RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-ppc64el-014 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:15:33 UTC 2017 ppc64le Buildd toolchain package versions: launchpad-buildd_144 python-lpbuildd_144 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.14. Syncing the system clock with the buildd NTP service... 25 Jun 05:12:25 ntpdate[1764]: adjust time server 10.211.37.1 offset 0.008309 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12801660', '/home/buildd/filecache-default/6f2309b02db3cfdb85003f9659f6426e55596487'] Unpacking chroot for build PACKAGEBUILD-12801660 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12801660'] Mounting chroot for build PACKAGEBUILD-12801660 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12801660', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-12801660 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12801660', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-12801660 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main ppc64el Packages [1126 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [565 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe ppc64el Packages [7957 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4756 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el Packages [77.0 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [49.0 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe ppc64el Packages [205 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [150 kB] Fetched 15.5 MB in 4s (3338 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: advancecomp apt apt-transport-https bash binutils bsdutils ca-certificates cpp-6 debianutils dmsetup dpkg dpkg-dev findutils g++-6 gcc-6 gcc-6-base init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libcc1-0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libip4tc0 libitm1 libkmod2 libkrb5-26-heimdal libldap-2.4-2 libldap-common libmount1 libperl5.24 libpng16-16 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount openssl passwd perl perl-base perl-modules-5.24 systemd systemd-sysv tzdata util-linux 77 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 47.3 MB of archives. After this operation, 967 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main ppc64el debianutils ppc64el 4.8.1.1 [85.9 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main ppc64el bash ppc64el 4.4-5ubuntu1 [644 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main ppc64el bsdutils ppc64el 1:2.29-1ubuntu3 [54.8 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main ppc64el dpkg ppc64el 1.18.24ubuntu1 [1122 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main ppc64el findutils ppc64el 4.6.0+git+20170606-2 [299 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main ppc64el login ppc64el 1:4.2-3.2ubuntu2 [301 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main ppc64el util-linux ppc64el 2.29-1ubuntu3 [881 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main ppc64el mount ppc64el 2.29-1ubuntu3 [126 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libperl5.24 ppc64el 5.24.1-4ubuntu1 [3307 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el perl ppc64el 5.24.1-4ubuntu1 [219 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el perl-base ppc64el 5.24.1-4ubuntu1 [1229 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el perl-modules-5.24 all 5.24.1-4ubuntu1 [2663 kB] Get:13 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el init-system-helpers all 1.48 [37.8 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main ppc64el gcc-7-base ppc64el 7.1.0-7ubuntu1 [18.5 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main ppc64el libgcc1 ppc64el 1:7.1.0-7ubuntu1 [29.7 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main ppc64el libstdc++6 ppc64el 7.1.0-7ubuntu1 [446 kB] Get:17 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libapt-pkg5.0 ppc64el 1.4.6 [820 kB] Get:18 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el apt ppc64el 1.4.6 [1132 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main ppc64el libip4tc0 ppc64el 1.6.0+snapshot20161117-6ubuntu1 [20.3 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main ppc64el libapparmor1 ppc64el 2.11.0-2ubuntu8 [29.4 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main ppc64el libaudit-common all 1:2.6.6-1ubuntu2 [4626 B] Get:22 http://ftpmaster.internal/ubuntu artful/main ppc64el libaudit1 ppc64el 1:2.6.6-1ubuntu2 [40.2 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main ppc64el libselinux1 ppc64el 2.6-3build1 [67.0 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main ppc64el libsemanage-common all 2.6-2build1 [6738 B] Get:25 http://ftpmaster.internal/ubuntu artful/main ppc64el libsemanage1 ppc64el 2.6-2build1 [75.7 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main ppc64el passwd ppc64el 1:4.2-3.2ubuntu2 [754 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main ppc64el libuuid1 ppc64el 2.29-1ubuntu3 [15.2 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main ppc64el libblkid1 ppc64el 2.29-1ubuntu3 [102 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main ppc64el libgcrypt20 ppc64el 1.7.7-2 [415 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main ppc64el libkmod2 ppc64el 24-1ubuntu1 [36.4 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main ppc64el libmount1 ppc64el 2.29-1ubuntu3 [107 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main ppc64el systemd ppc64el 233-8ubuntu1 [2256 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main ppc64el libsystemd0 ppc64el 233-8ubuntu1 [203 kB] Get:34 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el init ppc64el 1.48 [5808 B] Get:35 http://ftpmaster.internal/ubuntu artful/main ppc64el systemd-sysv ppc64el 233-8ubuntu1 [12.7 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main ppc64el libfdisk1 ppc64el 2.29-1ubuntu3 [132 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main ppc64el libsmartcols1 ppc64el 2.29-1ubuntu3 [64.2 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main ppc64el libudev1 ppc64el 233-8ubuntu1 [54.7 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.137-2ubuntu2 [128 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main ppc64el dmsetup ppc64el 2:1.02.137-2ubuntu2 [69.8 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main ppc64el libroken18-heimdal ppc64el 7.1.0+dfsg-13 [39.0 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main ppc64el libasn1-8-heimdal ppc64el 7.1.0+dfsg-13 [137 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main ppc64el libtasn1-6 ppc64el 4.12-2 [35.8 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main ppc64el libgnutls30 ppc64el 3.5.8-6ubuntu1 [576 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main ppc64el libheimbase1-heimdal ppc64el 7.1.0+dfsg-13 [28.4 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main ppc64el libhcrypto4-heimdal ppc64el 7.1.0+dfsg-13 [94.5 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main ppc64el libwind0-heimdal ppc64el 7.1.0+dfsg-13 [47.9 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main ppc64el libhx509-5-heimdal ppc64el 7.1.0+dfsg-13 [101 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main ppc64el libsqlite3-0 ppc64el 3.16.2-5 [439 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main ppc64el libkrb5-26-heimdal ppc64el 7.1.0+dfsg-13 [194 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main ppc64el libheimntlm0-heimdal ppc64el 7.1.0+dfsg-13 [15.6 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main ppc64el libgssapi3-heimdal ppc64el 7.1.0+dfsg-13 [86.5 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main ppc64el libldap-2.4-2 ppc64el 2.4.44+dfsg-5ubuntu1 [145 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main ppc64el libldap-common all 2.4.44+dfsg-5ubuntu1 [17.5 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main ppc64el libssl1.0.0 ppc64el 1.0.2g-1ubuntu13 [822 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main ppc64el tzdata all 2017b-2 [203 kB] Get:57 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el apt-transport-https ppc64el 1.4.6 [38.9 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main ppc64el openssl ppc64el 1.0.2g-1ubuntu13 [483 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main ppc64el ca-certificates all 20161130+nmu1 [186 kB] Get:60 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libpng16-16 ppc64el 1.6.29-3 [190 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main ppc64el advancecomp ppc64el 2.0-1 [255 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main ppc64el binutils ppc64el 2.28-6ubuntu1 [2336 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main ppc64el libgomp1 ppc64el 7.1.0-7ubuntu1 [69.3 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main ppc64el libitm1 ppc64el 7.1.0-7ubuntu1 [29.6 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main ppc64el libubsan0 ppc64el 7.1.0-7ubuntu1 [128 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main ppc64el libatomic1 ppc64el 7.1.0-7ubuntu1 [8468 B] Get:67 http://ftpmaster.internal/ubuntu artful/main ppc64el libasan3 ppc64el 6.3.0-19ubuntu1 [278 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main ppc64el g++-6 ppc64el 6.3.0-19ubuntu1 [6432 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main ppc64el libstdc++-6-dev ppc64el 6.3.0-19ubuntu1 [1442 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main ppc64el gcc-6 ppc64el 6.3.0-19ubuntu1 [6243 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main ppc64el libgcc-6-dev ppc64el 6.3.0-19ubuntu1 [659 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main ppc64el libcc1-0 ppc64el 7.1.0-7ubuntu1 [39.1 kB] Get:73 http://ftpmaster.internal/ubuntu artful/main ppc64el cpp-6 ppc64el 6.3.0-19ubuntu1 [5672 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main ppc64el gcc-6-base ppc64el 6.3.0-19ubuntu1 [17.4 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main ppc64el dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main ppc64el libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main ppc64el libusb-0.1-4 ppc64el 2:0.1.12-31 [16.0 kB] Get:78 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el linux-libc-dev ppc64el 4.11.0-8.13 [911 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.3 MB in 6s (6756 kB/s) (Reading database ... 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Selecting previously unselected package gcc-7-base:ppc64el. (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 ... 12321 files and directories currently installed.) Preparing to unpack .../gcc-7-base_7.1.0-7ubuntu1_ppc64el.deb ... Unpacking gcc-7-base:ppc64el (7.1.0-7ubuntu1) ... Setting up gcc-7-base:ppc64el (7.1.0-7ubuntu1) ... (Reading database ... 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Setting up systemd (233-8ubuntu1) ... Installing new version of config file /etc/systemd/resolved.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (Reading database ... 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Preparing to unpack .../37-libdpkg-perl_1.18.24ubuntu1_all.deb ... Unpacking libdpkg-perl (1.18.24ubuntu1) over (1.18.23ubuntu4) ... Preparing to unpack .../38-libusb-0.1-4_2%3a0.1.12-31_ppc64el.deb ... Unpacking libusb-0.1-4:ppc64el (2:0.1.12-31) over (2:0.1.12-30) ... Preparing to unpack .../39-linux-libc-dev_4.11.0-8.13_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (4.11.0-8.13) over (4.10.0-20.22) ... Setting up libgomp1:ppc64el (7.1.0-7ubuntu1) ... Setting up libatomic1:ppc64el (7.1.0-7ubuntu1) ... Setting up perl-modules-5.24 (5.24.1-4ubuntu1) ... Setting up libperl5.24:ppc64el (5.24.1-4ubuntu1) ... Setting up libcc1-0:ppc64el (7.1.0-7ubuntu1) ... Setting up apt-transport-https (1.4.6) ... Setting up libssl1.0.0:ppc64el (1.0.2g-1ubuntu13) ... Setting up libpng16-16:ppc64el (1.6.29-3) ... Setting up libldap-common (2.4.44+dfsg-5ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Jun 25 05:12:53 UTC 2017. Universal Time is now: Sun Jun 25 05:12:53 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (233-8ubuntu1) ... Setting up libubsan0:ppc64el (7.1.0-7ubuntu1) ... Setting up gcc-6-base:ppc64el (6.3.0-19ubuntu1) ... Setting up linux-libc-dev:ppc64el (4.11.0-8.13) ... Setting up advancecomp (2.0-1) ... Setting up libroken18-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up libdevmapper1.02.1:ppc64el (2:1.02.137-2ubuntu2) ... Setting up libtasn1-6:ppc64el (4.12-2) ... Setting up perl (5.24.1-4ubuntu1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up libheimbase1-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up openssl (1.0.2g-1ubuntu13) ... Setting up libsqlite3-0:ppc64el (3.16.2-5) ... Setting up dmsetup (2:1.02.137-2ubuntu2) ... Setting up binutils (2.28-6ubuntu1) ... Setting up cpp-6 (6.3.0-19ubuntu1) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 7 removed; done. Setting up libusb-0.1-4:ppc64el (2:0.1.12-31) ... Setting up libitm1:ppc64el (7.1.0-7ubuntu1) ... Setting up libasan3:ppc64el (6.3.0-19ubuntu1) ... Setting up libgcc-6-dev:ppc64el (6.3.0-19ubuntu1) ... Setting up libstdc++-6-dev:ppc64el (6.3.0-19ubuntu1) ... Setting up libwind0-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up init (1.48) ... Setting up libasn1-8-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up libhcrypto4-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up libgnutls30:ppc64el (3.5.8-6ubuntu1) ... Setting up libdpkg-perl (1.18.24ubuntu1) ... Setting up libhx509-5-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up gcc-6 (6.3.0-19ubuntu1) ... Setting up g++-6 (6.3.0-19ubuntu1) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up libkrb5-26-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up libheimntlm0-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up libgssapi3-heimdal:ppc64el (7.1.0+dfsg-13) ... Setting up libldap-2.4-2:ppc64el (2.4.44+dfsg-5ubuntu1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12801660', 'ppc64el', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=ppc64el', '--dist=artful-proposed', '--purge=never', '--nolog', 'r-base_3.4.0.20170622-1.dsc'] Initiating build PACKAGEBUILD-12801660 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:15:33 UTC 2017 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-ppc64el-014.buildd +==============================================================================+ | r-base 3.4.0.20170622-1 (ppc64el) 25 Jun 2017 05:12 | +==============================================================================+ Package: r-base Version: 3.4.0.20170622-1 Source Version: 3.4.0.20170622-1 Distribution: artful-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/r-base-Q05OXR/r-base-3.4.0.20170622' with '<>' I: NOTICE: Log filtering will replace 'build/r-base-Q05OXR' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12801660/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- r-base_3.4.0.20170622-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-KTL8b6/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-KTL8b6/apt_archive ./ InRelease Get:2 copy:/<>/resolver-KTL8b6/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-KTL8b6/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-KTL8b6/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-KTL8b6/apt_archive ./ Packages [531 B] Fetched 2864 B in 0s (237 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 780 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-KTL8b6/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [780 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 780 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (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 ... 12359 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk, mpack, bash-completion Filtered Build-Depends: gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk, mpack, bash-completion dpkg-deb: building package 'sbuild-build-depends-r-base-dummy' in '/<>/resolver-4Ai_Uk/apt_archive/sbuild-build-depends-r-base-dummy.deb'. Ign:1 copy:/<>/resolver-4Ai_Uk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4Ai_Uk/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-4Ai_Uk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4Ai_Uk/apt_archive ./ Sources [507 B] Get:5 copy:/<>/resolver-4Ai_Uk/apt_archive ./ Packages [801 B] Fetched 3427 B in 0s (317 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install r-base build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adwaita-icon-theme autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils ca-certificates-java debhelper default-jdk default-jdk-headless default-jre default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism file fontconfig fontconfig-config fonts-cabin fonts-comfortaa fonts-croscore fonts-crosextra-caladea fonts-crosextra-carlito fonts-dejavu-core fonts-dejavu-extra fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine fonts-lmodern fonts-lobster fonts-lobstertwo fonts-noto-hinted fonts-oflb-asana-math fonts-roboto-hinted fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix gettext gettext-base gfortran gfortran-6 gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme icu-devtools intltool-debian java-common libarchive-zip-perl libasound2 libasound2-data libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libblas-common libblas-dev libblas3 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 libcups2 libcupsimage2 libcurl3 libcurl4-openssl-dev libdatrie1 libdbus-1-3 libdrm-amdgpu1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libflac8 libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-6-dev libgfortran3 libgif7 libgirepository-1.0-1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu-dev libicu57 libijs-0.35 libjbig-dev libjbig0 libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libkpathsea6 liblapack-dev liblapack3 liblcms2-2 libllvm4.0 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmpdec2 libncurses5-dev libnspr4 libnss3 libogg0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpoppler64 libpotrace0 libptexenc1 libpthread-stubs0-dev libpulse0 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libreadline-dev librsvg2-2 librsvg2-common libsensors4 libsigsegv2 libsm-dev libsm6 libsndfile1 libsynctex1 libtcl8.6 libtexlua52 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtinfo-dev libtk8.6 libtool libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb1 libxcb1-dev libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont1 libxfont2 libxft-dev libxft2 libxi6 libxinerama1 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-8-jdk openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless pkg-config po-debconf poppler-data preview-latex-style python python-minimal python2.7 python2.7-minimal python3 python3-minimal python3.5 python3.5-minimal shared-mime-info t1utils tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-plain-generic tk8.6 tk8.6-dev ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ubuntu-mono ucf x11-common x11-utils x11-xkb-utils x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base xfonts-encodings xfonts-utils xkb-data xorg-sgml-doctools xserver-common xtrans-dev xvfb zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist whois vacation dh-make default-java-plugin fontforge gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-6-doc libgfortran3-dbg libcoarrays-dev groff libasound2-plugins alsa-utils liblapack-doc-man liblapack-doc libcairo2-doc cups-common libcurl4-doc libcurl3-dbg libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssl1.0-dev | libssl-dev libglib2.0-doc gvfs libice-doc icu-doc liblcms2-utils liblzma-doc ncurses-doc imagemagick libpango1.0-doc pcscd pulseaudio readline-doc librsvg2-bin lm-sensors libsm-doc libtool-doc gcj-jdk libxcb-doc libxext-doc libxt-doc m4-doc less www-browser mail-transport-agent inews openjdk-8-demo openjdk-8-source visualvm icedtea-8-plugin libnss-mdns fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei fonts-wqy-zenhei fonts-indic libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.5-venv python3.5-doc tcl-tclreadline tcl8.6-doc texinfo-doc-nonfree gv | postscript-viewer perl-tk xpdf-reader | pdf-viewer chktex dvidvi dvipng fragmaster lacheck latexdiff latexmk purifyeps xindy cm-super python-pygments libfile-which-perl libspreadsheet-parseexcel-perl texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby tk8.6-doc mesa-utils gvfs-bin Recommended packages: curl | wget | lynx-cur at-spi2-core bzip2-doc libcupsfilters1 dbus libarchive-cpio-perl libgdk-pixbuf2.0-bin libtxc-dxtn-s2tc | libtxc-dxtn-s2tc0 | libtxc-dxtn0 xdg-user-dirs fonts-droid-fallback libgail-common libgtk2.0-bin libpng-tools libltdl-dev tcpd libx11-doc libxml-sax-expat-perl xml-core libmail-sendmail-perl lmodern ruby wish ghostscript libfile-homedir-perl libyaml-tiny-perl ruby | ruby-interpreter texlive-fonts-extra-doc tex-gyre texlive-fonts-recommended-doc tipa texlive-latex-base-doc texlive-latex-extra-doc prosper texlive-latex-recommended-doc texlive-pictures-doc tk openjade xterm | x-terminal-emulator libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-xserver-utils The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: adwaita-icon-theme autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils ca-certificates-java debhelper default-jdk default-jdk-headless default-jre default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism file fontconfig fontconfig-config fonts-cabin fonts-comfortaa fonts-croscore fonts-crosextra-caladea fonts-crosextra-carlito fonts-dejavu-core fonts-dejavu-extra fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine fonts-lmodern fonts-lobster fonts-lobstertwo fonts-noto-hinted fonts-oflb-asana-math fonts-roboto-hinted fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix gettext gettext-base gfortran gfortran-6 gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme icu-devtools intltool-debian java-common libarchive-zip-perl libasound2 libasound2-data libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libblas-common libblas-dev libblas3 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 libcups2 libcupsimage2 libcurl3 libcurl4-openssl-dev libdatrie1 libdbus-1-3 libdrm-amdgpu1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libflac8 libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-6-dev libgfortran3 libgif7 libgirepository-1.0-1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu-dev libicu57 libijs-0.35 libjbig-dev libjbig0 libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libkpathsea6 liblapack-dev liblapack3 liblcms2-2 libllvm4.0 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmpdec2 libncurses5-dev libnspr4 libnss3 libogg0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpoppler64 libpotrace0 libptexenc1 libpthread-stubs0-dev libpulse0 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libreadline-dev librsvg2-2 librsvg2-common libsensors4 libsigsegv2 libsm-dev libsm6 libsndfile1 libsynctex1 libtcl8.6 libtexlua52 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtinfo-dev libtk8.6 libtool libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb1 libxcb1-dev libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont1 libxfont2 libxft-dev libxft2 libxi6 libxinerama1 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-8-jdk openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless pkg-config po-debconf poppler-data preview-latex-style python python-minimal python2.7 python2.7-minimal python3 python3-minimal python3.5 python3.5-minimal sbuild-build-depends-r-base-dummy shared-mime-info t1utils tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-plain-generic tk8.6 tk8.6-dev ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ubuntu-mono ucf x11-common x11-utils x11-xkb-utils x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base xfonts-encodings xfonts-utils xkb-data xorg-sgml-doctools xserver-common xtrans-dev xvfb zlib1g-dev 0 upgraded, 333 newly installed, 1 to remove and 0 not upgraded. Need to get 573 MB of archives. After this operation, 2013 MB of additional disk space will be used. Get:1 copy:/<>/resolver-4Ai_Uk/apt_archive ./ sbuild-build-depends-r-base-dummy 0.invalid.0 [1052 B] Get:2 http://ftpmaster.internal/ubuntu artful/main ppc64el libpython3.5-minimal ppc64el 3.5.3-3 [535 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libexpat1 ppc64el 2.2.1-2 [75.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main ppc64el python3.5-minimal ppc64el 3.5.3-3 [1654 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main ppc64el python3-minimal ppc64el 3.5.3-1ubuntu3 [23.4 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main ppc64el mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main ppc64el libmpdec2 ppc64el 2.4.2-1 [82.6 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main ppc64el libpython3.5-stdlib ppc64el 3.5.3-3 [2175 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main ppc64el python3.5 ppc64el 3.5.3-3 [179 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main ppc64el libpython3-stdlib ppc64el 3.5.3-1ubuntu3 [6868 B] Get:11 http://ftpmaster.internal/ubuntu artful/main ppc64el dh-python all 2.20170125 [83.7 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main ppc64el python3 ppc64el 3.5.3-1ubuntu3 [8708 B] Get:13 http://ftpmaster.internal/ubuntu artful/main ppc64el bash-completion all 1:2.1-4.3ubuntu1 [150 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main ppc64el libxau6 ppc64el 1:1.0.8-1 [7460 B] Get:15 http://ftpmaster.internal/ubuntu artful/main ppc64el libbsd0 ppc64el 0.8.3-1 [48.2 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main ppc64el libxdmcp6 ppc64el 1:1.1.2-3 [11.0 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb1 ppc64el 1.11.1-1ubuntu1 [37.6 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main ppc64el libx11-data all 2:1.6.4-3 [114 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main ppc64el libx11-6 ppc64el 2:1.6.4-3 [566 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main ppc64el libxext6 ppc64el 2:1.3.3-1 [30.7 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main ppc64el groff-base ppc64el 1.22.3-9 [1361 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main ppc64el bsdmainutils ppc64el 9.0.12ubuntu1 [179 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main ppc64el libpipeline1 ppc64el 1.4.1-2 [24.1 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main ppc64el man-db ppc64el 2.7.6.1-2 [890 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main ppc64el fonts-dejavu-core all 2.37-1 [1041 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main ppc64el fonts-freefont-ttf all 20120503-6 [4203 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main ppc64el ucf all 3.0036 [52.9 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main ppc64el fontconfig-config all 2.11.94-0ubuntu2 [49.9 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main ppc64el libfreetype6 ppc64el 2.6.3-3.2ubuntu1 [335 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main ppc64el libfontconfig1 ppc64el 2.11.94-0ubuntu2 [144 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main ppc64el fontconfig ppc64el 2.11.94-0ubuntu2 [178 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main ppc64el fonts-lato all 2.0-2 [2698 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main ppc64el libjpeg-turbo8 ppc64el 1.5.1-0ubuntu1 [150 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main ppc64el liblzo2-2 ppc64el 2.08-1.2 [67.2 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main ppc64el libogg0 ppc64el 1.3.2-1 [17.1 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main ppc64el libpcrecpp0v5 ppc64el 2:8.39-3 [15.8 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main ppc64el x11-common all 1:7.7+19ubuntu1 [22.1 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main ppc64el libice6 ppc64el 2:1.0.9-2 [38.0 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main ppc64el libsm6 ppc64el 2:1.2.2-1 [15.1 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main ppc64el libxfixes3 ppc64el 1:5.0.3-1 [10.6 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main ppc64el libxrender1 ppc64el 1:0.9.10-1 [17.6 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcursor1 ppc64el 1:1.1.14-1 [21.6 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main ppc64el libxdamage1 ppc64el 1:1.1.4-2 [6820 B] Get:44 http://ftpmaster.internal/ubuntu artful/main ppc64el libxft2 ppc64el 2.3.2-1 [39.3 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main ppc64el libxinerama1 ppc64el 2:1.1.3-1 [7160 B] Get:46 http://ftpmaster.internal/ubuntu artful/main ppc64el libxshmfence1 ppc64el 1.2-1 [5170 B] Get:47 http://ftpmaster.internal/ubuntu artful/main ppc64el libxss1 ppc64el 1:1.2.2-1 [7510 B] Get:48 http://ftpmaster.internal/ubuntu artful/main ppc64el libxxf86dga1 ppc64el 2:1.1.4-1 [11.3 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main ppc64el libxxf86vm1 ppc64el 1:1.1.4-1 [10.7 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main ppc64el java-common all 0.57ubuntu1 [7492 B] Get:51 http://ftpmaster.internal/ubuntu artful/main ppc64el default-jre-headless ppc64el 2:1.8-57ubuntu1 [4118 B] Get:52 http://ftpmaster.internal/ubuntu artful/main ppc64el libnspr4 ppc64el 2:4.13.1-0ubuntu1 [101 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main ppc64el libnss3 ppc64el 2:3.28.4-0ubuntu2 [1107 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main ppc64el ca-certificates-java all 20170531+nmu1 [12.1 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main ppc64el libavahi-common-data ppc64el 0.6.32-1ubuntu1 [22.1 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main ppc64el libavahi-common3 ppc64el 0.6.32-1ubuntu1 [19.5 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main ppc64el libdbus-1-3 ppc64el 1.10.18-1ubuntu2 [159 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main ppc64el libavahi-client3 ppc64el 0.6.32-1ubuntu1 [22.5 kB] Get:59 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libcups2 ppc64el 2.2.3-2 [197 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main ppc64el liblcms2-2 ppc64el 2.7-1ubuntu1 [164 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main ppc64el libjpeg8 ppc64el 8c-2ubuntu8 [2146 B] Get:62 http://ftpmaster.internal/ubuntu artful/main ppc64el libpcsclite1 ppc64el 1.8.21-1ubuntu1 [22.9 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main ppc64el libxi6 ppc64el 2:1.7.9-1 [29.0 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main ppc64el libxtst6 ppc64el 2:1.2.3-1 [13.5 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main ppc64el openjdk-8-jre-headless ppc64el 8u131-b11-2ubuntu1 [26.6 MB] Get:66 http://ftpmaster.internal/ubuntu artful/main ppc64el poppler-data all 0.4.7-8 [1449 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main ppc64el libpython2.7-minimal ppc64el 2.7.13-2 [338 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main ppc64el python2.7-minimal ppc64el 2.7.13-2 [1344 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main ppc64el python-minimal ppc64el 2.7.13-2 [28.2 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main ppc64el libpython2.7-stdlib ppc64el 2.7.13-2 [1907 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main ppc64el python2.7 ppc64el 2.7.13-2 [229 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main ppc64el libpython-stdlib ppc64el 2.7.13-2 [7776 B] Get:73 http://ftpmaster.internal/ubuntu artful/main ppc64el python ppc64el 2.7.13-2 [139 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main ppc64el libjbig0 ppc64el 2.1-3.1 [26.4 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main ppc64el libmagic-mgc ppc64el 1:5.30-1 [181 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main ppc64el libmagic1 ppc64el 1:5.30-1 [71.8 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main ppc64el file ppc64el 1:5.30-1 [22.5 kB] Get:78 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libelf1 ppc64el 0.168-1 [40.3 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main ppc64el xkb-data all 2.19-1ubuntu1 [311 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main ppc64el gettext-base ppc64el 0.19.8.1-2ubuntu1 [48.1 kB] Get:81 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libglib2.0-0 ppc64el 2.53.2-1 [1073 kB] Get:82 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libgirepository-1.0-1 ppc64el 1.53.2-2 [74.8 kB] Get:83 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el gir1.2-glib-2.0 ppc64el 1.53.2-2 [130 kB] Get:84 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libdrm2 ppc64el 2.4.81-2 [30.8 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main ppc64el libedit2 ppc64el 3.1-20170329-1 [79.6 kB] Get:86 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libglib2.0-data all 2.53.2-1 [5198 B] Get:87 http://ftpmaster.internal/ubuntu artful/main ppc64el libicu57 ppc64el 57.1-6 [7785 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main ppc64el libxml2 ppc64el 2.9.4+dfsg1-2.2ubuntu1 [609 kB] Get:89 http://ftpmaster.internal/ubuntu artful/main ppc64el libxmuu1 ppc64el 2:1.1.2-2 [9642 B] Get:90 http://ftpmaster.internal/ubuntu artful/main ppc64el shared-mime-info ppc64el 1.8-1 [421 kB] Get:91 http://ftpmaster.internal/ubuntu artful/main ppc64el xauth ppc64el 1:1.0.9-1ubuntu2 [21.5 kB] Get:92 http://ftpmaster.internal/ubuntu artful/main ppc64el hicolor-icon-theme all 0.15-1 [8378 B] Get:93 http://ftpmaster.internal/ubuntu artful/main ppc64el libtiff5 ppc64el 4.0.8-2 [154 kB] Get:94 http://ftpmaster.internal/ubuntu artful/main ppc64el libgdk-pixbuf2.0-common all 2.36.5-3 [4602 B] Get:95 http://ftpmaster.internal/ubuntu artful/main ppc64el libgdk-pixbuf2.0-0 ppc64el 2.36.5-3 [185 kB] Get:96 http://ftpmaster.internal/ubuntu artful/main ppc64el gtk-update-icon-cache ppc64el 3.22.15-0ubuntu2 [27.5 kB] Get:97 http://ftpmaster.internal/ubuntu artful/main ppc64el libpixman-1-0 ppc64el 0.34.0-1 [201 kB] Get:98 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-render0 ppc64el 1.11.1-1ubuntu1 [10.6 kB] Get:99 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-shm0 ppc64el 1.11.1-1ubuntu1 [5522 B] Get:100 http://ftpmaster.internal/ubuntu artful/main ppc64el libcairo2 ppc64el 1.14.8-1 [602 kB] Get:101 http://ftpmaster.internal/ubuntu artful/main ppc64el libcroco3 ppc64el 0.6.11-3 [74.4 kB] Get:102 http://ftpmaster.internal/ubuntu artful/main ppc64el libthai-data all 0.1.26-1 [131 kB] Get:103 http://ftpmaster.internal/ubuntu artful/main ppc64el libdatrie1 ppc64el 0.2.10-4 [16.8 kB] Get:104 http://ftpmaster.internal/ubuntu artful/main ppc64el libthai0 ppc64el 0.1.26-1 [17.2 kB] Get:105 http://ftpmaster.internal/ubuntu artful/main ppc64el libpango-1.0-0 ppc64el 1.40.5-1 [152 kB] Get:106 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libgraphite2-3 ppc64el 1.3.10-2 [66.8 kB] Get:107 http://ftpmaster.internal/ubuntu artful/main ppc64el libharfbuzz0b ppc64el 1.4.2-1 [205 kB] Get:108 http://ftpmaster.internal/ubuntu artful/main ppc64el libpangoft2-1.0-0 ppc64el 1.40.5-1 [33.5 kB] Get:109 http://ftpmaster.internal/ubuntu artful/main ppc64el libpangocairo-1.0-0 ppc64el 1.40.5-1 [20.2 kB] Get:110 http://ftpmaster.internal/ubuntu artful/main ppc64el librsvg2-2 ppc64el 2.40.16-2~svn1 [103 kB] Get:111 http://ftpmaster.internal/ubuntu artful/main ppc64el librsvg2-common ppc64el 2.40.16-2~svn1 [5224 B] Get:112 http://ftpmaster.internal/ubuntu artful/main ppc64el humanity-icon-theme all 0.6.13 [1288 kB] Get:113 http://ftpmaster.internal/ubuntu artful/main ppc64el ubuntu-mono all 16.10+17.10.20170619-0ubuntu1 [160 kB] Get:114 http://ftpmaster.internal/ubuntu artful/main ppc64el adwaita-icon-theme all 3.24.0-0ubuntu1 [3423 kB] Get:115 http://ftpmaster.internal/ubuntu artful/main ppc64el libsigsegv2 ppc64el 2.10-5 [14.2 kB] Get:116 http://ftpmaster.internal/ubuntu artful/main ppc64el m4 ppc64el 1.4.18-1 [202 kB] Get:117 http://ftpmaster.internal/ubuntu artful/main ppc64el autoconf all 2.69-10 [321 kB] Get:118 http://ftpmaster.internal/ubuntu artful/main ppc64el autotools-dev all 20161112.1 [39.5 kB] Get:119 http://ftpmaster.internal/ubuntu artful/main ppc64el automake all 1:1.15-6ubuntu1 [509 kB] Get:120 http://ftpmaster.internal/ubuntu artful/main ppc64el autopoint all 0.19.8.1-2ubuntu1 [411 kB] Get:121 http://ftpmaster.internal/ubuntu artful/main ppc64el libbison-dev ppc64el 2:3.0.4.dfsg-1build1 [339 kB] Get:122 http://ftpmaster.internal/ubuntu artful/main ppc64el bison ppc64el 2:3.0.4.dfsg-1build1 [263 kB] Get:123 http://ftpmaster.internal/ubuntu artful/main ppc64el libtool all 2.4.6-2 [194 kB] Get:124 http://ftpmaster.internal/ubuntu artful/main ppc64el dh-autoreconf all 14 [15.5 kB] Get:125 http://ftpmaster.internal/ubuntu artful/main ppc64el libarchive-zip-perl all 1.59-1 [84.0 kB] Get:126 http://ftpmaster.internal/ubuntu artful/main ppc64el libfile-stripnondeterminism-perl all 0.035-2 [13.3 kB] Get:127 http://ftpmaster.internal/ubuntu artful/main ppc64el libtimedate-perl all 2.3000-2 [37.5 kB] Get:128 http://ftpmaster.internal/ubuntu artful/main ppc64el dh-strip-nondeterminism all 0.035-2 [5018 B] Get:129 http://ftpmaster.internal/ubuntu artful/main ppc64el gettext ppc64el 0.19.8.1-2ubuntu1 [1111 kB] Get:130 http://ftpmaster.internal/ubuntu artful/main ppc64el intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:131 http://ftpmaster.internal/ubuntu artful/main ppc64el po-debconf all 1.0.20 [232 kB] Get:132 http://ftpmaster.internal/ubuntu artful/main ppc64el debhelper all 10.4ubuntu3 [876 kB] Get:133 http://ftpmaster.internal/ubuntu artful/main ppc64el libgtk2.0-common all 2.24.31-1ubuntu1 [124 kB] Get:134 http://ftpmaster.internal/ubuntu artful/main ppc64el libatk1.0-data all 2.22.0-1 [2844 B] Get:135 http://ftpmaster.internal/ubuntu artful/main ppc64el libatk1.0-0 ppc64el 2.22.0-1 [38.3 kB] Get:136 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcomposite1 ppc64el 1:0.4.4-2 [6940 B] Get:137 http://ftpmaster.internal/ubuntu artful/main ppc64el libxrandr2 ppc64el 2:1.5.1-1 [17.3 kB] Get:138 http://ftpmaster.internal/ubuntu artful/main ppc64el libgtk2.0-0 ppc64el 2.24.31-1ubuntu1 [1534 kB] Get:139 http://ftpmaster.internal/ubuntu artful/main ppc64el libglapi-mesa ppc64el 17.1.2-2ubuntu2 [27.5 kB] Get:140 http://ftpmaster.internal/ubuntu artful/main ppc64el libx11-xcb1 ppc64el 2:1.6.4-3 [9832 B] Get:141 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-dri2-0 ppc64el 1.11.1-1ubuntu1 [6692 B] Get:142 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-dri3-0 ppc64el 1.11.1-1ubuntu1 [5222 B] Get:143 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-glx0 ppc64el 1.11.1-1ubuntu1 [18.8 kB] Get:144 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-present0 ppc64el 1.11.1-1ubuntu1 [5270 B] Get:145 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-sync1 ppc64el 1.11.1-1ubuntu1 [8078 B] Get:146 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libdrm-amdgpu1 ppc64el 2.4.81-2 [19.4 kB] Get:147 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libdrm-nouveau2 ppc64el 2.4.81-2 [17.4 kB] Get:148 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libdrm-radeon1 ppc64el 2.4.81-2 [22.9 kB] Get:149 http://ftpmaster.internal/ubuntu artful/main ppc64el libllvm4.0 ppc64el 1:4.0.1-1 [11.1 MB] Get:150 http://ftpmaster.internal/ubuntu artful/main ppc64el libsensors4 ppc64el 1:3.4.0-4 [28.6 kB] Get:151 http://ftpmaster.internal/ubuntu artful/main ppc64el libgl1-mesa-dri ppc64el 17.1.2-2ubuntu2 [5367 kB] Get:152 http://ftpmaster.internal/ubuntu artful/main ppc64el libgl1-mesa-glx ppc64el 17.1.2-2ubuntu2 [129 kB] Get:153 http://ftpmaster.internal/ubuntu artful/main ppc64el libatspi2.0-0 ppc64el 2.22.0-5ubuntu4 [54.3 kB] Get:154 http://ftpmaster.internal/ubuntu artful/main ppc64el libatk-bridge2.0-0 ppc64el 2.22.0-1ubuntu1 [49.4 kB] Get:155 http://ftpmaster.internal/ubuntu artful/main ppc64el libfontenc1 ppc64el 1:1.1.3-1 [13.9 kB] Get:156 http://ftpmaster.internal/ubuntu artful/main ppc64el libxt6 ppc64el 1:1.1.5-1 [152 kB] Get:157 http://ftpmaster.internal/ubuntu artful/main ppc64el libxmu6 ppc64el 2:1.1.2-2 [43.4 kB] Get:158 http://ftpmaster.internal/ubuntu artful/main ppc64el libxpm4 ppc64el 1:3.5.12-1 [35.9 kB] Get:159 http://ftpmaster.internal/ubuntu artful/main ppc64el libxaw7 ppc64el 2:1.0.13-1 [176 kB] Get:160 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-shape0 ppc64el 1.11.1-1ubuntu1 [5658 B] Get:161 http://ftpmaster.internal/ubuntu artful/main ppc64el libxv1 ppc64el 2:1.0.11-1 [10.8 kB] Get:162 http://ftpmaster.internal/ubuntu artful/main ppc64el x11-utils ppc64el 7.7+3build1 [202 kB] Get:163 http://ftpmaster.internal/ubuntu artful/main ppc64el libatk-wrapper-java all 0.33.3-13 [34.1 kB] Get:164 http://ftpmaster.internal/ubuntu artful/main ppc64el libatk-wrapper-java-jni ppc64el 0.33.3-13 [24.1 kB] Get:165 http://ftpmaster.internal/ubuntu artful/main ppc64el libasound2-data all 1.1.3-5 [36.1 kB] Get:166 http://ftpmaster.internal/ubuntu artful/main ppc64el libasound2 ppc64el 1.1.3-5 [336 kB] Get:167 http://ftpmaster.internal/ubuntu artful/main ppc64el libgif7 ppc64el 5.1.4-0.4 [32.3 kB] Get:168 http://ftpmaster.internal/ubuntu artful/main