r-cran-ape →
3.1-1-1 →
armhf → 2014-05-31 07:11:31
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-cran-ape 3.1-1-1 (armhf) 31 May 2014 07:01 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-cran-ape
Version: 3.1-1-1
Source Version: 3.1-1-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-cran-ape-7DSkJz/r-cran-ape-3.1-1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-cran-ape-7DSkJz' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-72306588-63d4-4280-9ada-6a8a1f2bfef7' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7288 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8104 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.4 MB in 28s (545 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'r-cran-ape' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/r-cran-ape.git
Need to get 638 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main r-cran-ape 3.1-1-1 (dsc) [2017 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main r-cran-ape 3.1-1-1 (tar) [633 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main r-cran-ape 3.1-1-1 (diff) [3220 B]
Fetched 638 kB in 0s (4158 kB/s)
Download complete and in download only mode
Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-OAStLa/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 39 not upgraded.
Need to get 0 B/818 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11664 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9.0.0), r-base-dev (>= 3.1.0), r-cran-nlme, r-cran-lattice, cdbs
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9.0.0), r-base-dev (>= 3.1.0), r-cran-nlme, r-cran-lattice, cdbs
dpkg-deb: building package `sbuild-build-depends-r-cran-ape-dummy' in `/«BUILDDIR»/resolver-CL23Tk/apt_archive/sbuild-build-depends-r-cran-ape-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install r-cran-ape build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils cdbs cpp debhelper file fontconfig fontconfig-config
fonts-dejavu-core gcc gcc-4.9-base gettext gettext-base gfortran
gfortran-4.8 groff-base intltool-debian libasprintf0c2 libatomic1
libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libdatrie1 libdrm2
libexpat1 libffi6 libfontconfig1 libfreetype6 libgcc1 libgfortran-4.8-dev
libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgomp1
libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg8 libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libmagic1 libncurses5-dev
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-0
libpng12-dev libreadline-dev libreadline6-dev libsm6 libstdc++6 libtcl8.5
libthai-data libthai0 libtiff5 libtinfo-dev libtk8.5 libunistring0 libx11-6
libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0
libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1
libxdmcp6 libxext6 libxfixes3 libxft2 libxml2 libxrender1 libxshmfence1
libxss1 libxt6 libxxf86vm1 man-db po-debconf r-base-core r-base-dev
r-cran-lattice r-cran-nlme ucf unzip x11-common xdg-utils zip zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts cpp-doc dh-make gcc-multilib
manpages-dev autoconf automake1.9 libtool flex bison gdb gcc-doc gettext-doc
gfortran-doc gfortran-4.8-doc libgfortran3-dbg groff liblzma-doc ncurses-doc
ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
ttf-arphic-bkai00mp tcl8.5 tk8.5 less www-browser libmail-box-perl
r-doc-info r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base
texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
gvfs-bin
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libgl1-mesa-dri libglib2.0-data shared-mime-info xml-core
libmail-sendmail-perl r-recommended r-doc-html libfile-mimeinfo-perl
libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base gfortran gfortran-4.8 groff-base
intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2
libcroco3 libdatrie1 libdrm2 libexpat1 libffi6 libfontconfig1 libfreetype6
libgfortran-4.8-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg8 libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libmagic1 libncurses5-dev
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-0
libpng12-dev libreadline-dev libreadline6-dev libsm6 libtcl8.5 libthai-data
libthai0 libtiff5 libtinfo-dev libtk8.5 libunistring0 libx11-6 libx11-data
libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6
libxext6 libxfixes3 libxft2 libxml2 libxrender1 libxshmfence1 libxss1 libxt6
libxxf86vm1 man-db po-debconf r-base-core r-base-dev r-cran-lattice
r-cran-nlme sbuild-build-depends-r-cran-ape-dummy ucf unzip x11-common
xdg-utils zip zlib1g-dev
The following packages will be upgraded:
cpp gcc gcc-4.9-base libatomic1 libgcc1 libgomp1 libstdc++6
7 upgraded, 98 newly installed, 0 to remove and 32 not upgraded.
Need to get 52.6 MB/52.6 MB of archives.
