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586]
[1587] [1588] [1589] [1590] [1591] [1592] [1593]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\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 ,
[1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\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
[1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612]
[1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623]
[1624] [1625] [1626] [1627] [1628] [1629]
Underfull \vbox (badness 10000) has occurred while \output is active [1630]
Underfull \vbox (badness 10000) has occurred while \output is active [1631]
[1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642]
[1643]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

Underfull \hbox (badness 1735) in paragraph at lines 18581--18584
[]\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
[1644]
Underfull \hbox (badness 2343) in paragraph at lines 18594--18598
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

Underfull \hbox (badness 3471) in paragraph at lines 18594--18598
\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to

Underfull \hbox (badness 2662) in paragraph at lines 18602--18606
[]\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
[1645] [1646] [1647]
Overfull \hbox (15.73795pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1648]
[1649] [1650] [1651] [1652] [1653] [1654]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1664] [1665] [1666] [1667]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1668] [1669] [1670] [1671] [1672] [1673] [1674]
Underfull \hbox (badness 2503) in paragraph at lines 20381--20384
[]\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 ,

Underfull \hbox (badness 3919) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
[1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685]
[1686] [1687] [1688] [1689] [1690] [1691] [1692]
Underfull \hbox (badness 10000) in paragraph at lines 21485--21491
[]\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 ,
[1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703]
[1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714]
[1715]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723]
Overfull \hbox (27.74408pt too wide) in paragraph at lines 23399--23399
 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1724] [1725] [1726] [1727] [1728]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 4205) in paragraph at lines 23650--23653
\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
[1729] [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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 \T1/zi4/m/n/10 y[j] =
[1738]
Underfull \hbox (badness 3690) in paragraph at lines 24287--24291
[][][]\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
[1739] [1740] [1741] [1742] [1743] [1744] [1745]
Underfull \vbox (badness 10000) has occurred while \output is active [1746]
[1747]
Underfull \hbox (badness 2165) in paragraph at lines 24777--24782
[]\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 ,
[1748] [1749] [1750]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
[1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761]
[1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772]
[1773] [1774]
Underfull \vbox (badness 10000) has occurred while \output is active [1775]
Underfull \hbox (badness 3514) in paragraph at lines 26556--26561
[]\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
[1776] [1777] [1778] [1779]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26790--26790
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1780]
Underfull \hbox (badness 3514) in paragraph at lines 26826--26832
[]\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
[1781] [1782] [1783] [1784]
Underfull \hbox (badness 3514) in paragraph at lines 27040--27045
[]\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
[1785] [1786]
Underfull \hbox (badness 3514) in paragraph at lines 27127--27132
[]\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
[1787]
Underfull \hbox (badness 3514) in paragraph at lines 27192--27197
[]\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
[1788] [1789]
Underfull \hbox (badness 3514) in paragraph at lines 27286--27291
[]\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
[1790]
Underfull \hbox (badness 6691) in paragraph at lines 27378--27383
[]\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
[1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799]
Underfull \hbox (badness 4024) in paragraph at lines 27908--27911
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
[1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809]
Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\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
[1810] [1811] [1812]
Underfull \hbox (badness 5431) in paragraph at lines 28724--28727
[]\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
[1813] [1814] [1815] [1816] [1817] [1818]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1819] [1820] [1821] [1822] [1823]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834]
[1835] [1836] [1837] [1838] [1839] [1840] [1841] [1842]
Underfull \hbox (badness 3557) in paragraph at lines 30470--30474
[]\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 \T1/zi4
/m/n/10 interval =
[1843] [1844] [1845]
Underfull \vbox (badness 10000) has occurred while \output is active [1846]
[1847] [1848]
Underfull \hbox (badness 1337) in paragraph at lines 30834--30838
[]\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
[1849] [1850] [1851] [1852] [1853] [1854] [1855] [1856] [1857]
Underfull \hbox (badness 1337) in paragraph at lines 31361--31365
[]\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
[1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867])
(./stats4-pkg.tex [1868]
Chapter 11.
[1869] [1870] [1871] [1872] [1873] [1874]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1875] [1876] [1877])
(./tcltk-pkg.tex [1878]
Chapter 12.
[1879] [1880] [1881] [1882] [1883] [1884] [1885]
Underfull \vbox (badness 10000) has occurred while \output is active [1886]
Underfull \vbox (badness 10000) has occurred while \output is active [1887]
Underfull \hbox (badness 1546) in paragraph at lines 664--671
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898]
[1899]) (./tools-pkg.tex [1900]
Chapter 13.
[1901]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 72.

[1902]
Underfull \hbox (badness 3039) in paragraph at lines 164--167
[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1903] [1904]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

Underfull \hbox (badness 4967) in paragraph at lines 285--298
\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1905] [1906]
Underfull \hbox (badness 3039) in paragraph at lines 389--391
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
[1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917]
[1918]
Underfull \hbox (badness 4441) in paragraph at lines 1139--1149
\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-
[1919]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

Underfull \hbox (badness 7238) in paragraph at lines 1169--1171
[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous
[1920]
Underfull \hbox (badness 10000) in paragraph at lines 1206--1209
[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209
\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 ,
[1921] [1922] [1923] [1924] [1925]
Underfull \hbox (badness 2293) in paragraph at lines 1558--1560
[]\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
[1926] [1927]
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

Underfull \hbox (badness 1082) in paragraph at lines 1703--1705
[]\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
[1928] [1929] [1930] [1931]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD}
                                                   [1932] [1933] [1934]
[1935] [1936]
Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202
 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1937] [1938] [1939]
Underfull \hbox (badness 7981) in paragraph at lines 2371--2377
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1940] [1941] [1942] [1943] [1944] [1945] [1946]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
(Font)              using `T1/zi4/m/n' instead on input line 2846.

[1947] [1948] [1949] [1950] [1951]
Underfull \hbox (badness 1424) in paragraph at lines 3128--3130
[]\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
[1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] [1962]
Underfull \hbox (badness 10000) in paragraph at lines 3832--3834
[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1963] [1964]
Underfull \hbox (badness 10000) in paragraph at lines 3971--3974
[]\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
[1965] [1966]
Underfull \hbox (badness 1137) in paragraph at lines 4073--4075
[]\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
[1967] [1968] [1969] [1970] [1971]
Underfull \hbox (badness 1796) in paragraph at lines 4381--4386
[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1972]
Underfull \hbox (badness 1838) in paragraph at lines 4455--4461
[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

Underfull \hbox (badness 10000) in paragraph at lines 4455--4461
\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
[1973] [1974] [1975]
Underfull \hbox (badness 2197) in paragraph at lines 4671--4681
[]\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 :
[1976]
Underfull \hbox (badness 1571) in paragraph at lines 4734--4738
[]\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
[1977] [1978] [1979]) (./utils-pkg.tex [1980]
Chapter 14.
[1981]
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 ',
[1982] [1983] [1984] [1985] [1986]
Underfull \hbox (badness 10000) in paragraph at lines 376--381
\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
[1987] [1988] [1989] [1990] [1991]
Underfull \hbox (badness 10000) in paragraph at lines 717--723
[]\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 717--723
\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
[1992] [1993]
Underfull \hbox (badness 5847) in paragraph at lines 850--856
[]\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 850--856
\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
[1994]
Underfull \hbox (badness 3861) in paragraph at lines 918--923
[]\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 ,
[1995] [1996]
Underfull \hbox (badness 3323) in paragraph at lines 1089--1097
[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

Underfull \hbox (badness 3919) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 3735) in paragraph at lines 1089--1097
\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 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by
[1997]
Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1998] [1999]
Underfull \vbox (badness 3803) has occurred while \output is active [2000]
[2001] [2002] [2003] [2004]
Underfull \hbox (badness 1371) in paragraph at lines 1606--1608
[]\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
[2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014]
Underfull \hbox (badness 2057) in paragraph at lines 2215--2217
[]\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
[2015] [2016] [2017] [2018] [2019] [2020]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [2021] [2022]
Underfull \hbox (badness 1748) in paragraph at lines 2733--2736
[]\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
[2023] [2024] [2025] [2026] [2027] [2028] [2029]
Underfull \hbox (badness 5388) in paragraph at lines 3142--3146
[]\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 [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

Underfull \hbox (badness 2285) in paragraph at lines 3147--3150
[]\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 =
[2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040]
Underfull \hbox (badness 1430) in paragraph at lines 3906--3914
[]\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
[2041]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[2042] [2043]
Underfull \hbox (badness 10000) in paragraph at lines 4143--4145
[]\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
[2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054]
[2055]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [2056] [2057] [2058]
[2059] [2060] [2061] [2062] [2063]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073]
Underfull \hbox (badness 1371) in paragraph at lines 5996--5998
[]\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
[2074]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[2075] [2076] [2077]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[2078]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[2079] [2080]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[2081] [2082] [2083]
Underfull \hbox (badness 1325) in paragraph at lines 6632--6636
[]\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