ppc64el libasyncns0 ppc64el 0.8-6 [11.8 kB] Get:169 http://ftpmaster.internal/ubuntu artful/main ppc64el libflac8 ppc64el 1.3.2-1 [189 kB] Get:170 http://ftpmaster.internal/ubuntu artful/main ppc64el libvorbis0a ppc64el 1.3.5-4 [109 kB] Get:171 http://ftpmaster.internal/ubuntu artful/main ppc64el libvorbisenc2 ppc64el 1.3.5-4 [77.2 kB] Get:172 http://ftpmaster.internal/ubuntu artful/main ppc64el libsndfile1 ppc64el 1.0.28-2 [196 kB] Get:173 http://ftpmaster.internal/ubuntu artful/main ppc64el libwrap0 ppc64el 7.6.q-26 [47.1 kB] Get:174 http://ftpmaster.internal/ubuntu artful/main ppc64el libpulse0 ppc64el 1:10.0-1ubuntu2 [226 kB] Get:175 http://ftpmaster.internal/ubuntu artful/main ppc64el openjdk-8-jre ppc64el 8u131-b11-2ubuntu1 [63.9 kB] Get:176 http://ftpmaster.internal/ubuntu artful/main ppc64el default-jre ppc64el 2:1.8-57ubuntu1 [982 B] Get:177 http://ftpmaster.internal/ubuntu artful/main ppc64el openjdk-8-jdk-headless ppc64el 8u131-b11-2ubuntu1 [6262 kB] Get:178 http://ftpmaster.internal/ubuntu artful/main ppc64el default-jdk-headless ppc64el 2:1.8-57ubuntu1 [984 B] Get:179 http://ftpmaster.internal/ubuntu artful/main ppc64el openjdk-8-jdk ppc64el 8u131-b11-2ubuntu1 [464 kB] Get:180 http://ftpmaster.internal/ubuntu artful/main ppc64el default-jdk ppc64el 2:1.8-57ubuntu1 [968 B] Get:181 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-cabin all 1.5-2 [140 kB] Get:182 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-comfortaa all 2.003-1 [131 kB] Get:183 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-croscore all 20161116-1 [2134 kB] Get:184 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-crosextra-caladea all 20130214-1 [82.3 kB] Get:185 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-crosextra-carlito all 20130920-1 [742 kB] Get:186 http://ftpmaster.internal/ubuntu artful/main ppc64el fonts-dejavu-extra all 2.37-1 [1953 kB] Get:187 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-ebgaramond all 0.016-1 [474 kB] Get:188 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-ebgaramond-extra all 0.016-1 [2157 kB] Get:189 http://ftpmaster.internal/ubuntu artful/main ppc64el fonts-font-awesome all 4.7.0~dfsg-1 [513 kB] Get:190 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-freefont-otf all 20120503-6 [3053 kB] Get:191 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-gfs-artemisia all 1.1-5 [260 kB] Get:192 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-gfs-complutum all 1.1-6 [41.6 kB] Get:193 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-gfs-didot all 1.1-6 [278 kB] Get:194 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-gfs-neohellenic all 1.1-6 [215 kB] Get:195 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-gfs-olga all 1.1-5 [33.4 kB] Get:196 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-gfs-solomos all 1.1-5 [40.7 kB] Get:197 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-junicode all 0.7.8-2 [642 kB] Get:198 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-linuxlibertine all 5.3.0-2 [1688 kB] Get:199 http://ftpmaster.internal/ubuntu artful/main ppc64el fonts-lmodern all 2.004.5-3 [4551 kB] Get:200 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-lobster all 2.0-2 [38.7 kB] Get:201 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-lobstertwo all 2.0-2 [92.7 kB] Get:202 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-noto-hinted all 20161116-1 [5069 kB] Get:203 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-oflb-asana-math all 000.907-6 [246 kB] Get:204 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-roboto-hinted all 2:0~20160106-2 [2918 kB] Get:205 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-sil-gentium all 20081126:1.03-1 [247 kB] Get:206 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-sil-gentium-basic all 1.1-7 [379 kB] Get:207 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-sil-gentiumplus all 5.000-1 [2805 kB] Get:208 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-sil-gentiumplus-compact all 5.000-2 [1514 kB] Get:209 http://ftpmaster.internal/ubuntu artful/main ppc64el libgfortran3 ppc64el 6.3.0-19ubuntu1 [225 kB] Get:210 http://ftpmaster.internal/ubuntu artful/main ppc64el libgfortran-6-dev ppc64el 6.3.0-19ubuntu1 [268 kB] Get:211 http://ftpmaster.internal/ubuntu artful/main ppc64el gfortran-6 ppc64el 6.3.0-19ubuntu1 [6001 kB] Get:212 http://ftpmaster.internal/ubuntu artful/main ppc64el gfortran ppc64el 4:6.3.0-2ubuntu1 [1270 B] Get:213 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el gir1.2-freedesktop ppc64el 1.53.2-2 [8974 B] Get:214 http://ftpmaster.internal/ubuntu artful/main ppc64el libpangoxft-1.0-0 ppc64el 1.40.5-1 [15.2 kB] Get:215 http://ftpmaster.internal/ubuntu artful/main ppc64el gir1.2-pango-1.0 ppc64el 1.40.5-1 [21.5 kB] Get:216 http://ftpmaster.internal/ubuntu artful/main ppc64el icu-devtools ppc64el 57.1-6 [179 kB] Get:217 http://ftpmaster.internal/ubuntu artful/main ppc64el libblas-common ppc64el 3.7.0-2 [5654 B] Get:218 http://ftpmaster.internal/ubuntu artful/main ppc64el libblas3 ppc64el 3.7.0-2 [178 kB] Get:219 http://ftpmaster.internal/ubuntu artful/main ppc64el libblas-dev ppc64el 3.7.0-2 [190 kB] Get:220 http://ftpmaster.internal/ubuntu artful/main ppc64el libbz2-dev ppc64el 1.0.6-8.1 [40.9 kB] Get:221 http://ftpmaster.internal/ubuntu artful/main ppc64el libcairo-gobject2 ppc64el 1.14.8-1 [17.0 kB] Get:222 http://ftpmaster.internal/ubuntu artful/main ppc64el libcairo-script-interpreter2 ppc64el 1.14.8-1 [56.5 kB] Get:223 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libexpat1-dev ppc64el 2.2.1-2 [124 kB] Get:224 http://ftpmaster.internal/ubuntu artful/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-0ubuntu1 [173 kB] Get:225 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libpng-dev ppc64el 1.6.29-3 [174 kB] Get:226 http://ftpmaster.internal/ubuntu artful/main ppc64el libfreetype6-dev ppc64el 2.6.3-3.2ubuntu1 [5215 kB] Get:227 http://ftpmaster.internal/ubuntu artful/main ppc64el pkg-config ppc64el 0.29.1-0ubuntu2 [44.1 kB] Get:228 http://ftpmaster.internal/ubuntu artful/main ppc64el libfontconfig1-dev ppc64el 2.11.94-0ubuntu2 [675 kB] Get:229 http://ftpmaster.internal/ubuntu artful/main ppc64el xorg-sgml-doctools all 1:1.11-1 [12.9 kB] Get:230 http://ftpmaster.internal/ubuntu artful/main ppc64el x11proto-core-dev all 7.0.31-1 [700 kB] Get:231 http://ftpmaster.internal/ubuntu artful/main ppc64el libxau-dev ppc64el 1:1.0.8-1 [9358 B] Get:232 http://ftpmaster.internal/ubuntu artful/main ppc64el libxdmcp-dev ppc64el 1:1.1.2-3 [26.1 kB] Get:233 http://ftpmaster.internal/ubuntu artful/main ppc64el x11proto-input-dev all 2.3.2-1 [118 kB] Get:234 http://ftpmaster.internal/ubuntu artful/main ppc64el x11proto-kb-dev all 1.0.7-1 [226 kB] Get:235 http://ftpmaster.internal/ubuntu artful/main ppc64el xtrans-dev all 1.3.5-1 [70.5 kB] Get:236 http://ftpmaster.internal/ubuntu artful/main ppc64el libpthread-stubs0-dev ppc64el 0.3-4 [3894 B] Get:237 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb1-dev ppc64el 1.11.1-1ubuntu1 [73.8 kB] Get:238 http://ftpmaster.internal/ubuntu artful/main ppc64el libx11-dev ppc64el 2:1.6.4-3 [651 kB] Get:239 http://ftpmaster.internal/ubuntu artful/main ppc64el x11proto-render-dev all 2:0.11.1-2 [20.1 kB] Get:240 http://ftpmaster.internal/ubuntu artful/main ppc64el libxrender-dev ppc64el 1:0.9.10-1 [24.1 kB] Get:241 http://ftpmaster.internal/ubuntu artful/main ppc64el x11proto-xext-dev all 7.3.0-1 [212 kB] Get:242 http://ftpmaster.internal/ubuntu artful/main ppc64el libxext-dev ppc64el 2:1.3.3-1 [86.5 kB] Get:243 http://ftpmaster.internal/ubuntu artful/main ppc64el libice-dev ppc64el 2:1.0.9-2 [48.6 kB] Get:244 http://ftpmaster.internal/ubuntu artful/main ppc64el libsm-dev ppc64el 2:1.2.2-1 [16.6 kB] Get:245 http://ftpmaster.internal/ubuntu artful/main ppc64el libpixman-1-dev ppc64el 0.34.0-1 [233 kB] Get:246 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-render0-dev ppc64el 1.11.1-1ubuntu1 [14.9 kB] Get:247 http://ftpmaster.internal/ubuntu artful/main ppc64el libxcb-shm0-dev ppc64el 1.11.1-1ubuntu1 [6534 B] Get:248 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libglib2.0-bin ppc64el 2.53.2-1 [68.5 kB] Get:249 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libglib2.0-dev-bin ppc64el 2.53.2-1 [86.9 kB] Get:250 http://ftpmaster.internal/ubuntu artful/main ppc64el libpcre16-3 ppc64el 2:8.39-3 [143 kB] Get:251 http://ftpmaster.internal/ubuntu artful/main ppc64el libpcre32-3 ppc64el 2:8.39-3 [134 kB] Get:252 http://ftpmaster.internal/ubuntu artful/main ppc64el libpcre3-dev ppc64el 2:8.39-3 [514 kB] Get:253 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libglib2.0-dev ppc64el 2.53.2-1 [1509 kB] Get:254 http://ftpmaster.internal/ubuntu artful/main ppc64el libcairo2-dev ppc64el 1.14.8-1 [670 kB] Get:255 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libcupsimage2 ppc64el 2.2.3-2 [19.7 kB] Get:256 http://ftpmaster.internal/ubuntu artful/main ppc64el libcurl3 ppc64el 7.52.1-5ubuntu1 [182 kB] Get:257 http://ftpmaster.internal/ubuntu artful/main ppc64el libcurl4-openssl-dev ppc64el 7.52.1-5ubuntu1 [268 kB] Get:258 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libgraphite2-dev ppc64el 1.3.10-2 [14.6 kB] Get:259 http://ftpmaster.internal/ubuntu artful/main ppc64el libijs-0.35 ppc64el 0.35-12 [15.0 kB] Get:260 http://ftpmaster.internal/ubuntu artful/main ppc64el libjbig2dec0 ppc64el 0.13-4.1 [56.6 kB] Get:261 http://ftpmaster.internal/ubuntu artful/main ppc64el libpaper1 ppc64el 1.1.24+nmu5ubuntu1 [13.4 kB] Get:262 http://ftpmaster.internal/ubuntu artful/main ppc64el libgs9-common all 9.19~dfsg+1-0ubuntu10 [2988 kB] Get:263 http://ftpmaster.internal/ubuntu artful/main ppc64el libgs9 ppc64el 9.19~dfsg+1-0ubuntu10 [2285 kB] Get:264 http://ftpmaster.internal/ubuntu artful/main ppc64el libharfbuzz-icu0 ppc64el 1.4.2-1 [5330 B] Get:265 http://ftpmaster.internal/ubuntu artful/main ppc64el libharfbuzz-gobject0 ppc64el 1.4.2-1 [12.5 kB] Get:266 http://ftpmaster.internal/ubuntu artful/main ppc64el libicu-dev ppc64el 57.1-6 [18.3 MB] Get:267 http://ftpmaster.internal/ubuntu artful/main ppc64el libharfbuzz-dev ppc64el 1.4.2-1 [280 kB] Get:268 http://ftpmaster.internal/ubuntu artful/main ppc64el libjpeg-turbo8-dev ppc64el 1.5.1-0ubuntu1 [309 kB] Get:269 http://ftpmaster.internal/ubuntu artful/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu8 [1606 B] Get:270 http://ftpmaster.internal/ubuntu artful/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu8 [1602 B] Get:271 http://ftpmaster.internal/ubuntu artful/main ppc64el libkpathsea6 ppc64el 2017.20170613.44572-2 [52.9 kB] Get:272 http://ftpmaster.internal/ubuntu artful/main ppc64el liblapack3 ppc64el 3.7.0-2 [1918 kB] Get:273 http://ftpmaster.internal/ubuntu artful/main ppc64el liblapack-dev ppc64el 3.7.0-2 [2009 kB] Get:274 http://ftpmaster.internal/ubuntu artful/main ppc64el libtinfo-dev ppc64el 6.0+20160625-1ubuntu1 [89.1 kB] Get:275 http://ftpmaster.internal/ubuntu artful/main ppc64el libncurses5-dev ppc64el 6.0+20160625-1ubuntu1 [195 kB] Get:276 http://ftpmaster.internal/ubuntu artful/main ppc64el libxft-dev ppc64el 2.3.2-1 [51.4 kB] Get:277 http://ftpmaster.internal/ubuntu artful/main ppc64el libpango1.0-dev ppc64el 1.40.5-1 [311 kB] Get:278 http://ftpmaster.internal/ubuntu artful/main ppc64el libpaper-utils ppc64el 1.1.24+nmu5ubuntu1 [8368 B] Get:279 http://ftpmaster.internal/ubuntu artful/main ppc64el libpoppler64 ppc64el 0.48.0-2ubuntu2 [781 kB] Get:280 http://ftpmaster.internal/ubuntu artful/main ppc64el libpotrace0 ppc64el 1.14-2 [18.3 kB] Get:281 http://ftpmaster.internal/ubuntu artful/main ppc64el libptexenc1 ppc64el 2017.20170613.44572-2 [35.4 kB] Get:282 http://ftpmaster.internal/ubuntu artful/main ppc64el libreadline-dev ppc64el 7.0-0ubuntu2 [163 kB] Get:283 http://ftpmaster.internal/ubuntu artful/main ppc64el libsynctex1 ppc64el 2017.20170613.44572-2 [39.4 kB] Get:284 http://ftpmaster.internal/ubuntu artful/main ppc64el libtcl8.6 ppc64el 8.6.6+dfsg-1 [869 kB] Get:285 http://ftpmaster.internal/ubuntu artful/main ppc64el libtexlua52 ppc64el 2017.20170613.44572-2 [96.3 kB] Get:286 http://ftpmaster.internal/ubuntu artful/universe ppc64el libtext-unidecode-perl all 1.30-1 [99.0 kB] Get:287 http://ftpmaster.internal/ubuntu artful/main ppc64el libjbig-dev ppc64el 2.1-3.1 [25.3 kB] Get:288 http://ftpmaster.internal/ubuntu artful/main ppc64el liblzma-dev ppc64el 5.2.2-1.2 [157 kB] Get:289 http://ftpmaster.internal/ubuntu artful/main ppc64el libtiffxx5 ppc64el 4.0.8-2 [5988 B] Get:290 http://ftpmaster.internal/ubuntu artful/main ppc64el libtiff5-dev ppc64el 4.0.8-2 [289 kB] Get:291 http://ftpmaster.internal/ubuntu artful/main ppc64el libtk8.6 ppc64el 8.6.6-1 [684 kB] Get:292 http://ftpmaster.internal/ubuntu artful/main ppc64el libxfont1 ppc64el 1:1.5.2-4 [92.1 kB] Get:293 http://ftpmaster.internal/ubuntu artful/main ppc64el libxfont2 ppc64el 1:2.0.1-3 [90.1 kB] Get:294 http://ftpmaster.internal/ubuntu artful/main ppc64el libxkbfile1 ppc64el 1:1.0.9-2 [65.5 kB] Get:295 http://ftpmaster.internal/ubuntu artful/main ppc64el libxml-namespacesupport-perl all 1.11-1 [13.2 kB] Get:296 http://ftpmaster.internal/ubuntu artful/main ppc64el libxml-sax-base-perl all 1.07-1 [21.5 kB] Get:297 http://ftpmaster.internal/ubuntu artful/main ppc64el libxml-sax-perl all 0.99+dfsg-2ubuntu1 [64.6 kB] Get:298 http://ftpmaster.internal/ubuntu artful/main ppc64el libxml-libxml-perl ppc64el 2.0128+dfsg-1build1 [302 kB] Get:299 http://ftpmaster.internal/ubuntu artful/main ppc64el x11proto-scrnsaver-dev all 1.2.2-1 [25.0 kB] Get:300 http://ftpmaster.internal/ubuntu artful/main ppc64el libxss-dev ppc64el 1:1.2.2-1 [11.8 kB] Get:301 http://ftpmaster.internal/ubuntu artful/main ppc64el libxt-dev ppc64el 1:1.1.5-1 [406 kB] Get:302 http://ftpmaster.internal/ubuntu artful/main ppc64el libzzip-0-13 ppc64el 0.13.62-3.1 [24.5 kB] Get:303 http://ftpmaster.internal/ubuntu artful/universe ppc64el mpack ppc64el 1.6-8.1 [33.3 kB] Get:304 http://ftpmaster.internal/ubuntu artful/main ppc64el tex-common all 6.06 [545 kB] Get:305 http://ftpmaster.internal/ubuntu artful/main ppc64el preview-latex-style all 11.90-1ubuntu1 [184 kB] Get:306 http://ftpmaster.internal/ubuntu artful/main ppc64el t1utils ppc64el 1.39-2 [59.7 kB] Get:307 http://ftpmaster.internal/ubuntu artful/main ppc64el tcl8.6 ppc64el 8.6.6+dfsg-1 [14.4 kB] Get:308 http://ftpmaster.internal/ubuntu artful/main ppc64el tcl8.6-dev ppc64el 8.6.6+dfsg-1 [899 kB] Get:309 http://ftpmaster.internal/ubuntu artful-proposed/universe ppc64el texinfo ppc64el 6.4.0.dfsg.1-1 [753 kB] Get:310 http://ftpmaster.internal/ubuntu artful/main ppc64el texlive-binaries ppc64el 2017.20170613.44572-2 [8294 kB] Get:311 http://ftpmaster.internal/ubuntu artful/main ppc64el xdg-utils all 1.1.1-1ubuntu2 [59.6 kB] Get:312 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el texlive-base all 2017.20170623-1 [18.6 MB] Get:313 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el texlive-latex-base all 2017.20170623-1 [831 kB] Get:314 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el texlive-extra-utils all 2017.20170623-1 [20.2 MB] Get:315 http://ftpmaster.internal/ubuntu artful/universe ppc64el fonts-stix all 1.1.1-4 [591 kB] Get:316 http://ftpmaster.internal/ubuntu artful/universe ppc64el ttf-adf-accanthis all 0.20090423-2 [401 kB] Get:317 http://ftpmaster.internal/ubuntu artful/universe ppc64el ttf-adf-gillius all 0.20090423-2 [400 kB] Get:318 http://ftpmaster.internal/ubuntu artful/universe ppc64el ttf-adf-universalis all 0.20090423-2 [221 kB] Get:319 http://ftpmaster.internal/ubuntu artful-proposed/universe ppc64el texlive-fonts-extra all 2017.20170623-1 [268 MB] Get:320 http://ftpmaster.internal/ubuntu artful-proposed/universe ppc64el texlive-fonts-recommended all 2017.20170623-1 [5279 kB] Get:321 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el texlive-plain-generic all 2017.20170623-1 [23.4 MB] Get:322 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el texlive-generic-recommended all 2017.20170623-1 [15.7 kB] Get:323 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el texlive-latex-recommended all 2017.20170623-1 [14.8 MB] Get:324 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el texlive-pictures all 2017.20170623-1 [3953 kB] Get:325 http://ftpmaster.internal/ubuntu artful-proposed/universe ppc64el texlive-latex-extra all 2017.20170623-1 [10.3 MB] Get:326 http://ftpmaster.internal/ubuntu artful/main ppc64el tk8.6 ppc64el 8.6.6-1 [12.4 kB] Get:327 http://ftpmaster.internal/ubuntu artful/main ppc64el tk8.6-dev ppc64el 8.6.6-1 [693 kB] Get:328 http://ftpmaster.internal/ubuntu artful/main ppc64el x11-xkb-utils ppc64el 7.7+3 [161 kB] Get:329 http://ftpmaster.internal/ubuntu artful/main ppc64el xfonts-encodings all 1:1.0.4-2 [573 kB] Get:330 http://ftpmaster.internal/ubuntu artful/main ppc64el xfonts-utils ppc64el 1:7.7+4 [85.2 kB] Get:331 http://ftpmaster.internal/ubuntu artful/main ppc64el xfonts-base all 1:1.0.4+nmu1 [5914 kB] Get:332 http://ftpmaster.internal/ubuntu artful/main ppc64el xserver-common all 2:1.19.3-1ubuntu2 [27.6 kB] Get:333 http://ftpmaster.internal/ubuntu artful/universe ppc64el xvfb ppc64el 2:1.19.3-1ubuntu2 [799 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 573 MB in 30s (18.9 MB/s) (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 ... 12359 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package libpython3.5-minimal:ppc64el. (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 ... 12350 files and directories currently installed.) Preparing to unpack .../0-libpython3.5-minimal_3.5.3-3_ppc64el.deb ... Unpacking libpython3.5-minimal:ppc64el (3.5.3-3) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../1-libexpat1_2.2.1-2_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.2.1-2) ... Selecting previously unselected package python3.5-minimal. 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Unpacking sbuild-build-depends-r-base-dummy (0.invalid.0) ... Setting up libgs9-common (9.19~dfsg+1-0ubuntu10) ... Setting up libedit2:ppc64el (3.1-20170329-1) ... Setting up libkpathsea6:ppc64el (2017.20170613.44572-2) ... Setting up libtexlua52:ppc64el (2017.20170613.44572-2) ... Setting up ttf-adf-accanthis (0.20090423-2) ... Setting up libgtk2.0-common (2.24.31-1ubuntu1) ... Setting up libbz2-dev:ppc64el (1.0.6-8.1) ... Setting up libsynctex1:ppc64el (2017.20170613.44572-2) ... Setting up libasyncns0:ppc64el (0.8-6) ... Setting up libptexenc1:ppc64el (2017.20170613.44572-2) ... Setting up fonts-gfs-neohellenic (1.1-6) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up fonts-stix (1.1.1-4) ... Setting up fonts-comfortaa (2.003-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libxml-namespacesupport-perl (1.11-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up liblcms2-2:ppc64el (2.7-1ubuntu1) ... Setting up libjbig0:ppc64el (2.1-3.1) ... Setting up libpcsclite1:ppc64el (1.8.21-1ubuntu1) ... Setting up libsigsegv2:ppc64el (2.10-5) ... Setting up libpthread-stubs0-dev:ppc64el (0.3-4) ... Setting up libcurl3:ppc64el (7.52.1-5ubuntu1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up fonts-linuxlibertine (5.3.0-2) ... Setting up poppler-data (0.4.7-8) ... Setting up libblas-common (3.7.0-2) ... Setting up bash-completion (1:2.1-4.3ubuntu1) ... Setting up libelf1:ppc64el (0.168-1) ... Setting up libgfortran3:ppc64el (6.3.0-19ubuntu1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:ppc64el (2.53.2-1) ... No schema files found: doing nothing. Setting up libasound2-data (1.1.3-5) ... Setting up libxshmfence1:ppc64el (1.2-1) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up libtext-unidecode-perl (1.30-1) ... Setting up xkb-data (2.19-1ubuntu1) ... Setting up libgfortran-6-dev:ppc64el (6.3.0-19ubuntu1) ... Setting up java-common (0.57ubuntu1) ... Setting up fonts-oflb-asana-math (000.907-6) ... Setting up libtinfo-dev:ppc64el (6.0+20160625-1ubuntu1) ... Setting up fonts-lobster (2.0-2) ... Setting up fonts-gfs-solomos (1.1-5) ... Setting up libgdk-pixbuf2.0-common (2.36.5-3) ... Setting up libdatrie1:ppc64el (0.2.10-4) ... Setting up gettext-base (0.19.8.1-2ubuntu1) ... Setting up fonts-freefont-otf (20120503-6) ... Setting up libgif7:ppc64el (5.1.4-0.4) ... Setting up libjpeg-turbo8:ppc64el (1.5.1-0ubuntu1) ... Setting up libpipeline1:ppc64el (1.4.1-2) ... Setting up x11proto-kb-dev (1.0.7-1) ... Setting up libglapi-mesa:ppc64el (17.1.2-2ubuntu2) ... Setting up m4 (1.4.18-1) ... Setting up fonts-crosextra-carlito (20130920-1) ... Setting up libicu57:ppc64el (57.1-6) ... Setting up libbsd0:ppc64el (0.8.3-1) ... Setting up libnspr4:ppc64el (2:4.13.1-0ubuntu1) ... Setting up ucf (3.0036) ... Setting up fonts-ebgaramond-extra (0.016-1) ... Setting up libgirepository-1.0-1:ppc64el (1.53.2-2) ... Setting up fonts-font-awesome (4.7.0~dfsg-1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-2.2ubuntu1) ... Setting up mpack (1.6-8.1) ... Setting up fonts-junicode (0.7.8-2) ... Setting up libfreetype6:ppc64el (2.6.3-3.2ubuntu1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libasound2:ppc64el (1.1.3-5) ... Setting up libdrm2:ppc64el (2.4.81-2) ... Setting up libmagic1:ppc64el (1:5.30-1) ... Setting up libgraphite2-3:ppc64el (1.3.10-2) ... Setting up libjbig-dev:ppc64el (2.1-3.1) ... Setting up libcroco3:ppc64el (0.6.11-3) ... Setting up fonts-lato (2.0-2) ... Setting up libogg0:ppc64el (1.3.2-1) ... Setting up libncurses5-dev:ppc64el (6.0+20160625-1ubuntu1) ... Setting up fonts-gfs-complutum (1.1-6) ... Setting up fonts-cabin (1.5-2) ... Setting up libatk1.0-data (2.22.0-1) ... Setting up libxml-sax-base-perl (1.07-1) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Setting up libjbig2dec0:ppc64el (0.13-4.1) ... Setting up libx11-xcb1:ppc64el (2:1.6.4-3) ... Setting up libpixman-1-0:ppc64el (0.34.0-1) ... Setting up xtrans-dev (1.3.5-1) ... Setting up libllvm4.0:ppc64el (1:4.0.1-1) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up gir1.2-glib-2.0:ppc64el (1.53.2-2) ... Setting up libjpeg-turbo8-dev:ppc64el (1.5.1-0ubuntu1) ... Setting up libglib2.0-data (2.53.2-1) ... Setting up fonts-crosextra-caladea (20130214-1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up ttf-adf-gillius (0.20090423-2) ... Setting up autotools-dev (20161112.1) ... Setting up fonts-noto-hinted (20161116-1) ... Setting up libpixman-1-dev (0.34.0-1) ... Setting up t1utils (1.39-2) ... Setting up libatk1.0-0:ppc64el (2.22.0-1) ... Setting up fonts-ebgaramond (0.016-1) ... Processing triggers for systemd (233-8ubuntu1) ... Setting up libreadline-dev:ppc64el (7.0-0ubuntu2) ... Setting up fonts-croscore (20161116-1) ... Setting up libijs-0.35:ppc64el (0.35-12) ... Setting up libbison-dev:ppc64el (2:3.0.4.dfsg-1build1) ... Setting up libfontenc1:ppc64el (1:1.1.3-1) ... Setting up libexpat1-dev:ppc64el (2.2.1-2) ... Setting up libpotrace0 (1.14-2) ... Setting up libsensors4:ppc64el (1:3.4.0-4) ... Setting up shared-mime-info (1.8-1) ... Setting up libpcrecpp0v5:ppc64el (2:8.39-3) ... Setting up libpcre32-3:ppc64el (2:8.39-3) ... Setting up icu-devtools (57.1-6) ... Setting up libdrm-radeon1:ppc64el (2.4.81-2) ... Setting up fonts-gfs-didot (1.1-6) ... Setting up libpcre16-3:ppc64el (2:8.39-3) ... Setting up libtcl8.6:ppc64el (8.6.6+dfsg-1) ... Setting up libthai-data (0.1.26-1) ... Setting up liblzma-dev:ppc64el (5.2.2-1.2) ... Setting up bison (2:3.0.4.dfsg-1build1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libxdmcp6:ppc64el (1:1.1.2-3) ... Setting up fonts-gfs-artemisia (1.1-5) ... Setting up libdrm-nouveau2:ppc64el (2.4.81-2) ... Setting up bsdmainutils (9.0.12ubuntu1) ... 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 ttf-adf-universalis (0.20090423-2) ... Setting up fonts-dejavu-extra (2.37-1) ... Setting up fonts-freefont-ttf (20120503-6) ... Setting up libvorbis0a:ppc64el (1.3.5-4) ... Setting up x11-common (1:7.7+19ubuntu1) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libzzip-0-13:ppc64el (0.13.62-3.1) ... Setting up fonts-sil-gentium (20081126:1.03-1) ... Setting up xdg-utils (1.1.1-1ubuntu2) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Setting up hicolor-icon-theme (0.15-1) ... Setting up libglib2.0-bin (2.53.2-1) ... Setting up fonts-sil-gentium-basic (1.1-7) ... Setting up libgraphite2-dev (1.3.10-2) ... Setting up fonts-gfs-olga (1.1-5) ... Setting up libcurl4-openssl-dev:ppc64el (7.52.1-5ubuntu1) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libpython2.7-stdlib:ppc64el (2.7.13-2) ... Setting up libxau6:ppc64el (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up libmpdec2:ppc64el (2.4.2-1) ... Setting up libdbus-1-3:ppc64el (1.10.18-1ubuntu2) ... Setting up liblzo2-2:ppc64el (2.08-1.2) ... Setting up fonts-lmodern (2.004.5-3) ... Setting up libwrap0:ppc64el (7.6.q-26) ... Setting up libavahi-common-data:ppc64el (0.6.32-1ubuntu1) ... Setting up fonts-roboto-hinted (2:0~20160106-2) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libxml-sax-perl (0.99+dfsg-2ubuntu1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libjpeg8:ppc64el (8c-2ubuntu8) ... Setting up libpaper1:ppc64el (1.1.24+nmu5ubuntu1) ... Creating config file /etc/papersize with new version Setting up gfortran-6 (6.3.0-19ubuntu1) ... Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ... Setting up libpcre3-dev:ppc64el (2:8.39-3) ... Setting up fontconfig-config (2.11.94-0ubuntu2) ... Setting up tex-common (6.06) ... update-language: texlive-base not installed and configured, doing nothing! Setting up x11proto-core-dev (7.0.31-1) ... Setting up libdrm-amdgpu1:ppc64el (2.4.81-2) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up gir1.2-freedesktop:ppc64el (1.53.2-2) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libpython3.5-stdlib:ppc64el (3.5.3-3) ... Setting up fonts-lobstertwo (2.0-2) ... Setting up libflac8:ppc64el (1.3.2-1) ... Setting up libgl1-mesa-dri:ppc64el (17.1.2-2ubuntu2) ... Setting up python2.7 (2.7.13-2) ... Setting up libnss3:ppc64el (2:3.28.4-0ubuntu2) ... Setting up libxfont2:ppc64el (1:2.0.1-3) ... Setting up libharfbuzz0b:ppc64el (1.4.2-1) ... Setting up libtiff5:ppc64el (4.0.8-2) ... Setting up libxau-dev:ppc64el (1:1.0.8-1) ... Setting up preview-latex-style (11.90-1ubuntu1) ... Setting up autoconf (2.69-10) ... Setting up libthai0:ppc64el (0.1.26-1) ... Setting up libicu-dev (57.1-6) ... Setting up file (1:5.30-1) ... Setting up xfonts-encodings (1:1.0.4-2) ... Setting up libxfont1:ppc64el (1:1.5.2-4) ... Setting up libpython-stdlib:ppc64el (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libxdmcp-dev:ppc64el (1:1.1.2-3) ... Setting up libjpeg8-dev:ppc64el (8c-2ubuntu8) ... Setting up libjpeg-dev:ppc64el (8c-2ubuntu8) ... Setting up tcl8.6 (8.6.6+dfsg-1) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:ppc64el (2:1.0.9-2) ... Setting up libtiffxx5:ppc64el (4.0.8-2) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up x11proto-scrnsaver-dev (1.2.2-1) ... Setting up libavahi-common3:ppc64el (0.6.32-1ubuntu1) ... Setting up libxml-libxml-perl (2.0128+dfsg-1build1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libpng-dev:ppc64el (1.6.29-3) ... Setting up x11proto-render-dev (2:0.11.1-2) ... Setting up libvorbisenc2:ppc64el (1.3.5-4) ... Setting up libxcb1:ppc64el (1.11.1-1ubuntu1) ... Setting up x11proto-input-dev (2.3.2-1) ... Setting up libharfbuzz-gobject0:ppc64el (1.4.2-1) ... Setting up python (2.7.13-2) ... Setting up tcl8.6-dev:ppc64el (8.6.6+dfsg-1) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-3) ... Setting up gfortran (4:6.3.0-2ubuntu1) ... 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 libpython3-stdlib:ppc64el (3.5.3-1ubuntu3) ... Setting up libxcb-present0:ppc64el (1.11.1-1ubuntu1) ... Setting up libfontconfig1:ppc64el (2.11.94-0ubuntu2) ... Setting up libxcb-dri2-0:ppc64el (1.11.1-1ubuntu1) ... Setting up libsm6:ppc64el (2:1.2.2-1) ... Setting up libxcb-dri3-0:ppc64el (1.11.1-1ubuntu1) ... Setting up libxcb-glx0:ppc64el (1.11.1-1ubuntu1) ... Setting up libxcb-render0:ppc64el (1.11.1-1ubuntu1) ... Setting up libharfbuzz-icu0:ppc64el (1.4.2-1) ... Setting up po-debconf (1.0.20) ... Setting up libblas-dev (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libpoppler64:ppc64el (0.48.0-2ubuntu2) ... Setting up libtiff5-dev:ppc64el (4.0.8-2) ... Setting up libx11-6:ppc64el (2:1.6.4-3) ... Setting up xfonts-utils (1:7.7+4) ... Setting up libxmuu1:ppc64el (2:1.1.2-2) ... Setting up libxcb-sync1:ppc64el (1.11.1-1ubuntu1) ... Setting up libsndfile1:ppc64el (1.0.28-2) ... Setting up x11proto-xext-dev (7.3.0-1) ... Setting up libfreetype6-dev:ppc64el (2.6.3-3.2ubuntu1) ... Setting up libice-dev:ppc64el (2:1.0.9-2) ... Setting up libxcomposite1:ppc64el (1:0.4.4-2) ... Setting up libxcb-shm0:ppc64el (1.11.1-1ubuntu1) ... Setting up libxpm4:ppc64el (1:3.5.12-1) ... Setting up libxt6:ppc64el (1:1.1.5-1) ... Setting up libxcb-shape0:ppc64el (1.11.1-1ubuntu1) ... Setting up libxrender1:ppc64el (1:0.9.10-1) ... Setting up libxcb1-dev:ppc64el (1.11.1-1ubuntu1) ... Setting up libavahi-client3:ppc64el (0.6.32-1ubuntu1) ... Setting up texinfo (6.4.0.dfsg.1-1) ... Running mktexlsr. This may take some time. ... done. Setting up libx11-dev:ppc64el (2:1.6.4-3) ... Setting up libxft2:ppc64el (2.3.2-1) ... Setting up xfonts-base (1:1.0.4+nmu1) ... Setting up fontconfig (2.11.94-0ubuntu2) ... Regenerating fonts cache... done. Setting up libcups2:ppc64el (2.2.3-2) ... Setting up libxkbfile1:ppc64el (1:1.0.9-2) ... Setting up libfontconfig1-dev:ppc64el (2.11.94-0ubuntu2) ... Setting up liblapack-dev (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libsm-dev:ppc64el (2:1.2.2-1) ... Setting up libxdamage1:ppc64el (1:1.1.4-2) ... Setting up libxext6:ppc64el (2:1.3.3-1) ... Setting up libxfixes3:ppc64el (1:5.0.3-1) ... Setting up libatspi2.0-0:ppc64el (2.22.0-5ubuntu4) ... Setting up libxss1:ppc64el (1:1.2.2-1) ... Setting up libgdk-pixbuf2.0-0:ppc64el (2.36.5-3) ... Setting up libxcb-shm0-dev:ppc64el (1.11.1-1ubuntu1) ... Setting up libxrender-dev:ppc64el (1:0.9.10-1) ... Setting up libpulse0:ppc64el (1:10.0-1ubuntu2) ... Setting up libxtst6:ppc64el (2:1.2.3-1) ... Setting up libxmu6:ppc64el (2:1.1.2-2) ... Setting up xauth (1:1.0.9-1ubuntu2) ... Setting up libxcb-render0-dev:ppc64el (1.11.1-1ubuntu1) ... Setting up libcupsimage2:ppc64el (2.2.3-2) ... Setting up fonts-sil-gentiumplus-compact (5.000-2) ... Setting up libxft-dev (2.3.2-1) ... Setting up gtk-update-icon-cache (3.22.15-0ubuntu2) ... Setting up libxcursor1:ppc64el (1:1.1.14-1) ... Setting up libxxf86dga1:ppc64el (2:1.1.4-1) ... Setting up libxext-dev:ppc64el (2:1.3.3-1) ... Setting up libpango-1.0-0:ppc64el (1.40.5-1) ... Setting up libatk-bridge2.0-0:ppc64el (2.22.0-1ubuntu1) ... Setting up libxv1:ppc64el (2:1.0.11-1) ... Setting up fonts-sil-gentiumplus (5.000-1) ... Setting up libxxf86vm1:ppc64el (1:1.1.4-1) ... Setting up libgs9:ppc64el (9.19~dfsg+1-0ubuntu10) ... Setting up libxrandr2:ppc64el (2:1.5.1-1) ... Setting up libxi6:ppc64el (2:1.7.9-1) ... Setting up libxaw7:ppc64el (2:1.0.13-1) ... Setting up libcairo2:ppc64el (1.14.8-1) ... Setting up libxinerama1:ppc64el (2:1.1.3-1) ... Setting up libxt-dev:ppc64el (1:1.1.5-1) ... Setting up x11-xkb-utils (7.7+3) ... Setting up libcairo-script-interpreter2:ppc64el (1.14.8-1) ... Setting up libtk8.6:ppc64el (8.6.6-1) ... Setting up libcairo-gobject2:ppc64el (1.14.8-1) ... Setting up texlive-binaries (2017.20170613.44572-2) ... 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 libxss-dev:ppc64el (1:1.2.2-1) ... Setting up libpangoft2-1.0-0:ppc64el (1.40.5-1) ... Setting up libgl1-mesa-glx:ppc64el (17.1.2-2ubuntu2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/mesa/ld.so.conf to provide /etc/ld.so.conf.d/powerpc64le-linux-gnu_GL.conf (powerpc64le-linux-gnu_gl_conf) in auto mode Setting up xserver-common (2:1.19.3-1ubuntu2) ... Setting up tk8.6 (8.6.6-1) ... Setting up xvfb (2:1.19.3-1ubuntu2) ... Setting up tk8.6-dev:ppc64el (8.6.6-1) ... Setting up libpangoxft-1.0-0:ppc64el (1.40.5-1) ... Setting up x11-utils (7.7+3build1) ... Setting up libpangocairo-1.0-0:ppc64el (1.40.5-1) ... Setting up gir1.2-pango-1.0:ppc64el (1.40.5-1) ... Setting up libatk-wrapper-java (0.33.3-13) ... Setting up librsvg2-2:ppc64el (2.40.16-2~svn1) ... Setting up librsvg2-common:ppc64el (2.40.16-2~svn1) ... Setting up libatk-wrapper-java-jni:ppc64el (0.33.3-13) ... Processing triggers for tex-common (6.06) ... update-language: texlive-base not installed and configured, doing nothing! texlive-base is not ready, skipping fmtutil --all call Setting up texlive-base (2017.20170623-1) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Processing triggers for tex-common (6.06) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up texlive-fonts-recommended (2017.20170623-1) ... Setting up texlive-plain-generic (2017.20170623-1) ... Setting up texlive-generic-recommended (2017.20170623-1) ... Setting up texlive-latex-base (2017.20170623-1) ... Setting up texlive-fonts-extra (2017.20170623-1) ... Processing triggers for tex-common (6.06) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up texlive-latex-recommended (2017.20170623-1) ... Setting up texlive-extra-utils (2017.20170623-1) ... Setting up texlive-pictures (2017.20170623-1) ... Processing triggers for tex-common (6.06) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up texlive-latex-extra (2017.20170623-1) ... Processing triggers for tex-common (6.06) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up openjdk-8-jre-headless:ppc64el (8u131-b11-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up adwaita-icon-theme (3.24.0-0ubuntu1) ... 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 libgtk2.0-0:ppc64el (2.24.31-1ubuntu1) ... Setting up ca-certificates-java (20170531+nmu1) ... Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:PSCProcert.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Certinomis_-_Autorité_Racine.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Microsec_e-Szigno_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Equifax_Secure_CA.pem Adding debian:Certplus_Root_CA_G1.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Certplus_Root_CA_G2.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Swisscom_Root_CA_2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Swisscom_Root_EV_CA_2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:ACCVRAIZ1.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:SecureTrust_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:S-TRUST_Universal_Root_CA.pem Adding debian:IGC_A.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:Secure_Global_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:NetLock_Arany_=Class_Gold=_FÅ‘tanúsítvány.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:TÃœRKTRUST_Elektronik_Sertifika_Hizmet_SaÄŸlayıcısı_H5.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:TÃœRKTRUST_Elektronik_Sertifika_Hizmet_SaÄŸlayıcısı_H6.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:ACEDICOM_Root.pem Adding debian:ComSign_CA.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:CNNIC_ROOT.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Taiwan_GRCA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:OpenTrust_Root_CA_G1.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:AC_Raíz_Certicámara_S.A..pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:AddTrust_External_Root.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:TÃœBÄ°TAK_UEKAE_Kök_Sertifika_Hizmet_SaÄŸlayıcısı_-_Sürüm_3.pem Adding debian:Juur-SK.pem Adding debian:OpenTrust_Root_CA_G3.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_SaÄŸlayıcısı.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:Certum_Root_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:EC-ACC.pem Adding debian:CA_Disig_Root_R1.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Izenpe.com.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem Adding debian:AffirmTrust_Networking.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certigna.pem Adding debian:OpenTrust_Root_CA_G2.pem done. Setting up dh-autoreconf (14) ... Setting up python3 (3.5.3-1ubuntu3) ... Setting up libglib2.0-dev-bin (2.53.2-1) ... Setting up openjdk-8-jdk-headless:ppc64el (8u131-b11-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/javah to provide /usr/bin/javah (javah) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode Setting up humanity-icon-theme (0.6.13) ... Setting up libglib2.0-dev:ppc64el (2.53.2-1) ... Setting up openjdk-8-jre:ppc64el (8u131-b11-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up libharfbuzz-dev:ppc64el (1.4.2-1) ... Setting up dh-python (2.20170125) ... Setting up default-jre-headless (2:1.8-57ubuntu1) ... Setting up default-jdk-headless (2:1.8-57ubuntu1) ... Setting up debhelper (10.4ubuntu3) ... Setting up libcairo2-dev (1.14.8-1) ... Setting up openjdk-8-jdk:ppc64el (8u131-b11-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-ppc64el/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up ubuntu-mono (16.10+17.10.20170619-0ubuntu1) ... Setting up default-jre (2:1.8-57ubuntu1) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up libpango1.0-dev (1.40.5-1) ... Setting up default-jdk (2:1.8-57ubuntu1) ... Setting up sbuild-build-depends-r-base-dummy (0.invalid.0) ... (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 ... 109749 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libgdk-pixbuf2.0-0:ppc64el (2.36.5-3) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Processing triggers for systemd (233-8ubuntu1) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-81-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.28-6ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.3.0-19ubuntu1 gcc-6_6.3.0-19ubuntu1 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-19ubuntu1 libstdc++6_7.1.0-7ubuntu1 linux-libc-dev_4.11.0-8.13 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 adwaita-icon-theme_3.24.0-0ubuntu1 apt_1.4.6 apt-transport-https_1.4.6 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu99 base-passwd_3.5.43 bash_4.4-5ubuntu1 bash-completion_1:2.1-4.3ubuntu1 binutils_2.28-6ubuntu1 bison_2:3.0.4.dfsg-1build1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 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python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1ubuntu3 python3-minimal_3.5.3-1ubuntu3 python3.5_3.5.3-3 python3.5-minimal_3.5.3-3 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-base-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 shared-mime-info_1.8-1 systemd_233-8ubuntu1 systemd-sysv_233-8ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 t1utils_1.39-2 tar_1.29b-1.1 tcl8.6_8.6.6+dfsg-1 tcl8.6-dev_8.6.6+dfsg-1 tex-common_6.06 texinfo_6.4.0.dfsg.1-1 texlive-base_2017.20170623-1 texlive-binaries_2017.20170613.44572-2 texlive-extra-utils_2017.20170623-1 texlive-fonts-extra_2017.20170623-1 texlive-fonts-recommended_2017.20170623-1 texlive-generic-recommended_2017.20170623-1 texlive-latex-base_2017.20170623-1 texlive-latex-extra_2017.20170623-1 texlive-latex-recommended_2017.20170623-1 texlive-pictures_2017.20170623-1 texlive-plain-generic_2017.20170623-1 tk8.6_8.6.6-1 tk8.6-dev_8.6.6-1 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 ttf-adf-universalis_0.20090423-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 ubuntu-mono_16.10+17.10.20170619-0ubuntu1 ucf_3.0036 util-linux_2.29-1ubuntu3 x11-common_1:7.7+19ubuntu1 x11-utils_7.7+3build1 x11-xkb-utils_7.7+3 x11proto-core-dev_7.0.31-1 x11proto-input-dev_2.3.2-1 x11proto-kb-dev_1.0.7-1 x11proto-render-dev_2:0.11.1-2 x11proto-scrnsaver-dev_1.2.2-1 x11proto-xext-dev_7.3.0-1 xauth_1:1.0.9-1ubuntu2 xdg-utils_1.1.1-1ubuntu2 xfonts-base_1:1.0.4+nmu1 xfonts-encodings_1:1.0.4-2 xfonts-utils_1:7.7+4 xkb-data_2.19-1ubuntu1 xorg-sgml-doctools_1:1.11-1 xserver-common_2:1.19.3-1ubuntu2 xtrans-dev_1.3.5-1 xvfb_2:1.19.3-1ubuntu2 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jun 24 17:16:58 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-base_3.4.0.20170622-1.dsc dpkg-source: info: extracting r-base in r-base-3.4.0.20170622 dpkg-source: info: unpacking r-base_3.4.0.20170622.orig.tar.gz dpkg-source: info: unpacking r-base_3.4.0.20170622-1.debian.tar.xz dpkg-source: info: applying unset_R_LIBS_USER Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package r-base dpkg-buildpackage: info: source version 3.4.0.20170622-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build r-base-3.4.0.20170622 dpkg-buildpackage: info: host architecture ppc64el 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 dh_clean: Compatibility levels before 9 are deprecated (level 7 in use) debian/rules build-arch *** configure *** #automake #autoconf dh_testdir R_TEXI2DVICMD=emulation \ R_PAPERSIZE=letter \ R_BROWSER=xdg-open \ R_GZIPCMD="/bin/gzip -n" \ PAGER=/usr/bin/pager \ PERL=/usr/bin/perl \ JAVA_HOME=/usr/lib/jvm/default-java \ R_UNZIPCMD=/usr/bin/unzip \ R_ZIPCMD=/usr/bin/zip \ R_PRINTCMD=/usr/bin/lpr \ LIBnn=lib \ AWK=/usr/bin/awk \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ FC=gfortran \ CFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong" \ FCFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong" \ CPPFLAGS= \ LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" \ FLIBS= \ rsharedir=/usr/share/R/share \ rincludedir=/usr/share/R/include \ rdocdir=/usr/share/R/doc \ ./configure --prefix=/usr \ --with-cairo \ --with-jpeglib \ --with-readline \ --with-tcltk \ --with-system-bzlib \ --with-system-pcre \ --with-system-zlib \ --mandir=/usr/share/man \ --infodir=/usr/share/info \ --datadir=/usr/share/R/share \ --includedir=/usr/share/R/include \ --with-blas \ --with-lapack \ --enable-R-profiling \ --enable-R-shlib \ --enable-memory-profiling \ --without-recommended-packages \ --build powerpc64le-linux-gnu configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib checking build system type... powerpc64le-unknown-linux-gnu checking host system type... powerpc64le-unknown-linux-gnu loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking for working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking whether ln -s works... yes checking for bison... bison -y checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for which... /usr/bin/which checking for 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-std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether gcc -std=gnu99 needs -traditional... no checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking how to run the C preprocessor... gcc -std=gnu99 -E defining F77 to be gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g can compile C++ code... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc -std=gnu99 accepts -fvisibility... yes checking whether gfortran accepts -fvisibility... yes checking for gcc... gcc checking whether we are using the GNU Objective C compiler... no checking whether gcc accepts -g... no checking for Objective C++ compiler... trying some possibilities checking whether g++ can compile ObjC++... no checking whether can compile ObjC++... no no working ObjC++ compiler found checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc -std=gnu99... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert powerpc64le-unknown-linux-gnu file names to powerpc64le-unknown-linux-gnu format... func_convert_file_noop checking how to convert powerpc64le-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... /usr/bin/awk checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes checking if gcc -std=gnu99 static flag -static works... yes checking if gcc -std=gnu99 supports -c -o file.o... yes checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes checking whether the gcc -std=gnu99 linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking whether rl_callback_sigcleanup exists and is declared... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking glob.h usability... yes checking glob.h presence... yes checking for glob.h... yes checking grp.h usability... yes checking grp.h presence... yes checking for grp.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for strings.h... (cached) yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking dl.h usability... no checking dl.h presence... no checking for dl.h... no checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking floatingpoint.h usability... no checking floatingpoint.h presence... no checking for floatingpoint.h... no checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking stdalign.h usability... yes checking stdalign.h presence... yes checking for stdalign.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdbool.h usability... yes checking stdbool.h presence... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking return type of signal handlers... void checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for gcc -std=gnu99 option to accept ISO C99... none needed checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) none needed checking for inline... inline checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of double... 8 checking size of size_t... 8 checking size of long double... 16 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes checking for gcc -std=gnu99 option to support OpenMP... -fopenmp checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/powerpc64le-linux-gnu/6 -L/usr/lib/gcc/powerpc64le-linux-gnu/6/../../../powerpc64le-linux-gnu -L/usr/lib/gcc/powerpc64le-linux-gnu/6/../../../../lib -L/lib/powerpc64le-linux-gnu -L/lib/../lib -L/usr/lib/powerpc64le-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/powerpc64le-linux-gnu/6/../../.. -lgfortran -lm checking how to get verbose linking output from gcc -std=gnu99... -v checking for C libraries of gcc -std=gnu99... -L/usr/lib/gcc/powerpc64le-linux-gnu/6 -L/usr/lib/gcc/powerpc64le-linux-gnu/6/../../../powerpc64le-linux-gnu -L/usr/lib/gcc/powerpc64le-linux-gnu/6/../../../../lib -L/lib/powerpc64le-linux-gnu -L/lib/../lib -L/usr/lib/powerpc64le-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/powerpc64le-linux-gnu/6/../../.. -lgcc_s checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking whether gfortran appends underscores to external names... yes checking whether gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether gfortran and gcc -std=gnu99 agree on int and double... yes checking whether gfortran and gcc -std=gnu99 agree on double complex... yes checking for gfortran option to support OpenMP... -fopenmp checking whether g++ accepts -M for generating dependencies... yes checking for g++ option to support OpenMP... -fopenmp checking whether we can compute ObjC Make dependencies... no checking for xmkmf... no checking whether g++ supports C++98 features by default... no checking whether g++ supports C++98 features with -std=gnu++98... yes checking whether g++ supports C++11 features by default... no checking whether g++ supports C++11 features with -std=gnu++11... yes checking whether g++ supports C++14 features by default... yes checking whether g++ supports C++17 features by default... no checking whether g++ supports C++17 features with -std=gnu++17... no checking whether g++ supports C++17 features with -std=gnu++1z... no checking whether g++ supports C++17 features with -std=c++17... no checking whether g++ supports C++17 features with -std=c++1z... no configure: No compiler with C++17 support was found checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log1pl exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether nearbyint exists and is declared... yes checking whether nearbyintl exists and is declared... yes checking whether powl exists and is declared... yes checking whether rint exists and is declared... yes checking whether rintl exists and is declared... yes checking whether va_copy exists and is declared... yes checking for isblank... yes checking sunmath.h usability... no checking sunmath.h presence... no checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for 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whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking for 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... yes checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes checking for dgemm_... no checking for ATL_xerbla in -latlas... no checking for dgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for dgemm_ in -lblas... 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(cached) yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... 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(cached) yes checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking for gfortran option to support OpenMP... -fopenmp checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for ranlib... (cached) ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... no checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking for ld used by gcc -std=gnu99... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.0.4, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... yes using as R_SHELL for scripts ... /bin/bash configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/f77_f2c config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib R is now configured for powerpc64le-unknown-linux-gnu Source directory: . Installation directory: /usr C compiler: gcc -std=gnu99 -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g Fortran 77 compiler: gfortran -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong Default C++ compiler: g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++98 compiler: g++ -std=gnu++98 -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++11 compiler: g++ -std=gnu++11 -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++14 compiler: g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++17 compiler: Fortran 90/95 compiler: gfortran -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong" \ FCFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" \ PKG_BUILT_STAMP="""" \ R_GZIPCMD="/bin/gzip -n" \ R make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' creating src/scripts/R.fe make[4]: Entering directory '/<>/src/scripts' mkdir -p -- ../../bin make[4]: Leaving directory '/<>/src/scripts' make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' mkdir -p -- ../../include make[4]: Entering directory '/<>/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/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 '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 '/<>/src/extra/tre' make[4]: Leaving directory '/<>/src/extra/tre' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/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 '/<>/src/appl' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uncmin.c -o uncmin.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dchdc.f -o dchdc.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpbfa.f -o dpbfa.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpbsl.f -o dpbsl.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpoco.f -o dpoco.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpodi.f -o dpodi.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpofa.f -o dpofa.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dposl.f -o dposl.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrdc.f -o dqrdc.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrls.f -o dqrls.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrsl.f -o dqrsl.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrutl.f -o dqrutl.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dsvdc.f -o dsvdc.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dtrco.f -o dtrco.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 '/<>/src/appl' make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[4]: Entering directory '/<>/src/nmath' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c expm1.c -o expm1.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signrank.c -o signrank.o ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[4]: Leaving directory '/<>/src/nmath' make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/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 '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/<>"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/<>/src/unix' make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/src/main' config.status: creating src/main/Makefile making CommandLineArgs.d from CommandLineArgs.c making Rdynload.d from Rdynload.c making Renviron.d from Renviron.c making RNG.d from RNG.c making agrep.d from agrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making radixsort.d from radixsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making times.d from times.c making unique.d from unique.c making util.d from util.c making version.d from version.c making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[4]: Entering directory '/<>/src/main' gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c main.c -o main.o main.c: In function ‘dummy_ii’: main.c:1669:12: warning: function returns address of local variable [-Wreturn-local-addr] return (uintptr_t) ⅈ ^~~~~~~~~~~~~~~ gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_her_glyph.c -o g_her_glyph.o gfortran -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c xxxpr.f -o xxxpr.o gcc -std=gnu99 -shared -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lblas -lgfortran -lm -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[5]: Entering directory '/<>/src/main' mkdir -p -- /<>/bin/exec mkdir -p -- /<>/lib make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmain.c -o Rmain.o gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R.bin Rmain.o -lR make[5]: Entering directory '/<>/src/main' make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/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 '/<>/src/modules/internet' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR make[6]: Entering directory '/<>/src/modules/internet' mkdir -p -- /<>/modules make[6]: Leaving directory '/<>/src/modules/internet' make[5]: Leaving directory '/<>/src/modules/internet' make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' making Lapack.d from Lapack.c make[5]: Entering directory '/<>/src/modules/lapack' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Lapack.c -o Lapack.o gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o lapack.so Lapack.o -lR -llapack -lblas -lgfortran -lm make[6]: Entering directory '/<>/src/modules/lapack' make[6]: Leaving directory '/<>/src/modules/lapack' make[5]: Leaving directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/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 '/<>/src/modules/X11' gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/powerpc64le-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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/powerpc64le-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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/powerpc64le-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbitmap.c -o rbitmap.o gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/powerpc64le-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dataentry.c -o dataentry.o gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm make[5]: Leaving directory '/<>/src/modules/X11' make[5]: Entering directory '/<>/src/modules/X11' make[5]: Leaving directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' mkdir -p -- ../../library make[4]: Entering directory '/<>/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[4]: Leaving directory '/<>/src/library/profile' make[4]: Entering directory '/<>/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[5]: Entering directory '/<>/src/library/translations' make[5]: Leaving directory '/<>/src/library/translations' make[4]: Leaving directory '/<>/src/library/translations' make[4]: Entering directory '/<>/src/library/base' building package 'base' make[5]: Entering directory '/<>/src/library/base' mkdir -p -- ../../../library/base/demo make[5]: Leaving directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[5]: Entering directory '/<>/src/library/tools' mkdir -p -- ../../../library/tools/R make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' make[6]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramRd.c -o gramRd.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[7]: Leaving directory '/<>/src/library/tools/src' make[6]: Leaving directory '/<>/src/library/tools/src' make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[5]: Entering directory '/<>/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[5]: Leaving directory '/<>/src/library/compiler' make[5]: Entering directory '/<>/src/library/compiler' byte-compiling package 'compiler' make[5]: Leaving directory '/<>/src/library/compiler' make[4]: Leaving directory '/<>/src/library/compiler' make[4]: Entering directory '/<>/src/library/base' byte-compiling package 'base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' byte-compiling package 'tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[5]: Entering directory '/<>/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[6]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[7]: Leaving directory '/<>/src/library/utils/src' make[6]: Leaving directory '/<>/src/library/utils/src' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' byte-compiling package 'utils' make[5]: Leaving directory '/<>/src/library/utils' make[4]: Leaving directory '/<>/src/library/utils' make[4]: Entering directory '/<>/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[5]: Entering directory '/<>/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 '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[6]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devQuartz.c -o devQuartz.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[8]: Entering directory '/<>/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[9]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: Entering directory '/<>/src/library/grDevices/src/cairo' gcc -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../../../src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cairoBM.c -o cairoBM.o gcc -std=gnu99 -shared -L../../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -L../../../../../lib -lR -lm make[10]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[9]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[8]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[7]: Leaving directory '/<>/src/library/grDevices/src' make[6]: Leaving directory '/<>/src/library/grDevices/src' make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' byte-compiling package 'grDevices' make[5]: Leaving directory '/<>/src/library/grDevices' make[4]: Leaving directory '/<>/src/library/grDevices' make[4]: Entering directory '/<>/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[5]: Entering directory '/<>/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stem.c -o stem.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' byte-compiling package 'graphics' make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[5]: Entering directory '/<>/src/library/stats' mkdir -p -- ../../../library/stats/R make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c influence.c -o influence.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bsplvd.f -o bsplvd.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bvalue.f -o bvalue.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bvalus.f -o bvalus.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c loessf.f -o loessf.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c ppr.f -o ppr.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c qsbart.f -o qsbart.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sgram.f -o sgram.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sinerp.f -o sinerp.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sslvrg.f -o sslvrg.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c stxwx.f -o stxwx.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c hclust.f -o hclust.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c kmns.f -o kmns.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c eureka.f -o eureka.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c stl.f -o stl.o gfortran -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -ffloat-store -c portsrc.f -o portsrc.o gfortran -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c lminfl.f -o lminfl.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lblas -lgfortran -lm -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' byte-compiling package 'stats' make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[5]: Entering directory '/<>/src/library/methods' mkdir -p -- ../../../library/methods/R make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[5]: Entering directory '/<>/src/library/grid' mkdir -p -- ../../../library/grid/R make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c viewport.c -o viewport.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' byte-compiling package 'grid' make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[5]: Entering directory '/<>/src/library/splines' mkdir -p -- ../../../library/splines/R make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' making splines.d from splines.c gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fPIC -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' byte-compiling package 'splines' make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[5]: Entering directory '/<>/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' byte-compiling package 'stats4' make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[5]: Entering directory '/<>/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk_unix.c -o tcltk_unix.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib/powerpc64le-linux-gnu -ltcl8.6 -L/usr/lib/powerpc64le-linux-gnu -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR make[6]: Entering directory '/<>/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' byte-compiling package 'tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[5]: Entering directory '/<>/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fork.c -o fork.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' byte-compiling package 'parallel' make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' you should 'make docs' now ... make[1]: Leaving directory '/<>' (cd src/nmath/standalone; \ /usr/bin/make CFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -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 '/<>/src/nmath/standalone' (cd ../../include; /usr/bin/make Rmath.h) make[2]: Entering directory '/<>/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/<>/src/include' Copying source files make[2]: Entering directory '/<>/src/nmath/standalone' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c making std_unif.d from std_unif.c make[2]: Leaving directory '/<>/src/nmath/standalone' make[2]: Entering directory '/<>/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c expm1.c -o expm1.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.lo gcc -std=gnu99 -shared -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRmath.so -Wl,-soname,libRmath.so.1 mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo expm1.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm make[2]: Leaving directory '/<>/src/nmath/standalone' make[2]: Entering directory '/<>/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c expm1.c -o expm1.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.o ar -cr libRmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o ranlib libRmath.a make[2]: Leaving directory '/<>/src/nmath/standalone' make[1]: Leaving directory '/<>/src/nmath/standalone' R_GZIPCMD="/bin/gzip -n" \ /usr/bin/make docs R_CMD_BUILD_HELP_OPTS="--txt --example" make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' make[4]: Entering directory '/<>/src/scripts' make[4]: Leaving directory '/<>/src/scripts' make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' make[4]: Entering directory '/<>/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[4]: Leaving directory '/<>/src/extra/tre' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/src/appl' make[4]: Entering directory '/<>/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/<>/src/appl' make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/src/nmath' make[4]: Entering directory '/<>/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/<>/src/nmath' make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/<>"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/<>/src/unix' make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/lib/libR.so is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/bin/exec/R is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/src/modules/internet' make[5]: Entering directory '/<>/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/<>/src/modules/internet' make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' make[5]: Entering directory '/<>/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/src/modules/X11' make[5]: Entering directory '/<>/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 '/<>/src/modules/X11' make[5]: Entering directory '/<>/src/modules/X11' /<>/modules/R_X11.so is unchanged /<>/modules/R_de.so is unchanged make[5]: Leaving directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' make[4]: Entering directory '/<>/src/library/profile' building system startup profile make[4]: Leaving directory '/<>/src/library/profile' make[4]: Entering directory '/<>/src/library/translations' building package 'translations' make[5]: Entering directory '/<>/src/library/translations' make[5]: Leaving directory '/<>/src/library/translations' make[4]: Leaving directory '/<>/src/library/translations' make[4]: Entering directory '/<>/src/library/base' building package 'base' make[5]: Entering directory '/<>/src/library/base' all.R is unchanged make[5]: Leaving directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' building package 'tools' make[5]: Entering directory '/<>/src/library/tools' all.R is unchanged make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' make[6]: Entering directory '/<>/src/library/tools/src' make[7]: Entering directory '/<>/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/<>/src/library/tools/src' make[6]: Leaving directory '/<>/src/library/tools/src' make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/compiler' building package 'compiler' make[5]: Entering directory '/<>/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/<>/src/library/compiler' make[5]: Entering directory '/<>/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/compiler' make[4]: Leaving directory '/<>/src/library/compiler' make[4]: Entering directory '/<>/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/utils' building package 'utils' make[5]: Entering directory '/<>/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[6]: Entering directory '/<>/src/library/utils/src' make[7]: Entering directory '/<>/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/<>/src/library/utils/src' make[6]: Leaving directory '/<>/src/library/utils/src' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/utils' make[4]: Leaving directory '/<>/src/library/utils' make[4]: Entering directory '/<>/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/<>/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[6]: Entering directory '/<>/src/library/grDevices/src' make[7]: Entering directory '/<>/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/<>/src/library/grDevices/src/cairo' make[9]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[9]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[8]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[7]: Leaving directory '/<>/src/library/grDevices/src' make[6]: Leaving directory '/<>/src/library/grDevices/src' make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grDevices' make[4]: Leaving directory '/<>/src/library/grDevices' make[4]: Entering directory '/<>/src/library/graphics' building package 'graphics' make[5]: Entering directory '/<>/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/src/library/graphics/src' make[7]: Entering directory '/<>/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' make[5]: Entering directory '/<>/src/library/stats' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' make[7]: Entering directory '/<>/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' make[5]: Entering directory '/<>/src/library/methods' all.R is unchanged make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/src/library/methods/src' make[7]: Entering directory '/<>/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' make[5]: Entering directory '/<>/src/library/grid' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/src/library/grid/src' make[7]: Entering directory '/<>/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' make[5]: Entering directory '/<>/src/library/splines' all.R is unchanged make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' make[7]: Entering directory '/<>/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' make[5]: Entering directory '/<>/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/src/library/tcltk/src' make[6]: Entering directory '/<>/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' make[5]: Entering directory '/<>/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/src/library/parallel/src' make[7]: Entering directory '/<>/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' you should 'make docs' now ... make[2]: Entering directory '/<>/doc' creating doc/NEWS creating doc/NEWS.pdf make[3]: Entering directory '/<>/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 '/<>/doc/html' make[4]: Leaving directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' installing parsed Rd make[4]: Entering directory '/<>/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' building/updating package metadata ... make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' writing package indices make[4]: Entering directory '/<>/src/library' make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src/library' make[1]: Leaving directory '/<>' /usr/bin/make javaconf make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' make[4]: Entering directory '/<>/src/scripts' make[4]: Leaving directory '/<>/src/scripts' make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' make[4]: Entering directory '/<>/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[4]: Leaving directory '/<>/src/extra/tre' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/src/appl' make[4]: Entering directory '/<>/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/<>/src/appl' make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/src/nmath' make[4]: Entering directory '/<>/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/<>/src/nmath' make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/<>"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/<>/src/unix' make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/lib/libR.so is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/bin/exec/R is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/src/modules/internet' make[5]: Entering directory '/<>/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/<>/src/modules/internet' make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' make[5]: Entering directory '/<>/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/src/modules/X11' make[5]: Entering directory '/<>/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 '/<>/src/modules/X11' make[5]: Entering directory '/<>/src/modules/X11' /<>/modules/R_X11.so is unchanged /<>/modules/R_de.so is unchanged make[5]: Leaving directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' make[4]: Entering directory '/<>/src/library/profile' building system startup profile make[4]: Leaving directory '/<>/src/library/profile' make[4]: Entering directory '/<>/src/library/translations' building package 'translations' make[5]: Entering directory '/<>/src/library/translations' make[5]: Leaving directory '/<>/src/library/translations' make[4]: Leaving directory '/<>/src/library/translations' make[4]: Entering directory '/<>/src/library/base' building package 'base' make[5]: Entering directory '/<>/src/library/base' all.R is unchanged make[5]: Leaving directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' building package 'tools' make[5]: Entering directory '/<>/src/library/tools' all.R is unchanged make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' make[6]: Entering directory '/<>/src/library/tools/src' make[7]: Entering directory '/<>/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/<>/src/library/tools/src' make[6]: Leaving directory '/<>/src/library/tools/src' make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/compiler' building package 'compiler' make[5]: Entering directory '/<>/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/<>/src/library/compiler' make[5]: Entering directory '/<>/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/compiler' make[4]: Leaving directory '/<>/src/library/compiler' make[4]: Entering directory '/<>/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/utils' building package 'utils' make[5]: Entering directory '/<>/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[6]: Entering directory '/<>/src/library/utils/src' make[7]: Entering directory '/<>/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/<>/src/library/utils/src' make[6]: Leaving directory '/<>/src/library/utils/src' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/utils' make[4]: Leaving directory '/<>/src/library/utils' make[4]: Entering directory '/<>/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/<>/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[6]: Entering directory '/<>/src/library/grDevices/src' make[7]: Entering directory '/<>/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/<>/src/library/grDevices/src/cairo' make[9]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[9]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[8]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[7]: Leaving directory '/<>/src/library/grDevices/src' make[6]: Leaving directory '/<>/src/library/grDevices/src' make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grDevices' make[4]: Leaving directory '/<>/src/library/grDevices' make[4]: Entering directory '/<>/src/library/graphics' building package 'graphics' make[5]: Entering directory '/<>/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/src/library/graphics/src' make[7]: Entering directory '/<>/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' make[5]: Entering directory '/<>/src/library/stats' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' make[7]: Entering directory '/<>/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' make[5]: Entering directory '/<>/src/library/methods' all.R is unchanged make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/src/library/methods/src' make[7]: Entering directory '/<>/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' make[5]: Entering directory '/<>/src/library/grid' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/src/library/grid/src' make[7]: Entering directory '/<>/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' make[5]: Entering directory '/<>/src/library/splines' all.R is unchanged make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' make[7]: Entering directory '/<>/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' make[5]: Entering directory '/<>/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/src/library/tcltk/src' make[6]: Entering directory '/<>/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' make[5]: Entering directory '/<>/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/src/library/parallel/src' make[7]: Entering directory '/<>/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>' configuring Java ... Java interpreter : /usr/lib/jvm/default-java/jre/bin/java Java version : 1.8.0_131 Java home path : /usr/lib/jvm/default-java Java compiler : /usr/lib/jvm/default-java/bin/javac Java headers gen.: /usr/lib/jvm/default-java/bin/javah Java archive tool: /usr/lib/jvm/default-java/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/ppc64le/server -ljvm make[3]: Entering directory '/tmp/Rjavareconf.pscQBA' gcc -std=gnu99 -I/<>/include -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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/<>/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/jre/lib/ppc64le/server -ljvm -L/<>/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.pscQBA' JAVA_HOME : /usr/lib/jvm/default-java Java library path: $(JAVA_HOME)/jre/lib/ppc64le/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/jre/lib/ppc64le/server -ljvm Updating Java configuration in /<> Done. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' touch make-arch-stamp *** make-indep *** /usr/bin/make -k docs make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' make[4]: Entering directory '/<>/src/scripts' make[4]: Leaving directory '/<>/src/scripts' make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' make[4]: Entering directory '/<>/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[4]: Leaving directory '/<>/src/extra/tre' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/src/appl' make[4]: Entering directory '/<>/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/<>/src/appl' make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/src/nmath' make[4]: Entering directory '/<>/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/<>/src/nmath' make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/<>"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/<>/src/unix' make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/lib/libR.so is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/bin/exec/R is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/src/modules/internet' make[5]: Entering directory '/<>/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/<>/src/modules/internet' make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' make[5]: Entering directory '/<>/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/src/modules/X11' make[5]: Entering directory '/<>/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 '/<>/src/modules/X11' make[5]: Entering directory '/<>/src/modules/X11' /<>/modules/R_X11.so is unchanged /<>/modules/R_de.so is unchanged make[5]: Leaving directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' make[4]: Entering directory '/<>/src/library/profile' building system startup profile make[4]: Leaving directory '/<>/src/library/profile' make[4]: Entering directory '/<>/src/library/translations' building package 'translations' make[5]: Entering directory '/<>/src/library/translations' make[5]: Leaving directory '/<>/src/library/translations' make[4]: Leaving directory '/<>/src/library/translations' make[4]: Entering directory '/<>/src/library/base' building package 'base' make[5]: Entering directory '/<>/src/library/base' all.R is unchanged make[5]: Leaving directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' building package 'tools' make[5]: Entering directory '/<>/src/library/tools' all.R is unchanged make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' make[6]: Entering directory '/<>/src/library/tools/src' make[7]: Entering directory '/<>/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/<>/src/library/tools/src' make[6]: Leaving directory '/<>/src/library/tools/src' make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/compiler' building package 'compiler' make[5]: Entering directory '/<>/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/<>/src/library/compiler' make[5]: Entering directory '/<>/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/compiler' make[4]: Leaving directory '/<>/src/library/compiler' make[4]: Entering directory '/<>/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/utils' building package 'utils' make[5]: Entering directory '/<>/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' 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'graphics' make[5]: Entering directory '/<>/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/src/library/graphics/src' make[7]: Entering directory '/<>/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' make[5]: Entering directory '/<>/src/library/stats' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' make[7]: Entering directory '/<>/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' make[5]: Entering directory '/<>/src/library/methods' all.R is unchanged make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/src/library/methods/src' make[7]: Entering directory '/<>/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' make[5]: Entering directory '/<>/src/library/grid' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/src/library/grid/src' make[7]: Entering directory '/<>/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' make[5]: Entering directory '/<>/src/library/splines' all.R is unchanged make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' make[7]: Entering directory '/<>/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' make[5]: Entering directory '/<>/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/src/library/tcltk/src' make[6]: Entering directory '/<>/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' make[5]: Entering directory '/<>/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/src/library/parallel/src' make[7]: Entering directory '/<>/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/manual' make[4]: Entering directory '/<>/doc/html' make[4]: Leaving directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' installing parsed Rd make[4]: Entering directory '/<>/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory 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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 '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[1]: Leaving directory '/<>' (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 '/<>/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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2017-04-15> Babel <3.10> and hyphenation patterns for 3 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\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 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\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 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6481--6484 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6645--6651 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6707--6714 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7012--7018 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7012--7018 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7353--7357 \T1/zi4/m/n/10 status _ codes$[][] \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7446--7448 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7471--7474 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7726--7736 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7797--7807 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9470--9475 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9815--9820 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9815--9820 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9953--9957 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10368--10371 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10382--10390 []\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 2735) in paragraph at lines 10422--10429 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11486--11490 []\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 11486--11490 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12063--12072 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12063--12072 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12722--12725 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13134--13136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13205--13209 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13249--13251 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13389--13392 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13507--13511 [][][]\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 13518--13521 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13781--13785 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14543--14546 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14643--14645 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14649--14653 []\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 10000) in paragraph at lines 14688--14692 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14688--14692 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15277--15281 []\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 15277--15281 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15450--15455 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15698--15702 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16004--16011 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] Underfull \hbox (badness 3679) in paragraph at lines 16402--16404 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16957--16960 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17210--17212 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17800--17802 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17892--17908 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18306--18309 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18564--18566 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] Underfull \hbox (badness 1231) in paragraph at lines 19564--19569 \T1/ptm/m/n/10 ple-men-ta-tions of \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 use Op enSSL --- for ex-am-ple ma-cOS re-ports [304] Underfull \hbox (badness 10000) in paragraph at lines 19587--19593 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19587--19593 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [305] Underfull \hbox (badness 10000) in paragraph at lines 19660--19664 []\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 19660--19664 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19795--19802 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19795--19802 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19811--19816 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20544--20549 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21298--21300 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22330--22336 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22491--22499 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22762--22765 []\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 22762--22765 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23044--23047 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23250--23256 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23250--23256 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24210--24212 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24454--24460 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24454--24460 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25033--25041 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25042--25045 []\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 25061--25063 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25170--25180 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25181--25187 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25217--25222 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25227--25229 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25486--25492 []\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 25486--25492 \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 25486--25492 \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 25499--25502 []\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 25523--25525 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25555--25560 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25561--25572 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25573--25576 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25583--25595 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25597--25604 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26262--26266 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26839--26842 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27666--27671 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] [440] Underfull \hbox (badness 1533) in paragraph at lines 28475--28478 []\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 [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28637--28648 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30160--30164 []\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 30160--30164 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [467] Underfull \hbox (badness 6188) in paragraph at lines 30182--30184 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30730--30732 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31405--31409 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31645--31652 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31801--31806 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31828--31834 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31904--31909 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1072) in paragraph at lines 34942--34946 []\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 34947--34951 []\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 34975--34981 []\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 34975--34981 \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 34975--34981 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34987--34994 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 34987--34994 \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 34987--34994 \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 [542] [543] [544] [545] [546] Underfull \hbox (badness 10000) in paragraph at lines 35285--35291 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35285--35291 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] Underfull \hbox (badness 3333) in paragraph at lines 37121--37126 []\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 [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 1472) in paragraph at lines 37744--37747 []\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 [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 10000) in paragraph at lines 38609--38613 []\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., [601] [602] [603] [604] Underfull \hbox (badness 10000) in paragraph at lines 38857--38860 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [605] Underfull \hbox (badness 10000) in paragraph at lines 38975--38979 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39037--39041 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39544--39546 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40384--40387 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 40391--40399 []\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 40391--40399 \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 [628] [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40668--40671 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40896--40903 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41557--41559 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41663--41667 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41839--41844 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 41855--41860 []\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 [651] [652] [653] [654] [655] [656] [657] [658] [659] Underfull \hbox (badness 5417) in paragraph at lines 42412--42416 []\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 [660] Underfull \hbox (badness 10000) in paragraph at lines 42473--42477 []\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 [661]) (./compiler-pkg.tex [662] Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3490--3493 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3504--3506 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4327--4334 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4564--4566 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4614--4619 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4641--4649 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4690--4697 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4708--4710 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1057) in paragraph at lines 4819--4824 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4879--4881 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5003--5012 []\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 5003--5012 \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 5003--5012 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5071--5078 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5071--5078 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5213--5221 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5290--5294 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6139--6141 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6237--6239 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6528--6534 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6729--6731 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3923--3927 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4370--4375 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4401--4404 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4751--4757 []\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 4751--4757 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4882--4885 [938 >/library/graphics/help/figures/ mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4943--4945 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/ oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5133--5135 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6604--6605 [][] [965] [966 >/library/graphics/help/fi gures/pch.pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7313--7318 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7429--7432 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8667--8669 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8669--8671 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8749 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\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 [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\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 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9294--9296 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10220--10225 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] Underfull \hbox (badness 2142) in paragraph at lines 10562--10565 []\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 ^^@ [1477] Underfull \hbox (badness 1253) in paragraph at lines 10581--10584 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10643--10647 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11039--11042 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11058--11067 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 11365--11368 []\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 [1490] [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11519 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11650--11652 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12233--12235 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12240--12242 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12574--12578 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 4518) in paragraph at lines 13269--13274 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13916--13921 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] Underfull \hbox (badness 10000) in paragraph at lines 14054--14058 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14061--14063 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15123--15127 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 1584) in paragraph at lines 15635--15641 []\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 [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17272--17274 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 10000) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18183--18188 []\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 18188--18191 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1454) in paragraph at lines 18201--18205 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1602] Underfull \hbox (badness 2662) in paragraph at lines 18209--18213 []\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 [1603] [1604] Underfull \vbox (badness 3803) has occurred while \output is active [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18825--18828 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19311--19315 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19561--19563 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19564--19567 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19939--19942 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19966--19968 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Underfull \hbox (badness 10000) in paragraph at lines 21014--21020 []\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 , [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22352--22358 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22897--22897 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23147--23150 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23732--23735 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23783--23787 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24253--24259 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24450--24452 []\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 24463--24465 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24933--24938 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 25975--25980 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26037--26042 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26094--26099 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26155--26161 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26368--26373 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26424--26429 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1741] Underfull \hbox (badness 3514) in paragraph at lines 26481--26486 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26536--26541 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26605--26610 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27735--27737 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27945--27948 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28259--28263 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28376--28379 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28559--28562 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29685--29689 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30049--30053 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30533--30537 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30610--30615 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30632--30634 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31014--31019 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\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 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\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 1196--1199 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1539--1541 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\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 1684--1686 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2183--2183 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2817. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3099--3101 []\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 [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3938--3941 []\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 [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4245--4251 []\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 4245--4251 \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 [1920] Underfull \hbox (badness 5726) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4474--4484 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4474--4484 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4536--4540 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] 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 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\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 546--552 \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 [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\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 660--666 \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 [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\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 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \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 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\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 [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\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 [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\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 [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5268--5270 []\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 [2012] Underfull \hbox (badness 1502) in paragraph at lines 5357--5362 []\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 5357--5362 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5530--5539 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5593--5596 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5730--5732 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5763--5767 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5871--5875 []\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 [2021] Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6027--6034 []\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 6027--6034 \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 6027--6034 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6107--6112 [][][]\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 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7524--7526 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7529--7534 []\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, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8084--8086 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8913--8916 []\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 [2069] Underfull \hbox (badness 3000) in paragraph at lines 9049--9054 [][][]\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 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9632--9637 [][][]\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 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10057--10061 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10057--10061 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10069--10073 []\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 10069--10073 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10363--10363 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10426--10428 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10602--10604 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10821--10825 []\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 10852--10858 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10970--10973 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. 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If [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11352--11356 []\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 11368--11371 []\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 [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11737--11742 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11746--11749 []\T1/ptm/m/n/10 the page width to be used. 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LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.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 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Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning input file refman.idx.................done (13376 entries accepted, 34 rejected). Sorting entries...........................................................................................................................................done (203405 comparisons). Generating output file refman.ind................done (13225 lines written, 49 warnings). Output written in refman.ind. Transcript written in refman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2017-04-15> Babel <3.10> and hyphenation patterns for 3 language(s) loaded. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\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 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\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 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6481--6484 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6645--6651 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6707--6714 \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 [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7012--7018 []\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 7012--7018 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7353--7357 \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7446--7448 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7471--7474 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7726--7736 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7797--7807 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9470--9475 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9815--9820 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9815--9820 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9953--9957 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10368--10371 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10382--10390 []\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 2735) in paragraph at lines 10422--10429 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11486--11490 []\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 11486--11490 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12063--12072 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12063--12072 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12722--12725 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13134--13136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13205--13209 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13249--13251 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13389--13392 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13507--13511 [][][]\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 13518--13521 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13781--13785 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14543--14546 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14643--14645 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14649--14653 []\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 10000) in paragraph at lines 14688--14692 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14688--14692 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15277--15281 []\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 15277--15281 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15450--15455 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15698--15702 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16004--16011 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] Underfull \hbox (badness 3679) in paragraph at lines 16402--16404 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16957--16960 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17210--17212 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17800--17802 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17892--17908 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18306--18309 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18564--18566 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] Underfull \hbox (badness 1231) in paragraph at lines 19564--19569 \T1/ptm/m/n/10 ple-men-ta-tions of \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 use Op enSSL --- for ex-am-ple ma-cOS re-ports [304] Underfull \hbox (badness 10000) in paragraph at lines 19587--19593 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19587--19593 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [305] Underfull \hbox (badness 10000) in paragraph at lines 19660--19664 []\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 19660--19664 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19795--19802 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19795--19802 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19811--19816 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20544--20549 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21298--21300 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22330--22336 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22491--22499 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22762--22765 []\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 22762--22765 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23044--23047 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23250--23256 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23250--23256 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24210--24212 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24454--24460 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24454--24460 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25033--25041 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25042--25045 []\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 25061--25063 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25170--25180 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25181--25187 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25217--25222 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25227--25229 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25486--25492 []\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 25486--25492 \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 25486--25492 \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 25499--25502 []\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 25523--25525 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25555--25560 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25561--25572 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25573--25576 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25583--25595 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25597--25604 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26262--26266 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26839--26842 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27666--27671 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] [440] Underfull \hbox (badness 1533) in paragraph at lines 28475--28478 []\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 [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28637--28648 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30160--30164 []\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 30160--30164 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [467] Underfull \hbox (badness 6188) in paragraph at lines 30182--30184 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30730--30732 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31405--31409 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31645--31652 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31801--31806 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31828--31834 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31904--31909 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1072) in paragraph at lines 34942--34946 []\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 34947--34951 []\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 34975--34981 []\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 34975--34981 \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 34975--34981 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34987--34994 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 34987--34994 \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 34987--34994 \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 [542] [543] [544] [545] [546] Underfull \hbox (badness 10000) in paragraph at lines 35285--35291 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35285--35291 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] Underfull \hbox (badness 3333) in paragraph at lines 37121--37126 []\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 [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 1472) in paragraph at lines 37744--37747 []\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 [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 10000) in paragraph at lines 38609--38613 []\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., [601] [602] [603] [604] Underfull \hbox (badness 10000) in paragraph at lines 38857--38860 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [605] Underfull \hbox (badness 10000) in paragraph at lines 38975--38979 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39037--39041 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39544--39546 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40384--40387 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 40391--40399 []\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 40391--40399 \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 [628] [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40668--40671 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40896--40903 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41557--41559 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41663--41667 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41839--41844 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 41855--41860 []\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 [651] [652] [653] [654] [655] [656] [657] [658] [659] Underfull \hbox (badness 5417) in paragraph at lines 42412--42416 []\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 [660] Underfull \hbox (badness 10000) in paragraph at lines 42473--42477 []\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 [661]) (./compiler-pkg.tex [662] Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3490--3493 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3504--3506 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4327--4334 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4564--4566 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4614--4619 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4641--4649 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4690--4697 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4708--4710 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1057) in paragraph at lines 4819--4824 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4879--4881 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5003--5012 []\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 5003--5012 \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 5003--5012 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5071--5078 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5071--5078 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5213--5221 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5290--5294 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6139--6141 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6237--6239 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6528--6534 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6729--6731 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3923--3927 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4370--4375 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4401--4404 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4751--4757 []\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 4751--4757 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4882--4885 [938 >/library/graphics/help/figures/ mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4943--4945 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/ oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5133--5135 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6604--6605 [][] [965] [966 >/library/graphics/help/fi gures/pch.pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7313--7318 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7429--7432 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8667--8669 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8669--8671 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8749 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\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 [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\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 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9294--9296 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10220--10225 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] Underfull \hbox (badness 2142) in paragraph at lines 10562--10565 []\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 ^^@ [1477] Underfull \hbox (badness 1253) in paragraph at lines 10581--10584 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10643--10647 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11039--11042 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11058--11067 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 11365--11368 []\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 [1490] [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11519 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11650--11652 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12233--12235 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12240--12242 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12574--12578 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 4518) in paragraph at lines 13269--13274 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13916--13921 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] Underfull \hbox (badness 10000) in paragraph at lines 14054--14058 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14061--14063 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15123--15127 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 1584) in paragraph at lines 15635--15641 []\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 [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17272--17274 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 10000) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18183--18188 []\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 18188--18191 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1454) in paragraph at lines 18201--18205 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1602] Underfull \hbox (badness 2662) in paragraph at lines 18209--18213 []\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 [1603] [1604] Underfull \vbox (badness 3803) has occurred while \output is active [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18825--18828 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19311--19315 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19561--19563 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19564--19567 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19939--19942 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19966--19968 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Underfull \hbox (badness 10000) in paragraph at lines 21014--21020 []\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 , [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22352--22358 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22897--22897 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23147--23150 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23732--23735 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23783--23787 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24253--24259 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24450--24452 []\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 24463--24465 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24933--24938 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 25975--25980 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26037--26042 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26094--26099 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26155--26161 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26368--26373 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26424--26429 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1741] Underfull \hbox (badness 3514) in paragraph at lines 26481--26486 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26536--26541 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26605--26610 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27735--27737 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27945--27948 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28259--28263 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28376--28379 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28559--28562 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29685--29689 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30049--30053 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30533--30537 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30610--30615 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30632--30634 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31014--31019 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\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 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\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 1196--1199 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1539--1541 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\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 1684--1686 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2183--2183 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2817. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3099--3101 []\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 [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3938--3941 []\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 [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4245--4251 []\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 4245--4251 \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 [1920] Underfull \hbox (badness 5726) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4474--4484 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4474--4484 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4536--4540 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] 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 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\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 546--552 \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 [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\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 660--666 \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 [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\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 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \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 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\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 [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\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 [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\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 [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5268--5270 []\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 [2012] Underfull \hbox (badness 1502) in paragraph at lines 5357--5362 []\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 5357--5362 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5530--5539 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5593--5596 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5730--5732 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5763--5767 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5871--5875 []\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 [2021] Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6027--6034 []\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 6027--6034 \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 6027--6034 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6107--6112 [][][]\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 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7524--7526 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7529--7534 []\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, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8084--8086 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8913--8916 []\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 [2069] Underfull \hbox (badness 3000) in paragraph at lines 9049--9054 [][][]\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 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9632--9637 [][][]\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 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10057--10061 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10057--10061 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10069--10073 []\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 10069--10073 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10363--10363 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10426--10428 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10602--10604 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10821--10825 []\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 10852--10858 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10970--10973 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. 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If [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11352--11356 []\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 11368--11371 []\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 [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11737--11742 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11746--11749 []\T1/ptm/m/n/10 the page width to be used. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\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 . 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Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\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 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\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 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6481--6484 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6645--6651 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6707--6714 \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 [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7012--7018 []\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 7012--7018 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7353--7357 \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7446--7448 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7471--7474 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7726--7736 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7797--7807 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9470--9475 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9815--9820 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9815--9820 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9953--9957 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10368--10371 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10382--10390 []\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 2735) in paragraph at lines 10422--10429 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11486--11490 []\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 11486--11490 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12063--12072 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12063--12072 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12722--12725 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13134--13136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13205--13209 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13249--13251 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13389--13392 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13507--13511 [][][]\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 13518--13521 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13781--13785 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14543--14546 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14643--14645 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14649--14653 []\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 10000) in paragraph at lines 14688--14692 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14688--14692 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15277--15281 []\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 15277--15281 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15450--15455 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15698--15702 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16004--16011 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] Underfull \hbox (badness 3679) in paragraph at lines 16402--16404 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16957--16960 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17210--17212 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17800--17802 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17892--17908 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18306--18309 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18564--18566 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] Underfull \hbox (badness 1231) in paragraph at lines 19564--19569 \T1/ptm/m/n/10 ple-men-ta-tions of \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 use Op enSSL --- for ex-am-ple ma-cOS re-ports [304] Underfull \hbox (badness 10000) in paragraph at lines 19587--19593 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19587--19593 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [305] Underfull \hbox (badness 10000) in paragraph at lines 19660--19664 []\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 19660--19664 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19795--19802 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19795--19802 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19811--19816 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20544--20549 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21298--21300 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22330--22336 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22491--22499 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22762--22765 []\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 22762--22765 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23044--23047 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23250--23256 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23250--23256 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24210--24212 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24454--24460 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24454--24460 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25033--25041 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25042--25045 []\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 25061--25063 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25170--25180 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25181--25187 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25217--25222 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25227--25229 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25486--25492 []\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 25486--25492 \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 25486--25492 \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 25499--25502 []\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 25523--25525 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25555--25560 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25561--25572 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25573--25576 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25583--25595 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25597--25604 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26262--26266 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26839--26842 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27666--27671 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] [440] Underfull \hbox (badness 1533) in paragraph at lines 28475--28478 []\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 [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28637--28648 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30160--30164 []\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 30160--30164 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [467] Underfull \hbox (badness 6188) in paragraph at lines 30182--30184 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30730--30732 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31405--31409 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31645--31652 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31801--31806 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31828--31834 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31904--31909 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1072) in paragraph at lines 34942--34946 []\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 34947--34951 []\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 34975--34981 []\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 34975--34981 \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 34975--34981 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34987--34994 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 34987--34994 \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 34987--34994 \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 [542] [543] [544] [545] [546] Underfull \hbox (badness 10000) in paragraph at lines 35285--35291 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35285--35291 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] Underfull \hbox (badness 3333) in paragraph at lines 37121--37126 []\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 [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 1472) in paragraph at lines 37744--37747 []\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 [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 10000) in paragraph at lines 38609--38613 []\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., [601] [602] [603] [604] Underfull \hbox (badness 10000) in paragraph at lines 38857--38860 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [605] Underfull \hbox (badness 10000) in paragraph at lines 38975--38979 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39037--39041 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39544--39546 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40384--40387 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 40391--40399 []\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 40391--40399 \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 [628] [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40668--40671 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40896--40903 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41557--41559 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41663--41667 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41839--41844 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 41855--41860 []\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 [651] [652] [653] [654] [655] [656] [657] [658] [659] Underfull \hbox (badness 5417) in paragraph at lines 42412--42416 []\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 [660] Underfull \hbox (badness 10000) in paragraph at lines 42473--42477 []\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 [661]) (./compiler-pkg.tex [662] Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3490--3493 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3504--3506 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4327--4334 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4564--4566 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4614--4619 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4641--4649 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4690--4697 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4708--4710 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1057) in paragraph at lines 4819--4824 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4879--4881 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5003--5012 []\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 5003--5012 \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 5003--5012 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5071--5078 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5071--5078 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5213--5221 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5290--5294 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6139--6141 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6237--6239 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6528--6534 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6729--6731 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3923--3927 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4370--4375 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4401--4404 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4751--4757 []\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 4751--4757 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4882--4885 [938 >/library/graphics/help/figures/ mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4943--4945 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/ oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5133--5135 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6604--6605 [][] [965] [966 >/library/graphics/help/fi gures/pch.pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7313--7318 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7429--7432 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8667--8669 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8669--8671 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8749 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\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 [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\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 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9294--9296 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10220--10225 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] Underfull \hbox (badness 2142) in paragraph at lines 10562--10565 []\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 ^^@ [1477] Underfull \hbox (badness 1253) in paragraph at lines 10581--10584 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10643--10647 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11039--11042 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11058--11067 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 11365--11368 []\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 [1490] [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11519 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11650--11652 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12233--12235 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12240--12242 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12574--12578 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 4518) in paragraph at lines 13269--13274 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13916--13921 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] Underfull \hbox (badness 10000) in paragraph at lines 14054--14058 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14061--14063 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15123--15127 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 1584) in paragraph at lines 15635--15641 []\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 [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17272--17274 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 10000) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18183--18188 []\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 18188--18191 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1454) in paragraph at lines 18201--18205 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1602] Underfull \hbox (badness 2662) in paragraph at lines 18209--18213 []\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 [1603] [1604] Underfull \vbox (badness 3803) has occurred while \output is active [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18825--18828 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19311--19315 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19561--19563 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19564--19567 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19939--19942 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19966--19968 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Underfull \hbox (badness 10000) in paragraph at lines 21014--21020 []\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 , [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22352--22358 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22897--22897 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23147--23150 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23732--23735 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23783--23787 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24253--24259 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24450--24452 []\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 24463--24465 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24933--24938 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 25975--25980 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26037--26042 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26094--26099 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26155--26161 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26368--26373 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26424--26429 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1741] Underfull \hbox (badness 3514) in paragraph at lines 26481--26486 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26536--26541 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26605--26610 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27735--27737 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27945--27948 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28259--28263 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28376--28379 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28559--28562 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29685--29689 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30049--30053 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30533--30537 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30610--30615 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30632--30634 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31014--31019 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\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 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\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 1196--1199 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1539--1541 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\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 1684--1686 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2183--2183 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2817. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3099--3101 []\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 [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3938--3941 []\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 [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4245--4251 []\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 4245--4251 \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 [1920] Underfull \hbox (badness 5726) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4474--4484 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4474--4484 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4536--4540 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] 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 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\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 546--552 \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 [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\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 660--666 \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 [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\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 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \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 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\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 [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\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 [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\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 [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5268--5270 []\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 [2012] Underfull \hbox (badness 1502) in paragraph at lines 5357--5362 []\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 5357--5362 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5530--5539 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5593--5596 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5730--5732 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5763--5767 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5871--5875 []\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 [2021] Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6027--6034 []\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 6027--6034 \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 6027--6034 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6107--6112 [][][]\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 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7524--7526 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7529--7534 []\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, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8084--8086 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8913--8916 []\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 [2069] Underfull \hbox (badness 3000) in paragraph at lines 9049--9054 [][][]\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 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9632--9637 [][][]\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 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10057--10061 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10057--10061 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10069--10073 []\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 10069--10073 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10363--10363 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10426--10428 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10602--10604 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10821--10825 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10852--10858 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10970--10973 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10974--10977 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2101] Underfull \hbox (badness 1009) in paragraph at lines 11046--11057 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11352--11356 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11368--11371 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11737--11742 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11746--11749 []\T1/ptm/m/n/10 the page width to be used. 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Transcript written on refman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1880--1892 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2026--2026 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2218--2229 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] Overfull \hbox (119.26523pt too wide) in paragraph at lines 2323--2334 []@textrm The de-fault com-pil-ers spec-i-fied are shown in file @texttt /Libra ry/Frameworks/R.framework/Resources/etc/Makeconf[]@textrm . [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2691--2691 []@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 2711--2711 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2712--2712 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3344--3344 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3953--3953 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] [52] [53] Appendix B [54] [55] [56] [57] [58] [59] Appendix C [60] [61] [62] [63] [64] [65] Overfull \hbox (78.17732pt too wide) in paragraph at lines 4948--4948 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [66] Overfull \hbox (106.92076pt too wide) in paragraph at lines 4986--4986 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 5122--5127 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5137--5137 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Content s/Home[] [69] [70] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5305--5305 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.5/lib:/usr/local/lib:/opt/ csw/lib"[] [71] Underfull \hbox (badness 10000) in paragraph at lines 5402--5408 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (14.94176pt too wide) in paragraph at lines 5411--5411 []@texttt PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgc onfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5418--5418 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [72] Underfull \hbox (badness 10000) in paragraph at lines 5499--5503 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [73] Underfull \hbox (badness 10000) in paragraph at lines 5528--5532 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/sparcv9[] @textrm or [74] [75] [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) Output written on R-admin.pdf (86 pages, 474193 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-admin.toc [-1] [-2]) [-3] (/<>/doc/manual/R-admin.toc) (/<>/doc/manual/R-admin.toc) Chapter 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] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1880--1892 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2026--2026 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2218--2229 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] Overfull \hbox (119.26523pt too wide) in paragraph at lines 2323--2334 []@textrm The de-fault com-pil-ers spec-i-fied are shown in file @texttt /Libra ry/Frameworks/R.framework/Resources/etc/Makeconf[]@textrm . [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2691--2691 []@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 2711--2711 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2712--2712 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3344--3344 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3953--3953 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] [52] Appendix B [53] [54] [55] [56] [57] [58] Appendix C [59] [60] [61] [62] [63] [64] Overfull \hbox (78.17732pt too wide) in paragraph at lines 4948--4948 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [65] Overfull \hbox (106.92076pt too wide) in paragraph at lines 4986--4986 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [66] [67] Underfull \hbox (badness 10000) in paragraph at lines 5122--5127 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5137--5137 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Content s/Home[] [68] [69] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5305--5305 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.5/lib:/usr/local/lib:/opt/ csw/lib"[] [70] Underfull \hbox (badness 10000) in paragraph at lines 5402--5408 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (14.94176pt too wide) in paragraph at lines 5411--5411 []@texttt PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgc onfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5418--5418 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [71] Underfull \hbox (badness 10000) in paragraph at lines 5499--5503 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [72] Underfull \hbox (badness 10000) in paragraph at lines 5528--5532 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/sparcv9[] @textrm or [73] [74] [75] Appendix D [76] [77] [78] (Function and variable index) [79] (Concept index) [80] (Environment variable index) [81] [82] ) (see the transcript file for additional information)pdfTeX warning (dest): name {83} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (87 pages, 519669 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-admin.toc [-1] [-2]) [-3] (/<>/doc/manual/R-admin.toc) (/<>/doc/manual/R-admin.toc) Chapter 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] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1880--1892 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2026--2026 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2218--2229 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] Overfull \hbox (119.26523pt too wide) in paragraph at lines 2323--2334 []@textrm The de-fault com-pil-ers spec-i-fied are shown in file @texttt /Libra ry/Frameworks/R.framework/Resources/etc/Makeconf[]@textrm . [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2691--2691 []@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 2711--2711 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2712--2712 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3344--3344 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3953--3953 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] [52] Appendix B [53] [54] [55] [56] [57] [58] Appendix C [59] [60] [61] [62] [63] [64] Overfull \hbox (78.17732pt too wide) in paragraph at lines 4948--4948 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [65] Overfull \hbox (106.92076pt too wide) in paragraph at lines 4986--4986 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [66] [67] Underfull \hbox (badness 10000) in paragraph at lines 5122--5127 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5137--5137 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Content s/Home[] [68] [69] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5305--5305 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.5/lib:/usr/local/lib:/opt/ csw/lib"[] [70] Underfull \hbox (badness 10000) in paragraph at lines 5402--5408 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (14.94176pt too wide) in paragraph at lines 5411--5411 []@texttt PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgc onfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5418--5418 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [71] Underfull \hbox (badness 10000) in paragraph at lines 5499--5503 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [72] Underfull \hbox (badness 10000) in paragraph at lines 5528--5532 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/sparcv9[] @textrm or [73] [74] [75] Appendix D [76] [77] [78] (Function and variable index) [79] (Concept index) [80] (Environment variable index) [81] [82] ) (see the transcript file for additional information) Output written on R-admin.pdf (87 pages, 519609 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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] No file R-data.vrs. (Concept index) [35] No file R-data.cps. [36] ) (see the transcript file for additional information) Output written on R-data.pdf (39 pages, 272960 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-data.toc [-1]) [-2] (/<>/doc/manual/R-data.toc) (/<>/doc/manual/R-data.toc) (Acknowledgements) (/<>/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 (7.16699pt too high) has occurred while \output is active [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 312860 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-data.toc [-1]) [-2] (/<>/doc/manual/R-data.toc) (/<>/doc/manual/R-data.toc) (Acknowledgements) (/<>/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 . 