Underfull \hbox (badness 4726) in paragraph at lines 6644--6650
\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of
[2084]
Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[2085]
Underfull \hbox (badness 3219) in paragraph at lines 6792--6799
[]\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 6792--6799
\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 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

Underfull \hbox (badness 1596) in paragraph at lines 6792--6799
[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently

Underfull \hbox (badness 2932) in paragraph at lines 6800--6803
[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[2086]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,
[2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097]
[2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] [2108]
[2109] [2110] [2111]
Underfull \hbox (badness 10000) in paragraph at lines 8436--8438
[]\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 2310) in paragraph at lines 8458--8463
[]\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,
[2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119]
Underfull \hbox (badness 1248) in paragraph at lines 8982--8986
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[2120]
Underfull \hbox (badness 1789) in paragraph at lines 9060--9062
[]\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
[2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130]
Underfull \vbox (badness 10000) has occurred while \output is active [2131]
[2132] [2133]
Underfull \hbox (badness 1097) in paragraph at lines 9897--9900
[]\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
[2134] [2135]
Underfull \hbox (badness 3000) in paragraph at lines 10033--10038
[][][]\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 ;
[2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144]
Underfull \hbox (badness 2134) in paragraph at lines 10616--10621
[][][]\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 ;

Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


Underfull \hbox (badness 10000) in paragraph at lines 10672--10677
\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153]
Underfull \hbox (badness 2469) in paragraph at lines 11165--11169
[]\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 11165--11169
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[2154] [2155] [2156] [2157] [2158]
Underfull \hbox (badness 4060) in paragraph at lines 11496--11499
[]\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 11519--11519
 []\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 '[] 
[2159] [2160] [2161] [2162]
Underfull \hbox (badness 2150) in paragraph at lines 11758--11760
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[2163] [2164] [2165] [2166]
Underfull \hbox (badness 10000) in paragraph at lines 11977--11981
[]\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 12008--12014
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2167] [2168] [2169]
Underfull \hbox (badness 1009) in paragraph at lines 12202--12214
[]\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

Underfull \hbox (badness 4779) in paragraph at lines 12239--12241
[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd
[2170]
Underfull \hbox (badness 1077) in paragraph at lines 12269--12276
\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2171] [2172] [2173] [2174] [2175] [2176]
Underfull \hbox (badness 3780) in paragraph at lines 12670--12674
[]\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 12686--12689
[]\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
[2177] [2178] [2179] [2180]
Underfull \hbox (badness 2302) in paragraph at lines 12891--12893
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2181] [2182] [2183] [2184]
Underfull \hbox (badness 10000) in paragraph at lines 13187--13192
[]\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 13196--13199
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2185] [2186]
Underfull \vbox (badness 10000) has occurred while \output is active [2187]
[2188] [2189] [2190] [2191]
Underfull \hbox (badness 2932) in paragraph at lines 13616--13623
[]\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,

Underfull \hbox (badness 1688) in paragraph at lines 13616--13623
\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2192] [2193] [2194] [2195] [2196]
Underfull \hbox (badness 6510) in paragraph at lines 13925--13929
[]\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 13932--13935
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 13932--13935
\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
[2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206]
Underfull \hbox (badness 10000) in paragraph at lines 14596--14601
[]\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 14596--14601
[][]\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 14602--14604
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2207]
Underfull \hbox (badness 10000) in paragraph at lines 14661--14664
[][][]\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 ,
[2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218]
[2219]
Underfull \hbox (badness 10000) in paragraph at lines 15434--15436
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2220] [2221] [2222] [2223]) [2224] (./fullrefman.ind [2225] [2226] [2227]
[2228] [2229] [2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238]
[2239] [2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249]
[2250] [2251] [2252] [2253] [2254] [2255] [2256] [2257] [2258] [2259] [2260]
[2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271]
[2272] [2273] [2274]
Overfull \hbox (33.3567pt too wide) in paragraph at lines 8854--8856
[]\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , 

[2275] [2276] [2277] [2278] [2279] [2280]
Overfull \hbox (20.8567pt too wide) in paragraph at lines 10177--10179
[]\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE 
[2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288]
Overfull \hbox (5.8567pt too wide) in paragraph at lines 11923--11925
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 11925--11927
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_results 

Overfull \hbox (5.8567pt too wide) in paragraph at lines 11927--11929
[]\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings 
[2289] [2290] [2291] [2292] [2293] [2294] [2295] [2296] [2297])
(./fullrefman.aux)

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

 )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed 
one

pdfTeX warning (dest): name{Rfn.lmList} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.profile.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mcd} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cov.mve} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Insurance} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparse.model.matrix} has been referenced but do
es not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lqs} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.lme} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.logLik.gls} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rlm} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.loglm} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.nlsList} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.daisy} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.nls} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.confint.glm} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sammon} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isoMDS} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.width.SJ} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bcv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ucv} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.bandwidth.nrd} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.agnes} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.diana} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.lme} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rpart} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.sparseMatrix} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but 
does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.rBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cBind} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n
ot exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.panel.identify} has been referenced but does no
t exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.trellis.focus} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi
st, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r
eplaced by a fixed one

pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not 
exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e
xist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/
texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4b.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cmextra/cmbsy7.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmmib10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr5.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/share/texlive/texm
f-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist/
fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on fullrefman.pdf (2328 pages, 6262394 bytes).
Transcript written on fullrefman.log.
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[1]: Leaving directory '/build/r-base-3.6.1'
/usr/bin/make -k vignettes
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/m4'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/m4'
make[2]: Entering directory '/build/r-base-3.6.1/tools'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tools'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/html'
make[3]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/etc'
make[2]: Leaving directory '/build/r-base-3.6.1/etc'
make[2]: Entering directory '/build/r-base-3.6.1/share'
make[2]: Leaving directory '/build/r-base-3.6.1/share'
make[2]: Entering directory '/build/r-base-3.6.1/src'
make[3]: Entering directory '/build/r-base-3.6.1/src/scripts'
make[4]: Entering directory '/build/r-base-3.6.1/src/scripts'
make[4]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Entering directory '/build/r-base-3.6.1/src/include'
make[4]: Entering directory '/build/r-base-3.6.1/src/include/R_ext'
make[4]: Nothing to be done for 'R'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/include/R_ext'
make[3]: Leaving directory '/build/r-base-3.6.1/src/include'
make[3]: Entering directory '/build/r-base-3.6.1/src/extra'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: 'Makedeps' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[5]: 'libtre.a' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[3]: Leaving directory '/build/r-base-3.6.1/src/extra'
make[3]: Entering directory '/build/r-base-3.6.1/src/appl'
make[4]: Entering directory '/build/r-base-3.6.1/src/appl'
make[4]: 'libappl.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[4]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[4]: 'libnmath.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Entering directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
make[4]: 'libunix.a' is up to date.
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[4]: Entering directory '/build/r-base-3.6.1/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-z,relro -DR_HOME='"/build/r-base-3.6.1"' \
  -o Rscript ./Rscript.c
make[4]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Entering directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
/build/r-base-3.6.1/lib/libR.so is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[5]: Entering directory '/build/r-base-3.6.1/src/main'
/build/r-base-3.6.1/bin/exec/R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Entering directory '/build/r-base-3.6.1/src/modules'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
make[5]: 'internet.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[5]: 'lapack.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: 'R_X11.so' is up to date.
make[5]: 'R_de.so' is up to date.
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[5]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
/build/r-base-3.6.1/modules/R_X11.so is unchanged
/build/r-base-3.6.1/modules/R_de.so is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[3]: Leaving directory '/build/r-base-3.6.1/src/modules'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/profile'
building system startup profile
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/profile'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/translations'
building package 'translations'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/translations'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/translations'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
building package 'base'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/base'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
building package 'tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/tools/src'
../../../../library/tools/libs/tools.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tools/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tools'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
building package 'compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/compiler'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/compiler'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Nothing to be done for 'mklazycomp'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tools'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/utils'
building package 'utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
all.R is unchanged
make[5]: Nothing to be done for 'iconvlist'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/utils/src'
../../../../library/utils/libs/utils.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/utils/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
installing 'sysdata.rda'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/utils'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/utils'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
building package 'grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src'
../../../../library/grDevices/libs/grDevices.so is unchanged
make[8]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: Entering directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[10]: 'cairo.so' is up to date.
make[10]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[9]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[8]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src/cairo'
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grDevices'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grDevices'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
building package 'graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/graphics/src'
../../../../library/graphics/libs/graphics.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/graphics/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/graphics'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/graphics'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats'
building package 'stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/stats/src'
../../../../library/stats/libs/stats.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/stats/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
building package 'datasets'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/datasets'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/datasets'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/methods'
building package 'methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/methods/src'
../../../../library/methods/libs/methods.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/methods/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/methods'
make[5]: Nothing to be done for 'RfilesLazy'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/methods'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/grid'
building package 'grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/grid/src'
../../../../library/grid/libs/grid.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/grid/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/grid'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/grid'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/splines'
building package 'splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/splines/src'
../../../../library/splines/libs/splines.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/splines/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/splines'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/splines'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
building package 'stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/stats4'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/stats4'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
building package 'tcltk'
all.R is unchanged
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/tcltk/src'
../../../../library/tcltk/libs/tcltk.so is unchanged
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk/src'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/tcltk'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/tcltk'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
building package 'parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
all.R is unchanged
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[6]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
make[7]: Entering directory '/build/r-base-3.6.1/src/library/parallel/src'
../../../../library/parallel/libs/parallel.so is unchanged
make[7]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[6]: Leaving directory '/build/r-base-3.6.1/src/library/parallel/src'
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Entering directory '/build/r-base-3.6.1/src/library/parallel'
make[5]: Nothing to be done for 'mklazycomp'.
make[5]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/parallel'
make[4]: Entering directory '/build/r-base-3.6.1/src/library/base'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library/base'