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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 (7.16699pt too high) has occurred while \output is active [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 312861 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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] Overfull \vbox (0.24982pt too high) has occurred while \output is active [20] [21] [22] [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1889--1889 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [24] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2222--2222 []@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 2224--2224 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2366--2366 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [31] Underfull \hbox (badness 10000) in paragraph at lines 2473--2475 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [32] [33] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2595--2595 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [34] [35] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2720--2722 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4525--4525 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (36.62297pt too wide) in paragraph at lines 4526--4526 []@texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (36.62297pt too wide) in paragraph at lines 4527--4527 []@texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not availa ble")[] [59] [60] [61] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4757--4757 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [62] [63] [64] Overfull \hbox (30.87428pt too wide) in paragraph at lines 4967--4967 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4968--4968 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [65] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5062--5062 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [66] [67] [68] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5296--5296 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [69] [70] [71] Chapter 2 [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6556--6563 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 6875--6879 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7476--7476 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [99] [100] [101] Chapter 4 [102] [103] [104] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7853--7853 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [105] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7894--7894 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [106] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7998--7998 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [107] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8028--8037 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [108] [109] [110] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8307--8308 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [111] [112] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8427--8427 []@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 8455--8457 []@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 8469--8469 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [113] [114] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8591--8591 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [115] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8640--8640 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8643--8643 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [116] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8722--8722 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [117] [118] Chapter 5 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9689--9689 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9738--9738 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [130] [131] [132] [133] [134] [135] [136] [137] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10297--10297 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [138] [139] [140] [141] [142] [143] [144] [145] [146] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11069--11069 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [147] Underfull \hbox (badness 10000) in paragraph at lines 11130--11132 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [148] [149] [150] [151] [152] [153] [154] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11639--11639 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [155] [156] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11762--11762 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11767--11767 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11822--11822 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [157] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11834--11834 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [158] Overfull \hbox (26.43913pt too wide) in paragraph at lines 11933--11933 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12069--12069 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [161] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12151--12151 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [162] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12238--12238 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 13397--13401 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [176] [177] Warning: unbalanced parentheses in @def... [178] [179] [180] [181] [182] Chapter 7 [183] [184] Chapter 8 [185] [186] [187] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14274--14274 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [188] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14306--14306 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14322--14322 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [189] [190] [191] [192] Underfull \hbox (badness 10000) in paragraph at lines 14565--14572 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [193] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14948--14952 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [198] No file R-exts.vrs. (Concept index) [199] No file R-exts.cps. [200] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (203 pages, 884666 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/<>/doc/manual/R-exts.toc) (/<>/doc/manual/R-exts.toc) (Acknowledgements) (/<>/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 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1889--1889 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [24] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2222--2222 []@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 2224--2224 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2366--2366 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [31] Underfull \hbox (badness 10000) in paragraph at lines 2473--2475 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [32] [33] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2595--2595 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [34] [35] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2720--2722 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4525--4525 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (36.62297pt too wide) in paragraph at lines 4526--4526 []@texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (36.62297pt too wide) in paragraph at lines 4527--4527 []@texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not availa ble")[] [59] [60] [61] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4757--4757 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [62] [63] [64] Overfull \hbox (30.87428pt too wide) in paragraph at lines 4967--4967 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4968--4968 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [65] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5062--5062 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [66] [67] [68] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5296--5296 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [69] [70] [71] Chapter 2 [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6556--6563 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 6875--6879 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7476--7476 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [99] [100] [101] Chapter 4 [102] [103] [104] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7853--7853 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [105] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7894--7894 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [106] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7998--7998 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [107] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8028--8037 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [108] [109] [110] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8307--8308 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [111] [112] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8427--8427 []@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 8455--8457 []@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 8469--8469 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [113] [114] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8591--8591 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [115] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8640--8640 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8643--8643 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [116] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8722--8722 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [117] [118] Chapter 5 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9689--9689 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9738--9738 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [130] [131] [132] [133] [134] [135] [136] [137] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10297--10297 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [138] [139] [140] [141] [142] [143] [144] [145] [146] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11069--11069 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [147] Underfull \hbox (badness 10000) in paragraph at lines 11130--11132 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [148] [149] [150] [151] [152] [153] [154] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11639--11639 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [155] [156] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11762--11762 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11767--11767 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11822--11822 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [157] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11834--11834 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [158] Overfull \hbox (26.43913pt too wide) in paragraph at lines 11933--11933 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12069--12069 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [161] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12151--12151 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [162] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12238--12238 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 13397--13401 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [176] Warning: unbalanced parentheses in @def... [177] [178] [179] [180] [181] [182] Chapter 7 [183] [184] Chapter 8 [185] [186] [187] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14274--14274 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [188] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14306--14306 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14322--14322 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [189] [190] [191] [192] Underfull \hbox (badness 10000) in paragraph at lines 14565--14572 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [193] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14948--14952 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [198] [199] [200] [201] (Concept index) [202] [203] [204] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (211 pages, 947107 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/<>/doc/manual/R-exts.toc) (/<>/doc/manual/R-exts.toc) (Acknowledgements) (/<>/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 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1889--1889 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [24] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2222--2222 []@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 2224--2224 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2366--2366 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [31] Underfull \hbox (badness 10000) in paragraph at lines 2473--2475 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [32] [33] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2595--2595 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [34] [35] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2720--2722 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4525--4525 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (36.62297pt too wide) in paragraph at lines 4526--4526 []@texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (36.62297pt too wide) in paragraph at lines 4527--4527 []@texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not availa ble")[] [59] [60] [61] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4757--4757 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [62] [63] [64] Overfull \hbox (30.87428pt too wide) in paragraph at lines 4967--4967 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4968--4968 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [65] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5062--5062 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [66] [67] [68] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5296--5296 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [69] [70] [71] Chapter 2 [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6556--6563 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [86] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 6875--6879 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7476--7476 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [99] [100] [101] Chapter 4 [102] [103] [104] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7853--7853 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [105] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7894--7894 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [106] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7998--7998 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [107] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8028--8037 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [108] [109] [110] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8307--8308 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [111] [112] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8427--8427 []@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 8455--8457 []@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 8469--8469 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [113] [114] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8591--8591 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [115] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8640--8640 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8643--8643 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [116] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8722--8722 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [117] [118] Chapter 5 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9689--9689 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9738--9738 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [130] [131] [132] [133] [134] [135] [136] [137] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10297--10297 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [138] [139] [140] [141] [142] [143] [144] [145] [146] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11069--11069 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [147] Underfull \hbox (badness 10000) in paragraph at lines 11130--11132 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [148] [149] [150] [151] [152] [153] [154] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11639--11639 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [155] [156] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11762--11762 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11767--11767 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11822--11822 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [157] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11834--11834 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [158] Overfull \hbox (26.43913pt too wide) in paragraph at lines 11933--11933 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12069--12069 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [161] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12151--12151 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [162] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12238--12238 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 13397--13401 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [176] Warning: unbalanced parentheses in @def... [177] [178] [179] [180] [181] [182] Chapter 7 [183] [184] Chapter 8 [185] [186] [187] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14274--14274 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [188] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14306--14306 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14322--14322 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [189] [190] [191] [192] Underfull \hbox (badness 10000) in paragraph at lines 14565--14572 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [193] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14948--14952 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [198] [199] [200] [201] (Concept index) [202] [203] [204] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (211 pages, 947060 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3386--3394 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 367770 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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}] (/<>/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/<>/doc/manual/R-FAQ.toc) (/<>/doc/manual/R-FAQ.toc) Chapter 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] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3386--3394 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 384487 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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}] (/<>/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/<>/doc/manual/R-FAQ.toc) (/<>/doc/manual/R-FAQ.toc) Chapter 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] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3386--3394 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 384485 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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] >/doc/manual /images/hist.pdf> >/doc/manual/images /ecdf.pdf> [38] >/doc/manual/images/Q Q.pdf> [39] >/doc/manual/images/ice.p df> [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] >/doc/manual /images/fig11.pdf> [77] >/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-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb> Output written on R-intro.pdf (107 pages, 584238 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/<>/doc/manual/R-intro.toc) (/<>/doc/manual/R-intro.toc) (Preface) (/<>/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] >/doc/manual /images/hist.pdf> >/doc/manual/images /ecdf.pdf> [38] >/doc/manual/images/Q Q.pdf> [39] >/doc/manual/images/ice.p df> [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] >/doc/manual /images/fig11.pdf> [77] >/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) Output written on R-intro.pdf (113 pages, 633796 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/<>/doc/manual/R-intro.toc) (/<>/doc/manual/R-intro.toc) (Preface) (/<>/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] >/doc/manual /images/hist.pdf> >/doc/manual/images /ecdf.pdf> [38] >/doc/manual/images/Q Q.pdf> [39] >/doc/manual/images/ice.p df> [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] >/doc/manual /images/fig11.pdf> [77] >/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) Output written on R-intro.pdf (113 pages, 633855 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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1442--1442 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1443--1443 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1444--1444 [] @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 1445--1445 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [18] [19] [20] [21] [22] [23] Chapter 2 [24] [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1970--1970 [] @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 3617--3626 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3991--3999 @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 3991--3999 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] Chapter 9 [58] [59] Chapter 10 [60] Chapter 11 [61] Chapter 12 [62] [63] (Function and variable index) [64] [65] No file R-ints.vrs. (Concept index) [66] No file R-ints.cps. [67] ) (see the transcript file for additional information) Output written on R-ints.pdf (70 pages, 392793 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-ints.toc [-1] [-2]) [-3] (/<>/doc/manual/R-ints.toc) (/<>/doc/manual/R-ints.toc) Chapter 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] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1442--1442 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1443--1443 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1444--1444 [] @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 1445--1445 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [18] [19] [20] [21] [22] [23] Chapter 2 [24] [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1970--1970 [] @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 3617--3626 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3991--3999 @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 3991--3999 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] Chapter 9 [58] [59] Chapter 10 [60] Chapter 11 [61] Chapter 12 [62] [63] (Function and variable index) [64] [65] [66] (Concept index) [67] [68] ) (see the transcript file for additional information) Output written on R-ints.pdf (73 pages, 441234 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-ints.toc [-1] [-2]) [-3] (/<>/doc/manual/R-ints.toc) (/<>/doc/manual/R-ints.toc) Chapter 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] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1442--1442 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1443--1443 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1444--1444 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1445--1445 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [18] [19] [20] [21] [22] [23] Chapter 2 [24] [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1970--1970 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3991--3999 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] Chapter 9 [58] [59] Chapter 10 [60] Chapter 11 [61] Chapter 12 [62] [63] (Function and variable index) [64] [65] [66] (Concept index) [67] [68] ) (see the transcript file for additional information) Output written on R-ints.pdf (73 pages, 441235 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] No file R-lang.vrs. (Concept Index) [60] No file R-lang.cps. Appendix A [61] [62] ) (see the transcript file for additional information) Output written on R-lang.pdf (65 pages, 330554 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-lang.toc [-1] [-2]) [-3] (/<>/doc/manual/R-lang.toc) (/<>/doc/manual/R-lang.toc) Chapter 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] Overfull \vbox (81.99481pt too high) has occurred while \output is active Appendix A [62] [63] ) (see the transcript file for additional information) Output written on R-lang.pdf (68 pages, 379212 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2017-06-04.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/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 (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-lang.toc [-1] [-2]) [-3] (/<>/doc/manual/R-lang.toc) (/<>/doc/manual/R-lang.toc) Chapter 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] Overfull \vbox (81.99481pt too high) has occurred while \output is active Appendix A [62] [63] ) (see the transcript file for additional information) Output written on R-lang.pdf (68 pages, 379212 bytes). Transcript written on R-lang.log. make[1]: Leaving directory '/<>/doc/manual' /usr/bin/make -k pdf make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/manual' PDF/LaTeX documentation: full reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2017-04-15> Babel <3.10> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h 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/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)) Package hyperref Message: Driver (autodetected): hpdftex. 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(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\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 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\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 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6481--6484 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6645--6651 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6707--6714 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7012--7018 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7012--7018 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7353--7357 \T1/zi4/m/n/10 status _ codes$[][] \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7446--7448 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7471--7474 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7726--7736 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7797--7807 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9470--9475 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9815--9820 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9815--9820 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9953--9957 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10368--10371 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10382--10390 []\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 2735) in paragraph at lines 10422--10429 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11486--11490 []\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 11486--11490 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12063--12072 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12063--12072 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12722--12725 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13134--13136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13205--13209 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13249--13251 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13389--13392 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13507--13511 [][][]\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 13518--13521 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13781--13785 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14543--14546 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14643--14645 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14649--14653 []\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 10000) in paragraph at lines 14688--14692 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14688--14692 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15277--15281 []\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 15277--15281 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15450--15455 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15698--15702 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16004--16011 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] Underfull \hbox (badness 3679) in paragraph at lines 16402--16404 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16957--16960 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17210--17212 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17800--17802 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17892--17908 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18306--18309 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18564--18566 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] Underfull \hbox (badness 1231) in paragraph at lines 19564--19569 \T1/ptm/m/n/10 ple-men-ta-tions of \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 use Op enSSL --- for ex-am-ple ma-cOS re-ports [304] Underfull \hbox (badness 10000) in paragraph at lines 19587--19593 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19587--19593 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [305] Underfull \hbox (badness 10000) in paragraph at lines 19660--19664 []\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 19660--19664 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19795--19802 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19795--19802 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19811--19816 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20544--20549 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21298--21300 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22330--22336 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22491--22499 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22762--22765 []\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 22762--22765 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23044--23047 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23250--23256 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23250--23256 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24210--24212 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24454--24460 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24454--24460 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25033--25041 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25042--25045 []\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 25061--25063 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25170--25180 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25181--25187 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25217--25222 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25227--25229 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25486--25492 []\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 25486--25492 \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 25486--25492 \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 25499--25502 []\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 25523--25525 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25555--25560 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25561--25572 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25573--25576 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25583--25595 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25597--25604 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26262--26266 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26839--26842 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27666--27671 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] [440] Underfull \hbox (badness 1533) in paragraph at lines 28475--28478 []\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 [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28637--28648 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30160--30164 []\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 30160--30164 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [467] Underfull \hbox (badness 6188) in paragraph at lines 30182--30184 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30730--30732 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31405--31409 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31645--31652 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31801--31806 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31828--31834 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31904--31909 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1072) in paragraph at lines 34942--34946 []\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 34947--34951 []\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 34975--34981 []\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 34975--34981 \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 34975--34981 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34987--34994 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 34987--34994 \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 34987--34994 \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 [542] [543] [544] [545] [546] Underfull \hbox (badness 10000) in paragraph at lines 35285--35291 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35285--35291 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] Underfull \hbox (badness 3333) in paragraph at lines 37121--37126 []\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 [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 1472) in paragraph at lines 37744--37747 []\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 [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 10000) in paragraph at lines 38609--38613 []\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., [601] [602] [603] [604] Underfull \hbox (badness 10000) in paragraph at lines 38857--38860 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [605] Underfull \hbox (badness 10000) in paragraph at lines 38975--38979 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39037--39041 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39544--39546 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40384--40387 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 40391--40399 []\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 40391--40399 \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 [628] [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40668--40671 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40896--40903 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41557--41559 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41663--41667 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41839--41844 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 41855--41860 []\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 [651] [652] [653] [654] [655] [656] [657] [658] [659] Underfull \hbox (badness 5417) in paragraph at lines 42412--42416 []\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 [660] Underfull \hbox (badness 10000) in paragraph at lines 42473--42477 []\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 [661]) (./compiler-pkg.tex [662] Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3490--3493 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3504--3506 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4327--4334 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4564--4566 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4614--4619 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4641--4649 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4690--4697 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4708--4710 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1057) in paragraph at lines 4819--4824 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4879--4881 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5003--5012 []\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 5003--5012 \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 5003--5012 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5071--5078 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5071--5078 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5213--5221 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5290--5294 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6139--6141 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6237--6239 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6528--6534 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6729--6731 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3923--3927 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4370--4375 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4401--4404 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4751--4757 []\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 4751--4757 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4882--4885 [938 >/library/graphics/help/figures/ mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4943--4945 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/ oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5133--5135 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6604--6605 [][] [965] [966 >/library/graphics/help/fi gures/pch.pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7313--7318 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7429--7432 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8667--8669 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8669--8671 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8749 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\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 [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\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 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9294--9296 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10220--10225 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] Underfull \hbox (badness 2142) in paragraph at lines 10562--10565 []\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 ^^@ [1477] Underfull \hbox (badness 1253) in paragraph at lines 10581--10584 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10643--10647 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11039--11042 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11058--11067 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 11365--11368 []\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 [1490] [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11519 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11650--11652 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12233--12235 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12240--12242 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12574--12578 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 4518) in paragraph at lines 13269--13274 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13916--13921 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] Underfull \hbox (badness 10000) in paragraph at lines 14054--14058 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14061--14063 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15123--15127 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 1584) in paragraph at lines 15635--15641 []\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 [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17272--17274 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 10000) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18183--18188 []\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 18188--18191 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1454) in paragraph at lines 18201--18205 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1602] Underfull \hbox (badness 2662) in paragraph at lines 18209--18213 []\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 [1603] [1604] Underfull \vbox (badness 3803) has occurred while \output is active [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18825--18828 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19311--19315 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19561--19563 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19564--19567 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19939--19942 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19966--19968 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Underfull \hbox (badness 10000) in paragraph at lines 21014--21020 []\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 , [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22352--22358 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22897--22897 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23147--23150 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23732--23735 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23783--23787 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24253--24259 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24450--24452 []\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 24463--24465 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24933--24938 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 25975--25980 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26037--26042 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26094--26099 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26155--26161 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26368--26373 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26424--26429 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1741] Underfull \hbox (badness 3514) in paragraph at lines 26481--26486 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26536--26541 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26605--26610 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27735--27737 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27945--27948 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28259--28263 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28376--28379 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28559--28562 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29685--29689 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30049--30053 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30533--30537 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30610--30615 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30632--30634 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31014--31019 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\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 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\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 1196--1199 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1539--1541 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\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 1684--1686 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2183--2183 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2817. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3099--3101 []\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 [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3938--3941 []\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 [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4245--4251 []\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 4245--4251 \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 [1920] Underfull \hbox (badness 5726) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4474--4484 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4474--4484 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4536--4540 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] 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 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\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 546--552 \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 [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\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 660--666 \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 [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\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 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \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 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\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 [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\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 [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\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 [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5268--5270 []\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 [2012] Underfull \hbox (badness 1502) in paragraph at lines 5357--5362 []\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 5357--5362 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5530--5539 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5593--5596 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5730--5732 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5763--5767 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5871--5875 []\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 [2021] Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6027--6034 []\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 6027--6034 \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 6027--6034 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6107--6112 [][][]\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 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7524--7526 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7529--7534 []\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, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8084--8086 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8913--8916 []\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 [2069] Underfull \hbox (badness 3000) in paragraph at lines 9049--9054 [][][]\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 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9632--9637 [][][]\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 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10057--10061 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10057--10061 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10069--10073 []\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 10069--10073 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10363--10363 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10426--10428 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10602--10604 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10821--10825 []\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 10852--10858 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10970--10973 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. 