installing parsed NAMESPACE files
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src'
make[2]: Entering directory '/build/r-base-3.6.1/tests'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/build/r-base-3.6.1/tests'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
make[4]: Entering directory '/build/r-base-3.6.1/doc/html'
make[4]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
installing parsed Rd
make[4]: Entering directory '/build/r-base-3.6.1/src/library'
  base
  stats
  utils
  methods
  graphics
  grDevices
  datasets
  grid
  tools
  tcltk
  splines
  stats4
  compiler
  parallel
make[4]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
building/updating package metadata ...
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
writing package indices
make[4]: Entering directory '/build/r-base-3.6.1/src/library'
make[4]: Leaving directory '/build/r-base-3.6.1/src/library'
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Entering directory '/build/r-base-3.6.1/src/library/Recommended'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/r-base-3.6.1/src/library/Recommended'
make[2]: Entering directory '/build/r-base-3.6.1/src/library'
building/updating vignettes for package 'grid' ...
processing 'grid.Rnw'
building/updating vignettes for package 'parallel' ...
building/updating vignettes for package 'utils' ...
make[2]: Leaving directory '/build/r-base-3.6.1/src/library'
make[1]: Leaving directory '/build/r-base-3.6.1'
touch make-indep-stamp
*** check ***
xvfb-run make check-all
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
make[4]: Entering directory '/build/r-base-3.6.1/tests/Examples'
Testing examples for package 'base'
Testing examples for package 'tools'
  comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
Testing examples for package 'utils'
Testing examples for package 'grDevices'
  comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
Testing examples for package 'graphics'
  comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
Testing examples for package 'stats'
  comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... OK
Testing examples for package 'datasets'
  comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
Testing examples for package 'methods'
Testing examples for package 'grid'
  comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
Testing examples for package 'splines'
  comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
Testing examples for package 'stats4'
  comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
Testing examples for package 'tcltk'
Testing examples for package 'compiler'
Testing examples for package 'parallel'
make[4]: Leaving directory '/build/r-base-3.6.1/tests/Examples'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running strict specific tests
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'eval-etc.R' ... OK
  comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK
running code in 'simple-true.R' ... OK
  comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK
running code in 'arith-true.R' ... OK
  comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK
running code in 'arith.R' ... OK
  comparing 'arith.Rout' to './arith.Rout.save' ... OK
running code in 'lm-tests.R' ... OK
  comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK
running code in 'ok-errors.R' ... OK
  comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK
running code in 'method-dispatch.R' ... OK
  comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK
running code in 'any-all.R' ... OK
  comparing 'any-all.Rout' to './any-all.Rout.save' ... OK
running code in 'd-p-q-r-tests.R' ... OK
  comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
running sloppy specific tests
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'complex.R' ... OK
  comparing 'complex.Rout' to './complex.Rout.save' ... OK
running code in 'eval-etc-2.R' ... OK
  comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ...72,74c72,236
< Warning message:
< In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
<   there is no package called 'Matrix'
---
> > cat("Trying some Matrix objects, too\n")
> Trying some Matrix objects, too
> > D5. <- Diagonal(x = 5:1)
> > D5N <- D5.
> > D5N[5, 5] <- NA
> > example(Matrix)
> 
> Matrix> Matrix(0, 3, 2)             # 3 by 2 matrix of zeros -> sparse
> 3 x 2 sparse Matrix of class "dgCMatrix"
>         
> [1,] . .
> [2,] . .
> [3,] . .
> 
> Matrix> Matrix(0, 3, 2, sparse=FALSE)# -> 'dense'
> 3 x 2 Matrix of class "dgeMatrix"
>      [,1] [,2]
> [1,]    0    0
> [2,]    0    0
> [3,]    0    0
> 
> Matrix> Matrix(0, 2, 2, sparse=FALSE)# diagonal !
> 2 x 2 diagonal matrix of class "ddiMatrix"
>      [,1] [,2]
> [1,]    0    .
> [2,]    .    0
> 
> Matrix> Matrix(0, 2, 2, sparse=FALSE, doDiag=FALSE)# -> dense
> 2 x 2 Matrix of class "dsyMatrix"
>      [,1] [,2]
> [1,]    0    0
> [2,]    0    0
> 
> Matrix> Matrix(1:6, 3, 2)           # a 3 by 2 matrix (+ integer warning)
> 3 x 2 Matrix of class "dgeMatrix"
>      [,1] [,2]
> [1,]    1    4
> [2,]    2    5
> [3,]    3    6
> 
> Matrix> Matrix(1:6 + 1, nrow=3)
> 3 x 2 Matrix of class "dgeMatrix"
>      [,1] [,2]
> [1,]    2    5
> [2,]    3    6
> [3,]    4    7
> 
> Matrix> ## logical ones:
> Matrix> Matrix(diag(4) >  0)# -> "ldiMatrix" with diag = "U"
> 4 x 4 diagonal matrix of class "ldiMatrix"
>      [,1] [,2] [,3] [,4]
> [1,] TRUE    .    .    .
> [2,]    . TRUE    .    .
> [3,]    .    . TRUE    .
> [4,]    .    .    . TRUE
> 
> Matrix> Matrix(diag(4) >  0, sparse=TRUE)# -> sparse...
> 4 x 4 sparse Matrix of class "lsCMatrix"
>             
> [1,] | . . .
> [2,] . | . .
> [3,] . . | .
> [4,] . . . |
> 
> Matrix> Matrix(diag(4) >= 0)# -> "lsyMatrix" (of all 'TRUE')
> 4 x 4 Matrix of class "lsyMatrix"
>      [,1] [,2] [,3] [,4]
> [1,] TRUE TRUE TRUE TRUE
> [2,] TRUE TRUE TRUE TRUE
> [3,] TRUE TRUE TRUE TRUE
> [4,] TRUE TRUE TRUE TRUE
> 
> Matrix> ## triangular
> Matrix> l3 <- upper.tri(matrix(,3,3))
> 
> Matrix> (M <- Matrix(l3))  # -> "ltCMatrix"
> 3 x 3 sparse Matrix of class "ltCMatrix"
>           
> [1,] . | |
> [2,] . . |
> [3,] . . .
> 
> Matrix> Matrix(! l3)# -> "ltrMatrix"
> 3 x 3 Matrix of class "ltrMatrix"
>      [,1]  [,2]  [,3] 
> [1,]  TRUE     .     .
> [2,]  TRUE  TRUE     .
> [3,]  TRUE  TRUE  TRUE
> 
> Matrix> as(l3, "CsparseMatrix")
> 3 x 3 sparse Matrix of class "lgCMatrix"
>           
> [1,] . | |
> [2,] . . |
> [3,] . . .
> 
> Matrix> Matrix(1:9, nrow=3,
> Matrix+        dimnames = list(c("a", "b", "c"), c("A", "B", "C")))
> 3 x 3 Matrix of class "dgeMatrix"
>   A B C
> a 1 4 7
> b 2 5 8
> c 3 6 9
> 
> Matrix> (I3 <- Matrix(diag(3)))# identity, i.e., unit "diagonalMatrix"
> 3 x 3 diagonal matrix of class "ddiMatrix"
>      [,1] [,2] [,3]
> [1,]    1    .    .
> [2,]    .    1    .
> [3,]    .    .    1
> 
> Matrix> str(I3) # note the empty 'x' slot
> Formal class 'ddiMatrix' [package "Matrix"] with 4 slots
>   ..@ diag    : chr "U"
>   ..@ Dim     : int [1:2] 3 3
>   ..@ Dimnames:List of 2
>   .. ..$ : NULL
>   .. ..$ : NULL
>   ..@ x       : num(0) 
> 
> Matrix> (A <- cbind(a=c(2,1), b=1:2))# symmetric *apart* from dimnames
>      a b
> [1,] 2 1
> [2,] 1 2
> 
> Matrix> Matrix(A)                    # hence 'dgeMatrix'
> 2 x 2 Matrix of class "dgeMatrix"
>      a b
> [1,] 2 1
> [2,] 1 2
> 
> Matrix> (As <- Matrix(A, dimnames = list(NULL,NULL)))# -> symmetric
> 2 x 2 Matrix of class "dsyMatrix"
>      [,1] [,2]
> [1,]    2    1
> [2,]    1    2
> 
> Matrix> stopifnot(is(As, "symmetricMatrix"),
> Matrix+           is(Matrix(0, 3,3), "sparseMatrix"),
> Matrix+           is(Matrix(FALSE, 1,1), "sparseMatrix"))
> > i <- c(1, 3:8)
> > j <- c(2, 9, 6:10)
> > x <- 7 * (1:7)
> > A <- sparseMatrix(i, j, x = x)
> > sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)
> > tA <- sparseMatrix(i, j, x = x, triangular = TRUE)
> > AA <- sparseMatrix(c(1, 3:8), c(2, 9, 6:10), x = 7 * (1:7), dims = c(10, 
> +     20))
> > set.seed(1)
> > (perm <- sample(1:7))
> [1] 1 4 7 2 5 3 6
> > A1 <- sparseMatrix(i[perm], j[perm], x = x[perm])
> > args <- data.frame(i = c(i, 1), j = c(j, 2), x = c(x, 2))
> > Aa <- do.call(sparseMatrix, args)
> > A. <- do.call(sparseMatrix, c(args, list(use.last.ij = TRUE)))
> > nA <- do.call(sparseMatrix, args[c("i", "j")])
> > dn <- list(LETTERS[1:3], letters[1:5])
> > m <- sparseMatrix(i = c(3, 1, 3:2, 2:1), p = c(0:2, 4, 4, 6), x = 1:6, 
> +     dimnames = dn)
> > n <- sparseMatrix(i = 1:6, j = rev(2:7))
> > e <- sparseMatrix(dims = c(4, 6), i = {
> + }, j = {
> + })
> > sy <- sparseMatrix(i = c(2, 4, 3:5), j = c(4, 7:5, 5), x = 1:5, dims = c(7, 
> +     7), symmetric = TRUE)
76a239,290
> A: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, 
> 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list(
>     NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> A.: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, 
> 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list(
>     NULL, NULL), x = c(2, 21, 28, 35, 14, 42, 49), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> A1: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, 
> 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list(
>     NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> AA: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, 
> 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
> 7L, 7L, 7L, 7L), Dim = c(10L, 20L), Dimnames = list(NULL, NULL), 
>     x = c(7, 21, 28, 35, 14, 42, 49), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> Aa: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, 
> 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list(
>     NULL, NULL), x = c(9, 21, 28, 35, 14, 42, 49), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> As: new("dsyMatrix", x = c(2, 1, 1, 2), Dim = c(2L, 2L), Dimnames = list(
>     NULL, NULL), uplo = "U", factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> D5.: new("ddiMatrix", diag = "N", Dim = c(5L, 5L), Dimnames = list(
>     NULL, NULL), x = c(5, 4, 3, 2, 1))
>  --> checking list(*): Ok
> --=--=--=--=--
> D5N: new("ddiMatrix", diag = "N", Dim = c(5L, 5L), Dimnames = list(
>     NULL, NULL), x = c(5, 4, 3, 2, NA))
>  --> checking list(*): Ok
> --=--=--=--=--
> I3: new("ddiMatrix", diag = "U", Dim = c(3L, 3L), Dimnames = list(
>     NULL, NULL), x = numeric(0))
>  --> checking list(*): Ok
> --=--=--=--=--
> M: new("ltCMatrix", i = c(0L, 0L, 1L), p = c(0L, 0L, 1L, 3L), Dim = c(3L, 
> 3L), Dimnames = list(NULL, NULL), x = c(TRUE, TRUE, TRUE), uplo = "U", 
>     diag = "N")
>  --> checking list(*): Ok
> --=--=--=--=--
> args: structure(list(i = c(1, 3, 4, 5, 6, 7, 8, 1), j = c(2, 9, 6, 
> 7, 8, 9, 10, 2), x = c(7, 14, 21, 28, 35, 42, 49, 2)), class = "data.frame", row.names = c(NA, 
> -8L))
>  --> checking list(*): Ok
> --=--=--=--=--
178a393,399
> dn: list(c("A", "B", "C"), c("a", "b", "c", "d", "e"))
>  --> checking list(*): Ok
> --=--=--=--=--
> e: new("ngCMatrix", i = integer(0), p = c(0L, 0L, 0L, 0L, 0L, 0L, 
> 0L), Dim = c(4L, 6L), Dimnames = list(NULL, NULL), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
240a462,464
> i: c(1, 3, 4, 5, 6, 7, 8)
>  --> checking list(*): Ok
> --=--=--=--=--
260a485,505
> j: c(2, 9, 6, 7, 8, 9, 10)
>  --> checking list(*): Ok
> --=--=--=--=--
> l3: structure(c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, 
> FALSE), .Dim = c(3L, 3L))
>  --> checking list(*): Ok
> --=--=--=--=--
> m: new("dgCMatrix", i = c(2L, 0L, 1L, 2L, 0L, 1L), p = c(0L, 1L, 
> 2L, 4L, 4L, 6L), Dim = c(3L, 5L), Dimnames = list(c("A", "B", 
> "C"), c("a", "b", "c", "d", "e")), x = c(1, 2, 4, 3, 6, 5), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> n: new("ngCMatrix", i = 5:0, p = c(0L, 0L, 1L, 2L, 3L, 4L, 5L, 6L
> ), Dim = 6:7, Dimnames = list(NULL, NULL), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> nA: new("ngCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, 
> 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list(
>     NULL, NULL), factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
270a516,518
> perm: c(1L, 4L, 7L, 2L, 5L, 3L, 6L)
>  --> checking list(*): Ok
> --=--=--=--=--
312a561,580
> sA: new("dsCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, 
> 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list(
>     NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", 
>     factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> sy: new("dsCMatrix", i = c(1L, 3L, 4L, 2L, 3L), p = c(0L, 0L, 0L, 
> 0L, 1L, 3L, 4L, 5L), Dim = c(7L, 7L), Dimnames = list(NULL, NULL), 
>     x = c(1, 4, 5, 3, 2), uplo = "U", factors = list())
>  --> checking list(*): Ok
> --=--=--=--=--
> tA: new("dtCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, 
> 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list(
>     NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", 
>     diag = "N")
>  --> checking list(*): Ok
> --=--=--=--=--
> x: c(7, 14, 21, 28, 35, 42, 49)
>  --> checking list(*): Ok
> --=--=--=--=--
315,317c583,584
< 1 identical warnings:
< In library(package, lib.loc = lib.loc, character.only = TRUE,  ... :
<   there is no package called 'Matrix'
---
> Length  Class   Mode 
>      0   NULL   NULL 
 OK
running code in 'print-tests.R' ... OK
  comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK
running code in 'lapack.R' ... OK
  comparing 'lapack.Rout' to './lapack.Rout.save' ... OK
running code in 'datasets.R' ... OK
  comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
running code in 'datetime.R' ... OK
  comparing 'datetime.Rout' to './datetime.Rout.save' ... OK
running code in 'iec60559.R' ... OK
  comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[4]: Entering directory '/build/r-base-3.6.1/tests'
checking Sys.timezone ...
make[5]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'timezone.R' ... OK
make[5]: Leaving directory '/build/r-base-3.6.1/tests'
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running regression tests ...
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'array-subset.R' ... OK
running code in 'reg-tests-1a.R' ... OK
running code in 'reg-tests-1b.R' ... OK
running code in 'reg-tests-1c.R' ... OK
running code in 'reg-tests-1d.R' ... OK
running code in 'reg-tests-2.R' ... OK
  comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK
running code in 'reg-examples1.R' ... OK
running code in 'reg-examples2.R' ... OK
running code in 'reg-packages.R' ... OK
running code in 'p-qbeta-strict-tst.R' ... OK
running code in 'r-strict-tst.R' ... OK
running code in 'reg-IO.R' ... OK
  comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK
running code in 'reg-IO2.R' ... OK
  comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK
running code in 'reg-plot.R' ... OK
  comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK
running code in 'reg-S4-examples.R' ... OK
running code in 'reg-BLAS.R' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running tests of plotting Latin-1
  expect failure or some differences if not in a Latin-1 or UTF-8 locale
running code in 'reg-plot-latin1.R' ... FAILED
running code in 'reg-S4.R' ... OK
  comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ...606,608c606
< Warning message:
< In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
<   there is no package called 'Matrix'
---
> <sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
1249,1251c1247,1269
< Warning message:
< In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
<   there is no package called 'Matrix'
---
> > setClass("Z", representation(zz = "list"))
> > setClass("C", contains = c("Z", "dgCMatrix"))
> > setClass("C2", contains = "C")
> > setClass("C3", contains = "C2")
> > m <- matrix(c(0, 0, 2:0), 3, 5, dimnames = list(NULL, NULL))
> > (mC <- as(m, "dgCMatrix"))
> 3 x 5 sparse Matrix of class "dgCMatrix"
>               
> [1,] . 1 . . 2
> [2,] . . 2 . 1
> [3,] 2 . 1 . .
> > (cc <- as(mC, "C"))
> 3 x 5 sparse Matrix of class "C"
>               
> [1,] . 1 . . 2
> [2,] . . 2 . 1
> [3,] 2 . 1 . .
> > c2 <- as(mC, "C2")
> > c3 <- as(mC, "C3")
> > stopifnot(identical(capture.output(c2), sub("C3", "C2", capture.output(c3))), 
> +     identical(as(cc, "matrix"), m), identical(as(c2, "matrix"), m), identical(as(c3, 
> +         "matrix"), m))
> > invisible(lapply(c("Z", "C", "C2", "C3"), removeClass))
 OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running tests of Internet functions
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'internet.R' ... OK
  comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247
< Warning message:
< In nsl("cran.r-project.org") :
<   nsl() was unable to resolve host 'cran.r-project.org'
---
> > 
> > # test do_download (and "record" #{packages}):
> > ap <- available.packages(contrib.url("http://cran.r-project.org"))
> > ## IGNORE_RDIFF_END
> > 
> > # test url connections on http
> > zz <- url("http://cran.r-project.org/")
> > readLines(zz)
>  [1] "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">"
>  [2] "<html>"                                                                                                   
>  [3] "<head>"                                                                                                   
>  [4] "<title>The Comprehensive R Archive Network</title>"                                                       
>  [5] "<META HTTP-EQUIV=\"content-type\" CONTENT=\"text/html; charset=utf-8\">"                                  
>  [6] "<link rel=\"icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                           
>  [7] "<link rel=\"shortcut icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                  
>  [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"                                               
>  [9] "</head>"                                                                                                  
> [10] ""                                                                                                         
> [11] "<FRAMESET cols=\"1*, 4*\" style=\"border: none;\">"                                                       
> [12] "<FRAMESET rows=\"120, 1*\">"                                                                              
> [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>"                                                    
> [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>"                                              
> [15] "</FRAMESET>"                                                                                              
> [16] "<FRAME src=\"banner.shtml\" name=\"banner\" frameborder=0>"                                               
> [17] "<noframes>"                                                                                               
> [18] "<h1>The Comprehensive R Archive Network</h1>"                                                             
> [19] ""                                                                                                         
> [20] "Your browser seems not to support frames,"                                                                