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If [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11352--11356 []\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 11368--11371 []\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 [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11737--11742 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11746--11749 []\T1/ptm/m/n/10 the page width to be used. 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LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.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 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning input file fullrefman.idx.................done (13376 entries accepted, 34 rejected). Sorting entries...........................................................................................................................................done (203405 comparisons). Generating output file fullrefman.ind................done (13225 lines written, 49 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2017-04-15> Babel <3.10> and hyphenation patterns for 3 language(s) loaded. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\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 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\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 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6481--6484 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6645--6651 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6707--6714 \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 [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7012--7018 []\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 7012--7018 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7353--7357 \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7446--7448 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7471--7474 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7726--7736 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7797--7807 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9470--9475 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9815--9820 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9815--9820 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9953--9957 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10368--10371 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10382--10390 []\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 2735) in paragraph at lines 10422--10429 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11486--11490 []\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 11486--11490 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12063--12072 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12063--12072 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12722--12725 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13134--13136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13205--13209 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13249--13251 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13389--13392 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13507--13511 [][][]\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 13518--13521 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13781--13785 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14543--14546 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14643--14645 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14649--14653 []\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 10000) in paragraph at lines 14688--14692 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14688--14692 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15277--15281 []\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 15277--15281 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15450--15455 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15698--15702 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16004--16011 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] Underfull \hbox (badness 3679) in paragraph at lines 16402--16404 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16957--16960 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17210--17212 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17800--17802 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17892--17908 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18306--18309 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18564--18566 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] Underfull \hbox (badness 1231) in paragraph at lines 19564--19569 \T1/ptm/m/n/10 ple-men-ta-tions of \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 use Op enSSL --- for ex-am-ple ma-cOS re-ports [304] Underfull \hbox (badness 10000) in paragraph at lines 19587--19593 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19587--19593 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [305] Underfull \hbox (badness 10000) in paragraph at lines 19660--19664 []\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 19660--19664 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19795--19802 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19795--19802 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19811--19816 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20544--20549 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21298--21300 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22330--22336 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22491--22499 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22762--22765 []\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 22762--22765 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23044--23047 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23250--23256 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23250--23256 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24210--24212 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24454--24460 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24454--24460 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25033--25041 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25042--25045 []\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 25061--25063 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25170--25180 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25181--25187 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25217--25222 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25227--25229 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25486--25492 []\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 25486--25492 \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 25486--25492 \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 25499--25502 []\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 25523--25525 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25555--25560 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25561--25572 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25573--25576 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25583--25595 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25597--25604 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26262--26266 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26839--26842 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27666--27671 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] [440] Underfull \hbox (badness 1533) in paragraph at lines 28475--28478 []\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 [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28637--28648 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30160--30164 []\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 30160--30164 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [467] Underfull \hbox (badness 6188) in paragraph at lines 30182--30184 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30730--30732 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31405--31409 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31645--31652 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31801--31806 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31828--31834 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31904--31909 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1072) in paragraph at lines 34942--34946 []\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 34947--34951 []\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 34975--34981 []\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 34975--34981 \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 34975--34981 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34987--34994 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 34987--34994 \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 34987--34994 \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 [542] [543] [544] [545] [546] Underfull \hbox (badness 10000) in paragraph at lines 35285--35291 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35285--35291 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] Underfull \hbox (badness 3333) in paragraph at lines 37121--37126 []\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 [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 1472) in paragraph at lines 37744--37747 []\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 [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 10000) in paragraph at lines 38609--38613 []\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., [601] [602] [603] [604] Underfull \hbox (badness 10000) in paragraph at lines 38857--38860 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [605] Underfull \hbox (badness 10000) in paragraph at lines 38975--38979 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39037--39041 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39544--39546 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40384--40387 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 40391--40399 []\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 40391--40399 \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 [628] [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40668--40671 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40896--40903 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41557--41559 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41663--41667 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41839--41844 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 41855--41860 []\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 [651] [652] [653] [654] [655] [656] [657] [658] [659] Underfull \hbox (badness 5417) in paragraph at lines 42412--42416 []\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 [660] Underfull \hbox (badness 10000) in paragraph at lines 42473--42477 []\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 [661]) (./compiler-pkg.tex [662] Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3490--3493 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3504--3506 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4327--4334 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4564--4566 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4614--4619 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4641--4649 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4690--4697 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4708--4710 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1057) in paragraph at lines 4819--4824 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4879--4881 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5003--5012 []\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 5003--5012 \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 5003--5012 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5071--5078 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5071--5078 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5213--5221 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5290--5294 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6139--6141 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6237--6239 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6528--6534 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6729--6731 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3923--3927 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4370--4375 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4401--4404 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4751--4757 []\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 4751--4757 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4882--4885 [938 >/library/graphics/help/figures/ mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4943--4945 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/ oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5133--5135 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6604--6605 [][] [965] [966 >/library/graphics/help/fi gures/pch.pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7313--7318 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7429--7432 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8667--8669 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8669--8671 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8749 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\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 [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\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 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9294--9296 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10220--10225 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] Underfull \hbox (badness 2142) in paragraph at lines 10562--10565 []\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 ^^@ [1477] Underfull \hbox (badness 1253) in paragraph at lines 10581--10584 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10643--10647 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11039--11042 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11058--11067 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 11365--11368 []\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 [1490] [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11519 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11650--11652 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12233--12235 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12240--12242 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12574--12578 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 4518) in paragraph at lines 13269--13274 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13916--13921 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] Underfull \hbox (badness 10000) in paragraph at lines 14054--14058 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14061--14063 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15123--15127 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 1584) in paragraph at lines 15635--15641 []\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 [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17272--17274 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 10000) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18183--18188 []\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 18188--18191 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1454) in paragraph at lines 18201--18205 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1602] Underfull \hbox (badness 2662) in paragraph at lines 18209--18213 []\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 [1603] [1604] Underfull \vbox (badness 3803) has occurred while \output is active [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18825--18828 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19311--19315 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19561--19563 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19564--19567 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19939--19942 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19966--19968 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Underfull \hbox (badness 10000) in paragraph at lines 21014--21020 []\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 , [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22352--22358 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22897--22897 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23147--23150 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23732--23735 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23783--23787 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24253--24259 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24450--24452 []\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 24463--24465 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24933--24938 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 25975--25980 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26037--26042 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26094--26099 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26155--26161 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26368--26373 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26424--26429 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1741] Underfull \hbox (badness 3514) in paragraph at lines 26481--26486 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26536--26541 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26605--26610 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27735--27737 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27945--27948 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28259--28263 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28376--28379 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28559--28562 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29685--29689 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30049--30053 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30533--30537 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30610--30615 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30632--30634 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31014--31019 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\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 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\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 1196--1199 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1539--1541 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\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 1684--1686 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2183--2183 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2817. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3099--3101 []\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 [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3938--3941 []\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 [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4245--4251 []\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 4245--4251 \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 [1920] Underfull \hbox (badness 5726) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4474--4484 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4474--4484 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4536--4540 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] 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 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\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 546--552 \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 [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\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 660--666 \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 [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\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 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \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 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\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 [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\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 [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\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 [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5268--5270 []\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 [2012] Underfull \hbox (badness 1502) in paragraph at lines 5357--5362 []\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 5357--5362 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5530--5539 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5593--5596 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5730--5732 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5763--5767 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5871--5875 []\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 [2021] Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6027--6034 []\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 6027--6034 \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 6027--6034 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6107--6112 [][][]\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 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7524--7526 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7529--7534 []\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, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8084--8086 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8913--8916 []\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 [2069] Underfull \hbox (badness 3000) in paragraph at lines 9049--9054 [][][]\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 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9632--9637 [][][]\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 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10057--10061 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10057--10061 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10069--10073 []\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 10069--10073 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10363--10363 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10426--10428 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10602--10604 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10821--10825 []\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 10852--10858 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10970--10973 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. 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If [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11352--11356 []\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 11368--11371 []\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 [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11737--11742 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11746--11749 []\T1/ptm/m/n/10 the page width to be used. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\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 . 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Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\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 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\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 [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6481--6484 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6645--6651 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6645--6651 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6707--6714 \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 [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7012--7018 []\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 7012--7018 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7353--7357 \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7446--7448 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7471--7474 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7726--7736 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7797--7807 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9470--9475 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9815--9820 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9815--9820 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9953--9957 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10368--10371 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10382--10390 []\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 2735) in paragraph at lines 10422--10429 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11486--11490 []\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 11486--11490 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12063--12072 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12063--12072 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12722--12725 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13134--13136 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13205--13209 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13249--13251 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13389--13392 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13507--13511 [][][]\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 13518--13521 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13781--13785 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14543--14546 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14643--14645 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14649--14653 []\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 10000) in paragraph at lines 14688--14692 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14688--14692 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15277--15281 []\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 15277--15281 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15450--15455 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15698--15702 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16004--16011 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] Underfull \hbox (badness 3679) in paragraph at lines 16402--16404 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [254] [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16957--16960 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17210--17212 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17800--17802 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17892--17908 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18306--18309 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18564--18566 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] Underfull \hbox (badness 1231) in paragraph at lines 19564--19569 \T1/ptm/m/n/10 ple-men-ta-tions of \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 use Op enSSL --- for ex-am-ple ma-cOS re-ports [304] Underfull \hbox (badness 10000) in paragraph at lines 19587--19593 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19587--19593 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [305] Underfull \hbox (badness 10000) in paragraph at lines 19660--19664 []\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 19660--19664 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19795--19802 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19795--19802 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19811--19816 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20544--20549 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21298--21300 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22330--22336 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22491--22499 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22762--22765 []\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 22762--22765 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23044--23047 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23250--23256 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23250--23256 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23260--23263 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24210--24212 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24454--24460 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24454--24460 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25033--25041 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25042--25045 []\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 25061--25063 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25170--25180 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25181--25187 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25217--25222 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25227--25229 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25486--25492 []\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 25486--25492 \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 25486--25492 \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 25499--25502 []\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 25523--25525 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25555--25560 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25561--25572 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25573--25576 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25583--25595 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 25583--25595 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25597--25604 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25597--25604 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25944--25948 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26262--26266 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26839--26842 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27666--27671 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] [440] Underfull \hbox (badness 1533) in paragraph at lines 28475--28478 []\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 [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28637--28648 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30160--30164 []\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 30160--30164 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [467] Underfull \hbox (badness 6188) in paragraph at lines 30182--30184 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30730--30732 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31405--31409 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31645--31652 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31645--31652 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31801--31806 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31828--31834 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31904--31909 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] Underfull \hbox (badness 1072) in paragraph at lines 34942--34946 []\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 34947--34951 []\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 34975--34981 []\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 34975--34981 \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 34975--34981 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34987--34994 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 34987--34994 \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 34987--34994 \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 [542] [543] [544] [545] [546] Underfull \hbox (badness 10000) in paragraph at lines 35285--35291 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35285--35291 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] Underfull \hbox (badness 3333) in paragraph at lines 37121--37126 []\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 [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 1472) in paragraph at lines 37744--37747 []\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 [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 10000) in paragraph at lines 38609--38613 []\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., [601] [602] [603] [604] Underfull \hbox (badness 10000) in paragraph at lines 38857--38860 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [605] Underfull \hbox (badness 10000) in paragraph at lines 38975--38979 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39037--39041 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39544--39546 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40384--40387 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1990) in paragraph at lines 40391--40399 []\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 40391--40399 \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 [628] [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40668--40671 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40896--40903 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41557--41559 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41663--41667 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41839--41844 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 41855--41860 []\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 [651] [652] [653] [654] [655] [656] [657] [658] [659] Underfull \hbox (badness 5417) in paragraph at lines 42412--42416 []\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 [660] Underfull \hbox (badness 10000) in paragraph at lines 42473--42477 []\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 [661]) (./compiler-pkg.tex [662] Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2732--2733 [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3490--3493 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3504--3506 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4327--4334 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4564--4566 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4614--4619 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4641--4649 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4690--4697 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4698--4707 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4708--4710 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1057) in paragraph at lines 4819--4824 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4879--4881 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5003--5012 []\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 5003--5012 \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 5003--5012 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5071--5078 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5071--5078 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5213--5221 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5290--5294 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5742--5745 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6139--6141 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6237--6239 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6528--6534 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6729--6731 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3923--3927 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4370--4375 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4401--4404 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4751--4757 []\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 4751--4757 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4882--4885 [938 >/library/graphics/help/figures/ mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4943--4945 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/ oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5133--5135 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6604--6605 [][] [965] [966 >/library/graphics/help/fi gures/pch.pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7313--7318 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7429--7432 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8667--8669 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8669--8671 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8749 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\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 [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\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 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9294--9296 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10220--10225 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] Underfull \hbox (badness 2142) in paragraph at lines 10562--10565 []\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 ^^@ [1477] Underfull \hbox (badness 1253) in paragraph at lines 10581--10584 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10643--10647 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11039--11042 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 11058--11067 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 11365--11368 []\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 [1490] [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11519 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11650--11652 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12233--12235 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12240--12242 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12574--12578 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 4518) in paragraph at lines 13269--13274 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13916--13921 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] Underfull \hbox (badness 10000) in paragraph at lines 14054--14058 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14061--14063 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15123--15127 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 1584) in paragraph at lines 15635--15641 []\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 [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17272--17274 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 10000) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18183--18188 []\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 18188--18191 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1454) in paragraph at lines 18201--18205 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1602] Underfull \hbox (badness 2662) in paragraph at lines 18209--18213 []\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 [1603] [1604] Underfull \vbox (badness 3803) has occurred while \output is active [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18825--18828 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19311--19315 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19561--19563 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19564--19567 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19939--19942 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19966--19968 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Underfull \hbox (badness 10000) in paragraph at lines 21014--21020 []\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 , [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22352--22358 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22897--22897 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23147--23150 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23732--23735 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23783--23787 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24253--24259 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24450--24452 []\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 24463--24465 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24933--24938 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 25975--25980 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26037--26042 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26094--26099 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26155--26161 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26368--26373 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26424--26429 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1741] Underfull \hbox (badness 3514) in paragraph at lines 26481--26486 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26536--26541 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26605--26610 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27129--27132 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27735--27737 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27945--27948 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28259--28263 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28376--28379 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28559--28562 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29685--29689 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30049--30053 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30533--30537 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30610--30615 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30632--30634 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31014--31019 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1053--1055 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1131--1141 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1153--1155 []\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 1159--1161 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1196--1199 []\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 1196--1199 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1365--1367 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1539--1541 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1677--1682 []\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 1684--1686 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1881 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2183--2183 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2352--2358 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2817. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3099--3101 []\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 [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3799--3801 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3938--3941 []\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 [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4036--4038 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4245--4251 []\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 4245--4251 \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 [1920] Underfull \hbox (badness 5726) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4325--4330 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4474--4484 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4474--4484 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4536--4540 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] 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 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\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 546--552 \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 [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\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 660--666 \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 [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\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 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \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 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\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 [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\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 [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\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 [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4271 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5268--5270 []\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 [2012] Underfull \hbox (badness 1502) in paragraph at lines 5357--5362 []\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 5357--5362 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5530--5539 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5593--5596 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5730--5732 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5763--5767 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5871--5875 []\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 [2021] Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5954--5957 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6027--6034 []\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 6027--6034 \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 6027--6034 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6107--6112 [][][]\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 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7524--7526 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7529--7534 []\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, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8084--8086 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8913--8916 []\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 [2069] Underfull \hbox (badness 3000) in paragraph at lines 9049--9054 [][][]\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 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9632--9637 [][][]\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 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10057--10061 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10057--10061 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10069--10073 []\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 10069--10073 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10363--10363 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10426--10428 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10602--10604 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10821--10825 []\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 10852--10858 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10970--10973 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10974--10977 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2101] Underfull \hbox (badness 1009) in paragraph at lines 11046--11057 []\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 [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11352--11356 []\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 11368--11371 []\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 [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11737--11742 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11746--11749 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2113] [2114] [2115] [2116] [2117] Underfull \hbox (badness 10000) in paragraph at lines 12009--12011 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2118] [2119] Underfull \hbox (badness 1057) in paragraph at lines 12166--12173 []\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, [2120] [2121] [2122] [2123] Underfull \hbox (badness 6510) in paragraph at lines 12425--12429 []\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 12432--12435 [][][]$\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 12432--12435 \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 [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 10000) in paragraph at lines 12974--12976 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12977--12979 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2132] Underfull \hbox (badness 10000) in paragraph at lines 13007--13012 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13007--13012 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13007--13012 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by Underfull \hbox (badness 10000) in paragraph at lines 13036--13039 [][][]\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 , [2133] [2134] [2135] [2136] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13278--13281 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2137] [2138] Underfull \hbox (badness 1454) in paragraph at lines 13355--13359 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2139] Underfull \hbox (badness 10000) in paragraph at lines 13425--13427 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2140] [2141] [2142]) (./fullrefman.ind [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] Overfull \hbox (33.3567pt too wide) in paragraph at lines 8523--8525 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11508--11510 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11510--11512 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11512--11514 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213]) (./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.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 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Transcript written on fullrefman.log. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[1]: Leaving directory '/<>' /usr/bin/make -k vignettes make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' make[4]: Entering directory 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Entering directory '/<>/src/library/graphics/src' make[7]: Entering directory '/<>/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' make[5]: Entering directory '/<>/src/library/stats' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' make[7]: Entering directory '/<>/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' make[5]: Entering directory '/<>/src/library/methods' all.R is unchanged make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/src/library/methods/src' make[7]: Entering directory '/<>/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' make[5]: Entering directory '/<>/src/library/grid' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/src/library/grid/src' make[7]: Entering directory '/<>/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' make[5]: Entering directory '/<>/src/library/splines' all.R is unchanged make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' make[7]: Entering directory '/<>/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' make[5]: Entering directory '/<>/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/src/library/tcltk/src' make[6]: Entering directory '/<>/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' make[5]: Entering directory '/<>/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/src/library/parallel/src' make[7]: Entering directory '/<>/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/manual' make[4]: Entering directory '/<>/doc/html' make[4]: Leaving directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' installing parsed Rd make[4]: Entering directory '/<>/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' building/updating package metadata ... make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' writing package indices make[4]: Entering directory '/<>/src/library' make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src/library' make[2]: Entering directory '/<>/src/library/Recommended' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/src/library/Recommended' make[2]: Entering directory '/<>/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 '/<>/src/library' make[1]: Leaving directory '/<>' touch make-indep-stamp *** check *** xvfb-run make check-all make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/tests' make[3]: Entering directory '/<>/tests' make[4]: Entering directory '/<>/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 '/<>/tests/Examples' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running strict specific tests make[4]: Entering directory '/<>/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 '/<>/tests' running sloppy specific tests make[4]: Entering directory '/<>/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'print-tests.R' ... OK comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK running code in 'lapack.R' ... OK comparing 'lapack.Rout' to './lapack.Rout.save' ... 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 '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running regression tests ... make[4]: Entering directory '/<>/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 '/<>/tests' make[4]: Entering directory '/<>/tests' running tests of plotting Latin-1 expect failure or some differences if not in a Latin-1 or UTF-8 locale running code in 'reg-plot-latin1.R' ... OK comparing 'reg-plot-latin1.pdf' to './reg-plot-latin1.pdf.save' ... OK running code in 'reg-S4.R' ... OK comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ...650,652c650,653 < Warning message: < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : < there is no package called 'Matrix' --- > Note: method with signature 'numeric#dMatrix' chosen for function '>', > target signature 'numeric#ddiMatrix'. > "ANY#ddiMatrix" would also be valid > [ ] : .M.sub.i.logical() maybe inefficient OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of Internet functions make[4]: Entering directory '/<>/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247 < Warning message: < In nsl("cran.r-project.org") : < nsl() was unable to resolve host 'cran.r-project.org' --- > > > > # test do_download (and "record" #{packages}): > > ap <- available.packages(contrib.url("http://cran.r-project.org")) > > ## IGNORE_RDIFF_END > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "" > [2] "" > [3] "" > [4] "The Comprehensive R Archive Network" > [5] "" > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > [11] "" > [12] "" > [13] "" > [14] "" > [15] "" > [16] "" > [17] "" > [18] "<h1>The Comprehensive R Archive Network</h1>" > [19] "" > [20] "Your browser seems not to support frames," > [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN." > [22] "" > [23] "" > > close(zz) > > > > # and via read.table, test http and ftp. > > > > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of date-time printing expect platform-specific differences make[4]: Entering directory '/<>/tests' running code in 'datetime2.R' ... OK comparing 'datetime2.Rout' to './datetime2.Rout.save' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of documentation examples make[4]: Entering directory '/<>/tests' running code in 'R-intro.R' ... OK comparing 'R-intro.Rout' to './R-intro.Rout.save' ... OK make[4]: Leaving directory '/<>/tests' make[4]: Entering directory '/<>/tests' gcc -std=gnu99 -I/<>/include -DNDEBUG -fPIC -g -O3 -fdebug-prefix-map=/<>=. -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/<>/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R-exts.so R-exts.o -L/<>/lib -lR make[4]: Leaving directory '/<>/tests' make[4]: Entering directory '/<>/tests' running code in 'R-exts.R' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of consistency of as/is.* make[4]: Entering directory '/<>/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 '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of random deviate generation make[4]: Entering directory '/<>/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 '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running demos from base and stats make[4]: Entering directory '/<>/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 '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of primitives make[4]: Entering directory '/<>/tests' running code in 'primitives.R' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running regexp regression tests make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running more Internet and socket tests make[4]: Entering directory '/<>/tests' running code in 'internet2.R' ... OK running code in 'libcurl.R' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of CRAN tools (can be slow unless mirror is local) make[4]: Entering directory '/<>/tests' running code in 'CRANtools.R' ...Makefile.common:98: recipe for target 'CRANtools.Rout' failed make[4]: *** [CRANtools.Rout] Error 1 make[4]: Leaving directory '/<>/tests' Makefile.common:260: recipe for target 'test-CRANtools' failed make[3]: *** [test-CRANtools] Error 2 make[3]: Leaving directory '/<>/tests' Makefile.common:174: recipe for target 'test-all-devel' failed make[2]: *** [test-all-devel] Error 1 make[2]: Leaving directory '/<>/tests' Makefile:239: recipe for target 'check-all' failed make[1]: *** [check-all] Error 2 make[1]: Leaving directory '/<>' debian/rules:375: recipe for target 'check-stamp' failed make: [check-stamp] Error 2 (ignored) touch check-stamp fakeroot debian/rules binary-arch *** install-arch *** dh_testdir dh_testroot dh_prep -a dh_installdirs -A dh_installdirs: Compatibility levels before 9 are deprecated (level 7 in use) /<>/debian/r-base-core /usr/bin/make DESTDIR=/<>/debian/r-base-core install make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' installing doc ... mkdir -p -- /<>/debian/r-base-core/usr/share/R/doc mkdir -p -- /<>/debian/r-base-core/usr/share/man/man1 make[3]: Entering directory '/<>/doc/html' installing doc/html ... mkdir -p -- /<>/debian/r-base-core/usr/share/R/doc/html make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' installing doc/manual ... mkdir -p -- /<>/debian/r-base-core/usr/share/R/doc/manual mkdir -p -- /<>/debian/r-base-core/usr/share/R/doc/manual/images make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/etc installing etc ... make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' installing share ... mkdir -p -- /<>/debian/r-base-core/usr/share/R/share mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/R mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/dictionaries mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/encodings mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/java mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/licenses mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/make mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/Rd mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/Rd/macros mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/sh mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/texmf mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/texmf/tex/latex make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/bin make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' make[4]: Entering directory '/<>/src/include/R_ext' mkdir -p -- /<>/debian/r-base-core/usr/share/R/include/R_ext make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/blas' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/blas' make[4]: Entering directory '/<>/src/extra/tre' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/tre' make[4]: Entering directory '/<>/src/extra/xdr' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/xdr' make[4]: Entering directory '/<>/src/extra/intl' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/intl' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/src/appl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/src/nmath' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c mkdir -p -- /<>/debian/r-base-core/usr/lib/pkgconfig make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/src/main' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/bin/exec make[4]: Entering directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/lib make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/src/modules/internet' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/modules make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/library installing packages ... building HTML index ... make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/<>/tests' make[1]: Leaving directory '/<>' (cd src/unix; \ rm -vf Rscript /<>/debian/r-base-core/usr/bin/Rscript; \ /usr/bin/make CFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ RHOME=/usr/lib/R \ DESTDIR=/<>/debian/r-base-core \ install-Rscript ) removed 'Rscript' removed '/<>/debian/r-base-core/usr/bin/Rscript' make[1]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c make[1]: Leaving directory '/<>/src/unix' #ls -ltr /<>/debian/r-base-core/usr/bin/ #strings src/unix/Rscript cp -vax src/unix/Rscript /<>/debian/r-base-core/usr/bin/ 'src/unix/Rscript' -> '/<>/debian/r-base-core/usr/bin/Rscript' #ls -ltr /<>/debian/r-base-core/usr/bin/ #strings /<>/debian/r-base-core/usr/bin/Rscript (cd src/nmath/standalone; \ /usr/bin/make DESTDIR=/<>/debian/r-base-core install ) make[1]: Entering directory '/<>/src/nmath/standalone' make[2]: Entering directory '/<>/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/<>/src/include' /<>/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged make[1]: Leaving directory '/<>/src/nmath/standalone' chmod a+x /<>/debian/r-base-core/usr/share/R/share/sh/echo.sh rm -v /<>/debian/r-base-core/usr/lib/R/COPYING removed '/<>/debian/r-base-core/usr/lib/R/COPYING' (cd /<>/debian/r-base-core/usr/lib/R/; \ ln -s ../../share/common-licenses/GPL-2 COPYING) rm -v /<>/debian/r-base-core/usr/share/R/doc/COPYING removed '/<>/debian/r-base-core/usr/share/R/doc/COPYING' (cd /<>/debian/r-base-core/usr/share/R/doc; \ ln -s ../../../share/common-licenses/GPL-2 COPYING) # edd 03 Oct 2006 use link into /usr/share/, not /usr/lib/ (cd /<>/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: Compatibility levels before 9 are deprecated (level 7 in use) dh_movefiles --sourcedir=debian/r-base-core -pr-base-html dh_movefiles: Compatibility levels before 9 are deprecated (level 7 in use) dh_movefiles --sourcedir=debian/r-base-core -pr-base-latex dh_movefiles: Compatibility levels before 9 are deprecated (level 7 in use) make prefix=/<>/debian/r-base-core/usr \ rdocdir=/<>/debian/r-base-core/usr/share/R/doc \ install-pdf make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/doc/manual' installing R manuals in PDF format ... make[2]: Leaving directory '/<>/doc/manual' make[1]: Leaving directory '/<>' make prefix=/<>/debian/r-base-core/usr \ infodir=/<>/debian/r-base-core/usr/share/info install-info make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/doc/manual' mkdir -p -- /<>/debian/r-base-core/usr/share/info /usr/bin/install -c -m 644 "./dir" "/<>/debian/r-base-core/usr/share/info" installing R info pages ... updating '/<>/debian/r-base-core/usr/share/info/dir' ... you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually make[2]: Leaving directory '/<>/doc/manual' make[1]: Leaving directory '/<>' dh_movefiles --sourcedir=debian/r-base-core -pr-doc-pdf dh_movefiles: Compatibility levels before 9 are deprecated (level 7 in use) dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html dh_movefiles: Compatibility levels before 9 are deprecated (level 7 in use) touch install-indep-stamp gunzip -9v /<>/debian/r-base-core/usr/share/info/*.gz /<>/debian/r-base-core/usr/share/info/R-FAQ.info.gz: 67.0% -- replaced with /<>/debian/r-base-core/usr/share/info/R-FAQ.info /<>/debian/r-base-core/usr/share/info/R-admin.info.gz: 68.1% -- replaced with /<>/debian/r-base-core/usr/share/info/R-admin.info /<>/debian/r-base-core/usr/share/info/R-data.info.gz: 70.6% -- replaced with /<>/debian/r-base-core/usr/share/info/R-data.info /<>/debian/r-base-core/usr/share/info/R-exts.info-1.gz: 66.7% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info-1 /<>/debian/r-base-core/usr/share/info/R-exts.info-2.gz: 69.9% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info-2 /<>/debian/r-base-core/usr/share/info/R-exts.info-3.gz: 82.9% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info-3 /<>/debian/r-base-core/usr/share/info/R-exts.info.gz: 69.6% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info /<>/debian/r-base-core/usr/share/info/R-intro.info.gz: 70.0% -- replaced with /<>/debian/r-base-core/usr/share/info/R-intro.info /<>/debian/r-base-core/usr/share/info/R-ints.info.gz: 67.6% -- replaced with /<>/debian/r-base-core/usr/share/info/R-ints.info /<>/debian/r-base-core/usr/share/info/R-lang.info.gz: 71.6% -- replaced with /<>/debian/r-base-core/usr/share/info/R-lang.info dh_movefiles --sourcedir=debian/r-base-core -pr-doc-info dh_movefiles: Compatibility levels before 9 are deprecated (level 7 in use) rm -vf /<>/debian/r-doc-info/usr/share/info/dir \ /<>/debian/r-doc-info/usr/share/info/dir.old removed '/<>/debian/r-doc-info/usr/share/info/dir' dh_installdirs -pr-mathlib usr/include usr/lib \ usr/share/lintian/overrides \ usr/lib/pkgconfig dh_installdirs: Compatibility levels before 9 are deprecated (level 7 in use) dh_movefiles --sourcedir=debian/r-base-core -pr-mathlib dh_movefiles: Compatibility levels before 9 are deprecated (level 7 in use) (cd /<>/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 3060 -rw-rw-r-- 1 root root 2091390 Jun 25 05:26 libRmath.a -rwxrwxr-x 1 root root 1032872 Jun 25 05:26 libRmath.so drwxr-xr-x 2 root root 4096 Jun 25 05:26 pkgconfig 'libRmath.so' -> 'libRmath.so.1.0.0' 'libRmath.so.1' -> 'libRmath.so.1.0.0' 'libRmath.so' -> 'libRmath.so.1' install -m 0644 src/include/Rmath.h \ /<>/debian/r-mathlib/usr/include install -m 0644 debian/Rprofile.site /<>/debian/r-base-core/etc/R install -m 0644 debian/Renviron.site /<>/debian/r-base-core/etc/R (cd /<>/debian/r-base-core/usr/lib/R/etc; \ cat /<>/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 44 with fuzz 2 (offset 11 lines). done dh_bash-completion dh_bash-completion: Compatibility levels before 9 are deprecated (level 7 in use) # edd 12 Jan 2016 new location #install -m 0644 debian/R.bash-completion \ # debian/r-base-core/usr/share/bash-completion/completions/R (cd /<>/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: Compatibility levels before 9 are deprecated (level 7 in use) dh_installdocs -pr-mathlib doc/NEWS.* README \ debian/README.mathlib dh_installdocs: Compatibility levels before 9 are deprecated (level 7 in use) dh_installdocs -pr-base-core-dbg dh_installexamples -pr-mathlib src/nmath/standalone/test.c #dh_installmenu -a # (cd /<>/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .) (cd /<>/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .) (cd /<>/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/library .) install -p -m 0644 debian/r-base-core.lintian \ /<>/debian/r-base-core/usr/share/lintian/overrides/r-base-core install -p -m 0644 debian/r-recommended.lintian \ /<>/debian/r-recommended/usr/share/lintian/overrides/r-recommended install -p -m 0644 debian/r-mathlib.lintian \ /<>/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib dh_installchangelogs -a -k doc/NEWS dh_strip --sourcedir=/<>/debian/r-base-core --dbg-package=r-base-core-dbg Unknown option: sourcedir dh_strip: Compatibility levels before 9 are deprecated (level 7 in use) dh_strip --sourcedir=/<>/debian/r-mathlib Unknown option: sourcedir dh_strip: Compatibility levels before 9 are deprecated (level 7 in use) dh_compress -a dh_fixperms -a dh_link -a dh_makeshlibs -a dh_installdeb -a dh_installdeb: Compatibility levels before 9 are deprecated (level 7 in use) dh_perl -a dh_shlibdeps -a -l /<>/debian/r-base-core/usr/lib/R/lib dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtcl8.6.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtk8.6.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: 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' dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package r-base-core: unknown substitution variable ${perl:Depends} dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing r-base-core (in debian/r-base-core); do_strip: , oemstrip: pkgstriptranslations: processing r-base-core-dbg (in debian/r-base-core-dbg); do_strip: , oemstrip: pkgstriptranslations: processing r-mathlib (in debian/r-mathlib); do_strip: , oemstrip: debian/r-base-core/usr/share/applications/R.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-base-core/DEBIAN/control, package r-base-core, directory debian/r-base-core .. removing usr/share/doc/r-base-core/changelog.gz pkgstripfiles: processing control file: debian/r-mathlib/DEBIAN/control, package r-mathlib, directory debian/r-mathlib .. removing usr/share/doc/r-mathlib/changelog.gz INFO: pkgstripfiles: waiting for lock (r-mathlib) ... pkgstripfiles: Truncating usr/share/doc/r-base-core/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core ... WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/pch.png, ignoring WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/mai.png, ignoring WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/oma.png, ignoring ..opkgstripfiles: Truncating usr/share/doc/r-mathlib/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-mathlib ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.4.0.20170622-1_ppc64el.deb'. ooooooo pkgstripfiles: PNG optimization (8/0) for package r-base-core took 4 s dpkg-deb: building package 'r-base-core' in '../r-base-core_3.4.0.20170622-1_ppc64el.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-base-core-dbg/DEBIAN/control, package r-base-core-dbg, directory debian/r-base-core-dbg .. removing usr/share/doc/r-base-core-dbg/changelog.gz Searching for duplicated docs in dependency r-base-core... symlinking changelog.Debian.gz in r-base-core-dbg to file in r-base-core pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core-dbg ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-base-core-dbg' in '../r-base-core-dbg_3.4.0.20170622-1_ppc64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../r-base_3.4.0.20170622-1_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build r-base-3.4.0.20170622 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170625-0527 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ r-base_3.4.0.20170622-1_ppc64el.changes: ---------------------------------------- Format: 1.8 Date: Wed, 21 Jun 2017 16:04:14 -0500 Source: r-base Binary: r-base r-base-core r-base-dev r-mathlib r-base-html r-doc-pdf r-doc-html r-doc-info r-recommended r-base-core-dbg Architecture: ppc64el Version: 3.4.0.20170622-1 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Dirk Eddelbuettel Description: r-base - GNU R statistical computation and graphics system r-base-core - GNU R core of statistical computation and graphics system r-base-core-dbg - GNU R debug symbols for statistical comp. language and environmen r-base-dev - GNU R installation of auxiliary GNU R packages r-base-html - GNU R html docs for statistical computing system functions r-doc-html - GNU R html manuals for statistical computing system r-doc-info - GNU R info manuals statistical computing system r-doc-pdf - GNU R pdf manuals for statistical computing system r-mathlib - GNU R standalone mathematics library r-recommended - GNU R collection of recommended packages [metapackage] Changes: r-base (3.4.0.20170622-1) unstable; urgency=medium . * Initial beta build (r72852) of R 3.4.1 expected for June 30 . * debian/source/format: Set to '3.0 (quilt)' . * etc/Renviron.in: Patched to not set R_LIBS_USER by default * debian/Renviron.site: Mention possible R_LIBS_USER setting here Checksums-Sha1: 4ad43c459aed436f3b51e59a670dc52d16ca3ab3 3648068 r-base-core-dbg_3.4.0.20170622-1_ppc64el.deb 1b136b2516e6523f002695a8d8531a8a0f64a314 23178006 r-base-core_3.4.0.20170622-1_ppc64el.deb e6d1f1f04321e935a83ae30bcaff0c88ccd3d809 16284 r-base_3.4.0.20170622-1_ppc64el.buildinfo ffb8e787cc3ba931445c0859691f1eee5d921ae8 1574554 r-mathlib_3.4.0.20170622-1_ppc64el.deb Checksums-Sha256: 2a3cadf62681896773524901869cf18c9434236cd15e4b4119377a53c6d2b9d2 3648068 r-base-core-dbg_3.4.0.20170622-1_ppc64el.deb fd2e65c3eb0dab490e8b1f8e5e05d14616594201046eaa12e3ced6d80ce54542 23178006 r-base-core_3.4.0.20170622-1_ppc64el.deb 42ff766781baa4525b5a495e36fe40d8ee233dffb38914062e3c89f31e09ac56 16284 r-base_3.4.0.20170622-1_ppc64el.buildinfo 68fad62bf3eefdd3f36832cc1ba06072b0364222941f668df66a0496aef69b70 1574554 r-mathlib_3.4.0.20170622-1_ppc64el.deb Files: c09d3b425aa8fe47f470466c679e22a2 3648068 debug extra r-base-core-dbg_3.4.0.20170622-1_ppc64el.deb 235821d09d85df80f7e53cb9d5a95d95 23178006 gnu-r optional r-base-core_3.4.0.20170622-1_ppc64el.deb 64f01d2ece67a842cf7abc3fa257ff57 16284 gnu-r optional r-base_3.4.0.20170622-1_ppc64el.buildinfo 2fa6c9ae8fbfb178959446bf32cb23cf 1574554 gnu-r optional r-mathlib_3.4.0.20170622-1_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ r-base-core-dbg_3.4.0.20170622-1_ppc64el.deb -------------------------------------------- new debian package, version 2.0. size 3648068 bytes: control archive=1852 bytes. 1873 bytes, 39 lines control 1700 bytes, 21 lines md5sums Package: r-base-core-dbg Source: r-base Version: 3.4.0.20170622-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 16883 Depends: r-base-core (= 3.4.0.20170622-1), r-base-dev (= 3.4.0.20170622-1) Section: debug Priority: extra Homepage: http://www.r-project.org/ Description: GNU R debug symbols for statistical comp. language and environment R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'. . This package contains debugging symbol tables for the binaries and dynamic libraries in the r-base-core package. drwxr-xr-x root/root 0 2017-06-21 21:04 ./ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/bin/ -rw-r--r-- root/root 20616 2017-06-21 21:04 ./usr/lib/debug/usr/bin/Rscript drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/bin/ -rw-r--r-- root/root 20616 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/bin/Rscript drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/bin/exec/ -rw-r--r-- root/root 9264 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/bin/exec/R drwxr-xr-x root/root 0 2017-06-21 21:04 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21:04 ./usr/lib/debug/usr/lib/R/library/stats/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/stats/libs/ -rw-r--r-- root/root 2323280 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/stats/libs/stats.so drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/tcltk/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/tcltk/libs/ -rw-r--r-- root/root 222624 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/tcltk/libs/tcltk.so drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/tools/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/tools/libs/ -rw-r--r-- root/root 295352 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/tools/libs/tools.so drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/utils/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/debug/usr/lib/R/library/utils/libs/ -rw-r--r-- root/root 182912 2017-06-21 21:04 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20761 2010-08-05 18:01 ./usr/share/doc/r-base-core-dbg/copyright drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/share/lintian/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/share/lintian/overrides/ r-base-core_3.4.0.20170622-1_ppc64el.deb ---------------------------------------- new debian package, version 2.0. size 23178006 bytes: control archive=27777 bytes. 93 bytes, 5 lines conffiles 2790 bytes, 45 lines control 73358 bytes, 931 lines md5sums 2419 bytes, 68 lines * postinst #!/bin/sh 200 bytes, 5 lines * postrm #!/bin/sh 850 bytes, 37 lines * preinst #!/bin/sh 872 bytes, 29 lines * prerm #!/bin/sh Package: r-base-core Source: r-base Version: 3.4.0.20170622-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 37816 Depends: zip, unzip, libpaper-utils, xdg-utils, libblas3 | libblas.so.3, libbz2-1.0, libc6 (>= 2.23), libcairo2 (>= 1.6.0), libcurl3 (>= 7.28.0), libglib2.0-0 (>= 2.12.0), libgomp1 (>= 4.9), libicu57 (>= 57.1-1~), libjpeg8 (>= 8c), liblapack3 | liblapack.so.3, liblzma5 (>= 5.1.1alpha+20120614), libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libpcre3, libpng16-16 (>= 1.6.2-1), libreadline7 (>= 6.0), libtcl8.6 (>= 8.6.0), libtiff5 (>= 4.0.3), libtk8.6 (>= 8.6.0), libx11-6, libxt6, zlib1g (>= 1:1.1.4), ucf (>= 3.0), ca-certificates Recommends: r-recommended, r-base-dev, r-doc-html Suggests: ess, r-doc-info | r-doc-pdf, r-mathlib, r-base-html Conflicts: r-base-latex, r-cran-rcompgen, r-gnome Replaces: r-base (<= 1.4.1-1), r-base-latex (<= 2.9.2-4), r-cran-rcompgen (<= 0.1-17-1), r-gnome (<= 2.3.1), r-recommended (<< 1.9.0) Provides: r-api-3, r-base-latex, r-cran-rcompgen, r-gnome Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R core of statistical computation and graphics system R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'. . This package provides the core GNU R system from which only the optional documentation packages r-base-html, r-doc-html, r-doc-pdf and r-doc-info have been split off to somewhat reduce the size of this package. drwxr-xr-x root/root 0 2017-06-21 21:04 ./ drwxr-xr-x root/root 0 2017-06-21 21:04 ./etc/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./etc/R/ -rw-r--r-- root/root 8012 2017-06-21 21:04 ./etc/R/Makeconf -rw-r--r-- root/root 934 2017-06-21 21:04 ./etc/R/Renviron.site -rw-r--r-- root/root 792 2017-06-21 21:04 ./etc/R/Rprofile.site -rw-r--r-- root/root 805 2017-06-21 21:04 ./etc/R/ldpaths -rw-r--r-- root/root 1161 2017-06-21 21:04 ./etc/R/repositories drwxr-xr-x root/root 0 2017-06-21 21:04 ./etc/ld.so.conf.d/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/bin/ -rwxr-xr-x root/root 8722 2017-06-21 21:04 ./usr/bin/R -rwxr-xr-x root/root 67472 2017-06-21 21:04 ./usr/bin/Rscript drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/ drwxr-xr-x 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Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 2373 Depends: libc6 (>= 2.23) Recommends: r-base-core (= 3.4.0.20170622-1), r-base-dev (= 3.4.0.20170622-1) Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R standalone mathematics library R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'. . This package provides the libRmath shared and static libraries which can be called from standalone C or C++ code. drwxr-xr-x root/root 0 2017-06-21 21:04 ./ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/include/ -rw-r--r-- root/root 17985 2017-06-21 21:04 ./usr/include/Rmath.h drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/ -rw-r--r-- root/root 553382 2017-06-21 21:04 ./usr/lib/libRmath.a lrwxrwxrwx root/root 0 2017-06-21 21:04 ./usr/lib/libRmath.so -> libRmath.so.1 lrwxrwxrwx root/root 0 2017-06-21 21:04 ./usr/lib/libRmath.so.1 -> libRmath.so.1.0.0 -rw-r--r-- root/root 264264 2017-06-21 21:04 ./usr/lib/libRmath.so.1.0.0 drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/lib/pkgconfig/ -rw-r--r-- root/root 173 2017-06-21 21:04 ./usr/lib/pkgconfig/libRmath.pc drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/share/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/share/doc/r-mathlib/ -rw-r--r-- root/root 35933 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.0.gz -rw-r--r-- root/root 108753 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.1.gz -rw-r--r-- root/root 96628 2016-03-16 23:04 ./usr/share/doc/r-mathlib/NEWS.2.Rd.gz -rw-r--r-- root/root 229656 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.2.gz -rw-r--r-- root/root 90322 2017-06-21 21:04 ./usr/share/doc/r-mathlib/NEWS.Rd.gz lrwxrwxrwx root/root 0 2017-06-21 21:04 ./usr/share/doc/r-mathlib/NEWS.gz -> changelog.gz -rw-r--r-- root/root 476653 2017-06-21 21:04 ./usr/share/doc/r-mathlib/NEWS.pdf.gz -rw-r--r-- root/root 383568 2017-06-21 21:04 ./usr/share/doc/r-mathlib/NEWS.rds.gz -rw-r--r-- root/root 2107 2016-10-04 09:14 ./usr/share/doc/r-mathlib/README.gz -rw-r--r-- root/root 3026 2010-08-05 18:01 ./usr/share/doc/r-mathlib/README.mathlib -rw-r--r-- root/root 822 2017-06-21 21:04 ./usr/share/doc/r-mathlib/changelog.Debian.gz -rw-r--r-- root/root 20761 2010-08-05 18:01 ./usr/share/doc/r-mathlib/copyright drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/share/doc/r-mathlib/examples/ -rw-r--r-- root/root 1371 2015-08-25 22:18 ./usr/share/doc/r-mathlib/examples/test.c drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/share/lintian/ drwxr-xr-x root/root 0 2017-06-21 21:04 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 278 2017-03-06 11:52 ./usr/share/lintian/overrides/r-mathlib +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 384064 Build-Time: 676 Distribution: artful-proposed Host Architecture: ppc64el Install-Time: 167 Job: r-base_3.4.0.20170622-1.dsc Machine Architecture: ppc64el Package: r-base Package-Time: 845 Source-Version: 3.4.0.20170622-1 Space: 384064 Status: successful Version: 3.4.0.20170622-1 -------------------------------------------------------------------------------- Finished at 20170625-0527 Build needed 00:14:05, 384064k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12801660'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12801660/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12801660'] Unmounting chroot for build PACKAGEBUILD-12801660... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12801660'] Removing build PACKAGEBUILD-12801660