> [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN."                                           
> [22] "</noframes>"                                                                                              
> [23] "</FRAMESET>"                                                                                              
> > close(zz)
> > 
> > # and via read.table, test http and ftp.
> > 
> > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
>      V1  V2   V3    V4 V5
> 1     1 307  930 36.58  0
> 2     2 307  940 36.73  0
> 3     3 307  950 36.93  0
> 4     4 307 1000 37.15  0
> 5     5 307 1010 37.23  0
> 6     6 307 1020 37.24  0
> 7     7 307 1030 37.24  0
> 8     8 307 1040 36.90  0
> 9     9 307 1050 36.95  0
> 10   10 307 1100 36.89  0
> 11   11 307 1110 36.95  0
> 12   12 307 1120 37.00  0
> 13   13 307 1130 36.90  0
> 14   14 307 1140 36.99  0
> 15   15 307 1150 36.99  0
> 16   16 307 1200 37.01  0
> 17   17 307 1210 37.04  0
> 18   18 307 1220 37.04  0
> 19   19 307 1230 37.14  0
> 20   20 307 1240 37.07  0
> 21   21 307 1250 36.98  0
> 22   22 307 1300 37.01  0
> 23   23 307 1310 36.97  0
> 24   24 307 1320 36.97  0
> 25   25 307 1330 37.12  0
> 26   26 307 1340 37.13  0
> 27   27 307 1350 37.14  0
> 28   28 307 1400 37.15  0
> 29   29 307 1410 37.17  0
> 30   30 307 1420 37.12  0
> 31   31 307 1430 37.12  0
> 32   32 307 1440 37.17  0
> 33   33 307 1450 37.28  0
> 34   34 307 1500 37.28  0
> 35   35 307 1510 37.44  0
> 36   36 307 1520 37.51  0
> 37   37 307 1530 37.64  0
> 38   38 307 1540 37.51  0
> 39   39 307 1550 37.98  1
> 40   40 307 1600 38.02  1
> 41   41 307 1610 38.00  1
> 42   42 307 1620 38.24  1
> 43   43 307 1630 38.10  1
> 44   44 307 1640 38.24  1
> 45   45 307 1650 38.11  1
> 46   46 307 1700 38.02  1
> 47   47 307 1710 38.11  1
> 48   48 307 1720 38.01  1
> 49   49 307 1730 37.91  1
> 50   50 307 1740 37.96  1
> 51   51 307 1750 38.03  1
> 52   52 307 1800 38.17  1
> 53   53 307 1810 38.19  1
> 54   54 307 1820 38.18  1
> 55   55 307 1830 38.15  1
> 56   56 307 1840 38.04  1
> 57   57 307 1850 37.96  1
> 58   58 307 1900 37.84  1
> 59   59 307 1910 37.83  1
> 60   60 307 1920 37.84  1
> 61   61 307 1930 37.74  1
> 62   62 307 1940 37.76  1
> 63   63 307 1950 37.76  1
> 64   64 307 2000 37.64  1
> 65   65 307 2010 37.63  1
> 66   66 307 2020 38.06  1
> 67   67 307 2030 38.19  1
> 68   68 307 2040 38.35  1
> 69   69 307 2050 38.25  1
> 70   70 307 2100 37.86  1
> 71   71 307 2110 37.95  1
> 72   72 307 2120 37.95  1
> 73   73 307 2130 37.76  1
> 74   74 307 2140 37.60  1
> 75   75 307 2150 37.89  1
> 76   76 307 2200 37.86  1
> 77   77 307 2210 37.71  1
> 78   78 307 2220 37.78  1
> 79   79 307 2230 37.82  1
> 80   80 307 2240 37.76  1
> 81   81 307 2250 37.81  1
> 82   82 307 2300 37.84  1
> 83   83 307 2310 38.01  1
> 84   84 307 2320 38.10  1
> 85   85 307 2330 38.15  1
> 86   86 307 2340 37.92  1
> 87   87 307 2350 37.64  1
> 88   88 308    0 37.70  1
> 89   89 308   10 37.46  1
> 90   90 308   20 37.41  1
> 91   91 308   30 37.46  1
> 92   92 308   40 37.56  1
> 93   93 308   50 37.55  1
> 94   94 308  100 37.75  1
> 95   95 308  110 37.76  1
> 96   96 308  120 37.73  1
> 97   97 308  130 37.77  1
> 98   98 308  140 38.01  1
> 99   99 308  150 38.04  1
> 100 100 308  200 38.07  1
> > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
>      V1  V2   V3    V4 V5
> 1     1 307  930 36.58  0
> 2     2 307  940 36.73  0
> 3     3 307  950 36.93  0
> 4     4 307 1000 37.15  0
> 5     5 307 1010 37.23  0
> 6     6 307 1020 37.24  0
> 7     7 307 1030 37.24  0
> 8     8 307 1040 36.90  0
> 9     9 307 1050 36.95  0
> 10   10 307 1100 36.89  0
> 11   11 307 1110 36.95  0
> 12   12 307 1120 37.00  0
> 13   13 307 1130 36.90  0
> 14   14 307 1140 36.99  0
> 15   15 307 1150 36.99  0
> 16   16 307 1200 37.01  0
> 17   17 307 1210 37.04  0
> 18   18 307 1220 37.04  0
> 19   19 307 1230 37.14  0
> 20   20 307 1240 37.07  0
> 21   21 307 1250 36.98  0
> 22   22 307 1300 37.01  0
> 23   23 307 1310 36.97  0
> 24   24 307 1320 36.97  0
> 25   25 307 1330 37.12  0
> 26   26 307 1340 37.13  0
> 27   27 307 1350 37.14  0
> 28   28 307 1400 37.15  0
> 29   29 307 1410 37.17  0
> 30   30 307 1420 37.12  0
> 31   31 307 1430 37.12  0
> 32   32 307 1440 37.17  0
> 33   33 307 1450 37.28  0
> 34   34 307 1500 37.28  0
> 35   35 307 1510 37.44  0
> 36   36 307 1520 37.51  0
> 37   37 307 1530 37.64  0
> 38   38 307 1540 37.51  0
> 39   39 307 1550 37.98  1
> 40   40 307 1600 38.02  1
> 41   41 307 1610 38.00  1
> 42   42 307 1620 38.24  1
> 43   43 307 1630 38.10  1
> 44   44 307 1640 38.24  1
> 45   45 307 1650 38.11  1
> 46   46 307 1700 38.02  1
> 47   47 307 1710 38.11  1
> 48   48 307 1720 38.01  1
> 49   49 307 1730 37.91  1
> 50   50 307 1740 37.96  1
> 51   51 307 1750 38.03  1
> 52   52 307 1800 38.17  1
> 53   53 307 1810 38.19  1
> 54   54 307 1820 38.18  1
> 55   55 307 1830 38.15  1
> 56   56 307 1840 38.04  1
> 57   57 307 1850 37.96  1
> 58   58 307 1900 37.84  1
> 59   59 307 1910 37.83  1
> 60   60 307 1920 37.84  1
> 61   61 307 1930 37.74  1
> 62   62 307 1940 37.76  1
> 63   63 307 1950 37.76  1
> 64   64 307 2000 37.64  1
> 65   65 307 2010 37.63  1
> 66   66 307 2020 38.06  1
> 67   67 307 2030 38.19  1
> 68   68 307 2040 38.35  1
> 69   69 307 2050 38.25  1
> 70   70 307 2100 37.86  1
> 71   71 307 2110 37.95  1
> 72   72 307 2120 37.95  1
> 73   73 307 2130 37.76  1
> 74   74 307 2140 37.60  1
> 75   75 307 2150 37.89  1
> 76   76 307 2200 37.86  1
> 77   77 307 2210 37.71  1
> 78   78 307 2220 37.78  1
> 79   79 307 2230 37.82  1
> 80   80 307 2240 37.76  1
> 81   81 307 2250 37.81  1
> 82   82 307 2300 37.84  1
> 83   83 307 2310 38.01  1
> 84   84 307 2320 38.10  1
> 85   85 307 2330 38.15  1
> 86   86 307 2340 37.92  1
> 87   87 307 2350 37.64  1
> 88   88 308    0 37.70  1
> 89   89 308   10 37.46  1
> 90   90 308   20 37.41  1
> 91   91 308   30 37.46  1
> 92   92 308   40 37.56  1
> 93   93 308   50 37.55  1
> 94   94 308  100 37.75  1
> 95   95 308  110 37.76  1
> 96   96 308  120 37.73  1
> 97   97 308  130 37.77  1
> 98   98 308  140 38.01  1
> 99   99 308  150 38.04  1
> 100 100 308  200 38.07  1
> > 
 OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running tests of date-time printing
  expect platform-specific differences
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'datetime2.R' ... OK
  comparing 'datetime2.Rout' to './datetime2.Rout.save' ...10,11c10,11
<  [1] "1890-01-10 13:00:00 CET" "1891-01-10 13:00:00 CET"
<  [3] "1892-01-10 13:00:00 CET" "1893-01-10 13:00:00 CET"
---
>  [1] "1890-01-10 12:49:56 RMT" "1891-01-10 12:49:56 RMT"
>  [3] "1892-01-10 12:49:56 RMT" "1893-01-10 12:49:56 RMT"
24c24
<  [1] "1890-01-10 12:09:21 PMT" "1891-01-10 12:09:21 PMT"
---
>  [1] "1890-01-10 12:09:21 LMT" "1891-01-10 12:09:21 LMT"
37c37
<  [1] "1890-01-10 12:09:21 PMT" "1891-01-10 12:09:21 PMT"
---
>  [1] "1890-01-10 12:09:21 LMT" "1891-01-10 12:09:21 LMT"
68c68
<  [1] "1890-01-10 12:09:21 PMT"  "1895-01-10 12:09:21 PMT" 
---
>  [1] "1890-01-10 12:09:21 LMT"  "1895-01-10 12:09:21 PMT" 
78c78
< [1] "1890-01-10 12:09:21 PMT"
---
> [1] "1890-01-10 12:09:21 LMT"
 OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running tests of documentation examples
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'R-intro.R' ... OK
  comparing 'R-intro.Rout' to './R-intro.Rout.save' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[4]: Entering directory '/build/r-base-3.6.1/tests'
gcc -std=gnu99 -I"/build/r-base-3.6.1/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R-exts.c -o R-exts.o
gcc -std=gnu99 -shared -L/build/r-base-3.6.1/lib -Wl,-z,relro -o R-exts.so R-exts.o -L/build/r-base-3.6.1/lib -lR
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'R-exts.R' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running tests of consistency of as/is.*
make[4]: Entering directory '/build/r-base-3.6.1/tests'
creating 'isas-tests.R'
running code in 'isas-tests.R' ... OK
  comparing 'isas-tests.Rout' to './isas-tests.Rout.save' ... OK
rm isas-tests.R
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running tests of random deviate generation
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'p-r-random-tests.R' ... OK
  comparing 'p-r-random-tests.Rout' to './p-r-random-tests.Rout.save' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running demos from base and stats
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'demos.R' ... OK
  comparing 'demos.Rout' to './demos.Rout.save' ... OK
running code in 'demos2.R' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running tests of primitives
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'primitives.R' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running regexp regression tests
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running more Internet and socket tests
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'internet2.R' ... OK
running code in 'libcurl.R' ... OK
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: Entering directory '/build/r-base-3.6.1/tests'
running tests of CRAN tools
  (can be slow unless mirror is local)
make[4]: Entering directory '/build/r-base-3.6.1/tests'
running code in 'CRANtools.R' ...make[4]: *** [Makefile.common:106: CRANtools.Rout] Error 1
make[4]: Leaving directory '/build/r-base-3.6.1/tests'
make[3]: *** [Makefile.common:276: test-CRANtools] Error 2
make[3]: Leaving directory '/build/r-base-3.6.1/tests'
make[2]: *** [Makefile.common:180: test-all-devel] Error 1
make[2]: Leaving directory '/build/r-base-3.6.1/tests'
make[1]: *** [Makefile:241: check-all] Error 2
make[1]: Leaving directory '/build/r-base-3.6.1'
make: [debian/rules:387: check-stamp] Error 2 (ignored)
touch check-stamp
 fakeroot debian/rules binary
*** install-arch ***
dh_testdir
dh_testroot
dh_prep -a
dh_installdirs -A
/build/r-base-3.6.1/debian/r-base-core
/usr/bin/make DESTDIR=/build/r-base-3.6.1/debian/r-base-core install
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/m4'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/build/r-base-3.6.1/m4'
make[2]: Entering directory '/build/r-base-3.6.1/tools'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/build/r-base-3.6.1/tools'
make[2]: Entering directory '/build/r-base-3.6.1/doc'
installing doc ...
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/doc
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/man/man1
make[3]: Entering directory '/build/r-base-3.6.1/doc/html'
installing doc/html ...
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/doc/html
make[3]: Leaving directory '/build/r-base-3.6.1/doc/html'
make[3]: Entering directory '/build/r-base-3.6.1/doc/manual'
installing doc/manual ...
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/doc/manual
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/doc/manual/images
make[3]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[2]: Leaving directory '/build/r-base-3.6.1/doc'
make[2]: Entering directory '/build/r-base-3.6.1/etc'
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/etc
installing etc ...
make[2]: Leaving directory '/build/r-base-3.6.1/etc'
make[2]: Entering directory '/build/r-base-3.6.1/share'
installing share ...
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/R
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/dictionaries
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/encodings
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/java
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/licenses
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/make
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/Rd
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/Rd/macros
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/sh
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/texmf
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/texmf/tex/latex
make[2]: Leaving directory '/build/r-base-3.6.1/share'
make[2]: Entering directory '/build/r-base-3.6.1/src'
make[3]: Entering directory '/build/r-base-3.6.1/src/scripts'
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/bin
make[3]: Leaving directory '/build/r-base-3.6.1/src/scripts'
make[3]: Entering directory '/build/r-base-3.6.1/src/include'
make[4]: Entering directory '/build/r-base-3.6.1/src/include/R_ext'
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/R/include/R_ext
make[4]: Leaving directory '/build/r-base-3.6.1/src/include/R_ext'
make[3]: Leaving directory '/build/r-base-3.6.1/src/include'
make[3]: Entering directory '/build/r-base-3.6.1/src/extra'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/blas'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/blas'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/tre'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/tre'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/tzone'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/tzone'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/xdr'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/xdr'
make[4]: Entering directory '/build/r-base-3.6.1/src/extra/intl'
make[4]: Nothing to be done for 'install'.
make[4]: Leaving directory '/build/r-base-3.6.1/src/extra/intl'
make[3]: Leaving directory '/build/r-base-3.6.1/src/extra'
make[3]: Entering directory '/build/r-base-3.6.1/src/appl'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/build/r-base-3.6.1/src/appl'
make[3]: Entering directory '/build/r-base-3.6.1/src/nmath'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/build/r-base-3.6.1/src/nmath'
make[3]: Entering directory '/build/r-base-3.6.1/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \
  -o Rscript ./Rscript.c
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/lib/pkgconfig
make[3]: Leaving directory '/build/r-base-3.6.1/src/unix'
make[3]: Entering directory '/build/r-base-3.6.1/src/main'
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/bin/exec
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[4]: Entering directory '/build/r-base-3.6.1/src/main'
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/lib
make[4]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Leaving directory '/build/r-base-3.6.1/src/main'
make[3]: Entering directory '/build/r-base-3.6.1/src/modules'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/internet'
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/modules
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/internet'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/lapack'
make[4]: Entering directory '/build/r-base-3.6.1/src/modules/X11'
make[4]: Leaving directory '/build/r-base-3.6.1/src/modules/X11'
make[3]: Leaving directory '/build/r-base-3.6.1/src/modules'
make[3]: Entering directory '/build/r-base-3.6.1/src/library'
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/library
installing packages ...
  building HTML index ...
make[3]: Leaving directory '/build/r-base-3.6.1/src/library'
make[2]: Leaving directory '/build/r-base-3.6.1/src'
make[2]: Entering directory '/build/r-base-3.6.1/tests'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/build/r-base-3.6.1/tests'
make[1]: Leaving directory '/build/r-base-3.6.1'
(cd src/unix; 						\
	rm -vf Rscript /build/r-base-3.6.1/debian/r-base-core/usr/bin/Rscript;	\
	/usr/bin/make	CFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"		\
		CXXFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT"	\
		FFLAGS="-g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -D_REENTRANT"	\
		CC="gcc -std=gnu99"				\
		CXX=g++			\
		F77=gfortran			\
		RHOME=/usr/lib/R			\
		DESTDIR=/build/r-base-3.6.1/debian/r-base-core			\
		install-Rscript )
removed 'Rscript'
removed '/build/r-base-3.6.1/debian/r-base-core/usr/bin/Rscript'
make[1]: Entering directory '/build/r-base-3.6.1/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include   -DHAVE_CONFIG_H    -g -O2 -fdebug-prefix-map=/build/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \
  -o Rscript ./Rscript.c
make[1]: Leaving directory '/build/r-base-3.6.1/src/unix'
#ls -ltr /build/r-base-3.6.1/debian/r-base-core/usr/bin/
#strings src/unix/Rscript
cp -vax src/unix/Rscript /build/r-base-3.6.1/debian/r-base-core/usr/bin/
'src/unix/Rscript' -> '/build/r-base-3.6.1/debian/r-base-core/usr/bin/Rscript'
#ls -ltr /build/r-base-3.6.1/debian/r-base-core/usr/bin/
#strings /build/r-base-3.6.1/debian/r-base-core/usr/bin/Rscript
(cd src/nmath/standalone;				\
	/usr/bin/make DESTDIR=/build/r-base-3.6.1/debian/r-base-core install )
make[1]: Entering directory '/build/r-base-3.6.1/src/nmath/standalone'
make[2]: Entering directory '/build/r-base-3.6.1/src/include'
make[2]: 'Rmath.h' is up to date.
make[2]: Leaving directory '/build/r-base-3.6.1/src/include'
/build/r-base-3.6.1/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged
make[1]: Leaving directory '/build/r-base-3.6.1/src/nmath/standalone'
chmod a+x	/build/r-base-3.6.1/debian/r-base-core/usr/share/R/share/sh/echo.sh
rm -v	/build/r-base-3.6.1/debian/r-base-core/usr/lib/R/COPYING
removed '/build/r-base-3.6.1/debian/r-base-core/usr/lib/R/COPYING'
(cd /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/; \
	ln -s ../../share/common-licenses/GPL-2 COPYING)
rm -v	/build/r-base-3.6.1/debian/r-base-core/usr/share/R/doc/COPYING
removed '/build/r-base-3.6.1/debian/r-base-core/usr/share/R/doc/COPYING'
(cd /build/r-base-3.6.1/debian/r-base-core/usr/share/R/doc; \
	ln -s ../../../share/common-licenses/GPL-2 COPYING)
(cd /build/r-base-3.6.1/debian/r-base-core/usr/share/texmf/tex/latex && 	\
    ln -s ../../../R/share/texmf R)
dh_movefiles	--sourcedir=debian/r-base-core -pr-doc-html
dh_movefiles	--sourcedir=debian/r-base-core -pr-base-html
make		prefix=/build/r-base-3.6.1/debian/r-base-core/usr			\
		rdocdir=/build/r-base-3.6.1/debian/r-base-core/usr/share/R/doc	\
		install-pdf
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/doc/manual'
installing R manuals in PDF format ...
make[2]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[1]: Leaving directory '/build/r-base-3.6.1'
make		prefix=/build/r-base-3.6.1/debian/r-base-core/usr  \
		infodir=/build/r-base-3.6.1/debian/r-base-core/usr/share/info	install-info
make[1]: Entering directory '/build/r-base-3.6.1'
make[2]: Entering directory '/build/r-base-3.6.1/doc/manual'
mkdir -p -- /build/r-base-3.6.1/debian/r-base-core/usr/share/info
/usr/bin/install -c -m 644 "./dir" "/build/r-base-3.6.1/debian/r-base-core/usr/share/info"
installing R info pages ...
updating '/build/r-base-3.6.1/debian/r-base-core/usr/share/info/dir' ...
you need to adjust /build/r-base-3.6.1/debian/r-base-core/usr/share/info/dir manually
you need to adjust /build/r-base-3.6.1/debian/r-base-core/usr/share/info/dir manually
you need to adjust /build/r-base-3.6.1/debian/r-base-core/usr/share/info/dir manually
you need to adjust /build/r-base-3.6.1/debian/r-base-core/usr/share/info/dir manually
you need to adjust /build/r-base-3.6.1/debian/r-base-core/usr/share/info/dir manually
you need to adjust /build/r-base-3.6.1/debian/r-base-core/usr/share/info/dir manually
you need to adjust /build/r-base-3.6.1/debian/r-base-core/usr/share/info/dir manually
make[2]: Leaving directory '/build/r-base-3.6.1/doc/manual'
make[1]: Leaving directory '/build/r-base-3.6.1'
dh_movefiles	--sourcedir=debian/r-base-core -pr-doc-pdf
dh_movefiles	--sourcedir=debian/r-base-core -pr-doc-html
touch install-indep-stamp
gunzip -9v /build/r-base-3.6.1/debian/r-base-core/usr/share/info/*.gz
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-FAQ.info.gz:	 67.2% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-FAQ.info
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-admin.info.gz:	 68.0% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-admin.info
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-data.info.gz:	 70.6% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-data.info
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-exts.info-1.gz:	 66.6% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-exts.info-1
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-exts.info-2.gz:	 69.7% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-exts.info-2
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-exts.info-3.gz:	 83.3% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-exts.info-3
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-exts.info.gz:	 70.2% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-exts.info
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-intro.info.gz:	 70.0% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-intro.info
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-ints.info.gz:	 68.0% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-ints.info
/build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-lang.info.gz:	 71.6% -- replaced with /build/r-base-3.6.1/debian/r-base-core/usr/share/info/R-lang.info
dh_movefiles	--sourcedir=debian/r-base-core -pr-doc-info
rm -vf	/build/r-base-3.6.1/debian/r-doc-info/usr/share/info/dir		\
	/build/r-base-3.6.1/debian/r-doc-info/usr/share/info/dir.old
removed '/build/r-base-3.6.1/debian/r-doc-info/usr/share/info/dir'
dh_installdirs -pr-mathlib usr/include usr/lib \
				usr/share/lintian/overrides \
				usr/lib/pkgconfig
dh_movefiles	--sourcedir=debian/r-base-core -pr-mathlib
(cd /build/r-base-3.6.1/debian/r-mathlib/usr/lib; \
		ls -l ; \
		mv -v  libRmath.so 	     libRmath.so.1.0.0; \
		ln -sv libRmath.so.1.0.0 libRmath.so.1; \
		ln -sv libRmath.so.1  libRmath.so)
total 2088
-rw-r--r-- 1 root root 1323876 Jul  9 04:32 libRmath.a
-rwxr-xr-x 1 root root  803288 Jul  9 04:32 libRmath.so
drwxr-xr-x 2 root root    4096 Jul  9 04:32 pkgconfig
renamed 'libRmath.so' -> 'libRmath.so.1.0.0'
'libRmath.so.1' -> 'libRmath.so.1.0.0'
'libRmath.so' -> 'libRmath.so.1'
install -m 0644 src/include/Rmath.h			\
		/build/r-base-3.6.1/debian/r-mathlib/usr/include
install -m 0644 debian/Rprofile.site /build/r-base-3.6.1/debian/r-base-core/etc/R
install -m 0644 debian/Renviron.site /build/r-base-3.6.1/debian/r-base-core/etc/R
(cd /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/etc; \
	cat /build/r-base-3.6.1/debian/Renviron-R_LIBS.patch | patch --verbose;	\
	mv Makeconf repositories ldpaths ../../../../etc/R/;	\
	mv Renviron Renviron.ucf;				\
	ln -s  /etc/R/Makeconf	.;				\
	ln -s  /etc/R/Renviron	.;				\
	ln -s  /etc/R/Renviron.site .;				\
	ln -s  /etc/R/Rprofile.site .;				\
	ln -s  /etc/R/ldpaths   .;                              \
	ln -s  /etc/R/repositories .				)
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|--- Renviron.orig	2003-04-04 06:52:22.000000000 -0500
|+++ Renviron	2003-04-04 06:49:05.000000000 -0500
--------------------------
patching file Renviron
Using Plan A...
Hunk #1 succeeded at 46 with fuzz 2 (offset 13 lines).
done
dh_bash-completion
# edd 12 Jan 2016  new location
#install -m 0644 debian/R.bash-completion \
#	debian/r-base-core/usr/share/bash-completion/completions/R
(cd /build/r-base-3.6.1/debian/r-base-core/usr/lib/; \
	ln -sv R/lib/libR.so . )
'./libR.so' -> 'R/lib/libR.so'
(cd debian/icon-class-patch && munpack rlogo_icon.png.mpack)
rlogo_icon.png (application/octet-stream)
install -m 0644 debian/icon-class-patch/rlogo_icon.png	\
	debian/r-base-core/usr/share/icons/hicolor/48x48/apps
install -m 0644 debian/icon-class-patch/R.desktop		\
	debian/r-base-core/usr/share/applications
rm debian/icon-class-patch/rlogo_icon.png
touch install-arch-stamp
*** binary-arch ***
dh_testdir -a
dh_testroot -a
dh_installdocs -pr-base-core doc/NEWS.* README \
				debian/README.Atlas \
				debian/README.mathlib
dh_installdocs -pr-mathlib  doc/NEWS.* README \
				debian/README.mathlib
dh_installdocs -pr-base-core-dbg
dh_installexamples -pr-mathlib	src/nmath/standalone/test.c
#dh_installmenu -a
# (cd /build/r-base-3.6.1/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .)
(cd /build/r-base-3.6.1/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .)
(cd /build/r-base-3.6.1/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/library .)
install -p -m 0644  debian/r-base-core.lintian \
   /build/r-base-3.6.1/debian/r-base-core/usr/share/lintian/overrides/r-base-core
install -p -m 0644  debian/r-recommended.lintian \
   /build/r-base-3.6.1/debian/r-recommended/usr/share/lintian/overrides/r-recommended
install -p -m 0644  debian/r-mathlib.lintian \
   /build/r-base-3.6.1/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib
dh_installchangelogs -a	-k doc/NEWS
dh_strip --dbg-package=r-base-core-dbg
dh_compress -a
dh_fixperms -a
dh_link -a
dh_makeshlibs -a
dh_installdeb -a
dh_perl -a
dh_shlibdeps -a -l /build/r-base-3.6.1/debian/r-base-core/usr/lib/R/lib
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: 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 'libtcl8.6.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libtk8.6.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so'
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_X11.so debian/r-base-core/usr/lib/R/modules/R_de.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)
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_X11.so debian/r-base-core/usr/lib/R/modules/R_de.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/lib/libR.so debian/r-base-core/usr/lib/R/modules/lapack.so debian/r-base-core/usr/lib/R/library/stats/libs/stats.so were not linked against libgfortran.so.5 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_X11.so debian/r-base-core/usr/lib/R/modules/R_de.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/lib/libR.so was not linked against libpcre2-8.so.0 (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/lib/libR.so debian/r-base-core/usr/lib/R/modules/lapack.so debian/r-base-core/usr/lib/R/library/stats/libs/stats.so were not linked against libquadmath.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_X11.so debian/r-base-core/usr/lib/R/modules/R_de.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)
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package r-base-core: substitution variable ${perl:Depends} used, but is not defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'r-base-core-dbg' in '../r-base-core-dbg_3.6.1-2~bustercran.0_i386.deb'.
dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.6.1-2~bustercran.0_i386.deb'.
dpkg-deb: building package 'r-base-core' in '../r-base-core_3.6.1-2~bustercran.0_i386.deb'.
*** binary-indep ***
dh_testdir -i
dh_testroot -i
dh_link -i
dh_installdocs -i
dh_installdocs -v -pr-doc-html
	install -p -m0644 debian/copyright debian/r-doc-html/usr/share/doc/r-doc-html/copyright
	install -p -m0644 debian/r-doc-html.doc-base.exts debian/r-doc-html/usr/share/doc-base/r-extensions
	install -p -m0644 debian/r-doc-html.doc-base.admin debian/r-doc-html/usr/share/doc-base/r-admin
	install -p -m0644 debian/r-doc-html.doc-base.ints debian/r-doc-html/usr/share/doc-base/r-ints
	install -p -m0644 debian/r-doc-html.doc-base.data debian/r-doc-html/usr/share/doc-base/r-data
	install -p -m0644 debian/r-doc-html.doc-base.intro debian/r-doc-html/usr/share/doc-base/r-intro
	install -p -m0644 debian/r-doc-html.doc-base.faq debian/r-doc-html/usr/share/doc-base/r-faq
	install -p -m0644 debian/r-doc-html.doc-base.lang debian/r-doc-html/usr/share/doc-base/r-language
dh_installchangelogs -i
dh_installdirs -pr-base-dev usr/share/R/debian
install -p -m 0755  debian/r-cran.mk \
	/build/r-base-3.6.1/debian/r-base-dev/usr/share/R/debian
dh_compress -i
dh_fixperms -i
dh_installdeb -i
dh_gencontrol -i
dh_md5sums -i
dh_builddeb -i
dpkg-deb: building package 'r-base-html' in '../r-base-html_3.6.1-2~bustercran.0_all.deb'.
dpkg-deb: building package 'r-base' in '../r-base_3.6.1-2~bustercran.0_all.deb'.
dpkg-deb: building package 'r-doc-pdf' in '../r-doc-pdf_3.6.1-2~bustercran.0_all.deb'.
dpkg-deb: building package 'r-doc-html' in '../r-doc-html_3.6.1-2~bustercran.0_all.deb'.
dpkg-deb: building package 'r-base-dev' in '../r-base-dev_3.6.1-2~bustercran.0_all.deb'.
dpkg-deb: building package 'r-doc-info' in '../r-doc-info_3.6.1-2~bustercran.0_all.deb'.
dpkg-deb: building package 'r-recommended' in '../r-recommended_3.6.1-2~bustercran.0_all.deb'.
 dpkg-genbuildinfo
 dpkg-genchanges -sa >../r-base_3.6.1-2~bustercran.0_i386.changes
dpkg-genchanges: warning: the current version (3.6.1-2~bustercran.0) is earlier than the previous one (3.6.1-2)
dpkg-genchanges: info: including full source code in upload
 dpkg-source --after-build .
dpkg-buildpackage: info: full upload (original source is included)
I: copying local configuration
I: Copying back the cached apt archive contents
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /var/cache/pbuilder/buster-i386/build/11622 and its subdirectories
I: Current time: Tue Jul  9 06:32:48 CEST 2019
I: pbuilder-time-stamp: 1562646768