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Get:3 http://172.17.0.1/private/ jessie-staging/main libstdc++6 armhf 4.9.0-4 [234 kB]
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Get:5 http://172.17.0.1/private/ jessie-staging/main libgcc1 armhf 1:4.9.0-4 [39.4 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.7.1-1 [964 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-1 [29.0 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.18-1 [229 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
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Get:15 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.5.2-1 [397 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0029 [70.5 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.34-1 [1047 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.11.0-5 [273 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.11.0-5 [310 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libdrm2 armhf 2.4.54-1 [25.9 kB]
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Get:22 http://172.17.0.1/private/ jessie-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
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Get:30 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0 armhf 1.10-2 [23.2 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main libxcb-present0 armhf 1.10-2 [10.4 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main libxcb-sync1 armhf 1.10-2 [12.9 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libxfixes3 armhf 1:5.0.1-1 [21.0 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-1 [14.6 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libxext6 armhf 2:1.3.2-1 [51.1 kB]
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Get:38 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 10.1.2-1 [134 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.32.4-1 [476 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.10-2 [15.7 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.10-2 [10.8 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2+rpi1 [894 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1~rc1+r3.0.13-12 [17.6 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-3 [2247 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.8-1 [29.1 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libgfortran3 armhf 4.9.0-4 [154 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.4-2 [48.0 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0b armhf 0.9.28-1 [434 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+7 [287 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.8-2 [56.2 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d-2 [133 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.20-3 [157 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.20-3 [41.6 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-5 [401 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.36.3-1 [265 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.36.3-1 [199 kB]
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Get:68 http://172.17.0.1/private/ jessie-staging/main libtk8.5 armhf 8.5.15-4 [646 kB]
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Get:100 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7.1 [64.6 kB]
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Get:104 http://172.17.0.1/private/ jessie-staging/main r-cran-nlme armhf 3.1.117-1 [1986 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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No schema files found: doing nothing.
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.8-2) ...
Setting up libjpeg8:armhf (8d-2) ...
Setting up libthai-data (0.1.20-3) ...
Setting up libthai0:armhf (0.1.20-3) ...
Setting up fontconfig (2.11.0-5) ...
Regenerating fonts cache... done.
Setting up libpango-1.0-0:armhf (1.36.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.36.3-1) ...
Setting up libpangocairo-1.0-0:armhf (1.36.3-1) ...
Setting up libpaper1:armhf (1.1.24+nmu3) ...
Creating config file /etc/papersize with new version
Setting up libpcrecpp0:armhf (1:8.31-5) ...
Setting up libsm6:armhf (2:1.2.1-2) ...
Setting up libtcl8.5:armhf (8.5.15-4) ...
Setting up libjbig0:armhf (2.0-2.1) ...
Setting up libtiff5:armhf (4.0.3-8) ...
Setting up libxft2:armhf (2.3.1-2) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libtk8.5:armhf (8.5.15-4) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libxt6:armhf (1:1.1.4-1) ...
Setting up file (1:5.18-1) ...
Setting up gettext-base (0.18.3.2-1) ...
Setting up cdbs (0.4.123) ...
Setting up cpp (4:4.8.2-4) ...
Setting up gettext (0.18.3.2-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20140228) ...
Setting up gcc (4:4.8.2-4) ...
Setting up libgfortran-4.8-dev:armhf (4.8.2-21) ...
Setting up gfortran-4.8 (4.8.2-21) ...
Setting up gfortran (4:4.8.2-4) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
Setting up libblas3 (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libbz2-dev:armhf (1.0.6-5) ...
Setting up libjpeg8-dev:armhf (8d-2) ...
Setting up liblapack3 (3.5.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up liblapack-dev (3.5.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up liblzma-dev:armhf (5.1.1alpha+20120614-2) ...
Setting up libtinfo-dev:armhf (5.9+20140118-1) ...
Setting up libncurses5-dev:armhf (5.9+20140118-1) ...
Setting up libpaper-utils (1.1.24+nmu3) ...
Setting up libpcre3-dev:armhf (1:8.31-5) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up libpng12-dev (1.2.50-1) ...
Setting up libreadline6-dev:armhf (6.3-6) ...
Setting up libreadline-dev:armhf (6.3-6) ...
Setting up zip (3.0-8) ...
Setting up unzip (6.0-12) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7.1) ...
Setting up r-base-core (3.1.0-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.1.0-1) ...
Setting up r-cran-lattice (0.20-29-1) ...
Setting up r-cran-nlme (3.1.117-1) ...
Setting up sbuild-build-depends-r-cran-ape-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.18-5) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.14-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140425-1 dpkg-dev_1.17.6+rpi1 g++-4.8_4.8.2-21 gcc-4.8_4.8.2-21 libc6-dev_2.18-5 libstdc++-4.8-dev_4.8.2-21 libstdc++6_4.9.0-4 linux-libc-dev_3.13.10-1+rpi1
Package versions: apt_1.0.1 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.3-7 binutils_2.24.51.20140425-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.7 build-essential_11.6 bzip2_1.0.6-5 cdbs_0.4.123 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.8.2-4 cpp-4.8_4.8.2-21 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140228 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.18-1 findutils_4.4.2-8 fontconfig_2.11.0-5 fontconfig-config_2.11.0-5 fonts-dejavu-core_2.34-1 g++_4:4.8.2-3 g++-4.8_4.8.2-21 gcc_4:4.8.2-4 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.2-21 gcc-4.8-base_4.8.2-21 gcc-4.9-base_4.9.0-4 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gfortran_4:4.8.2-4 gfortran-4.8_4.8.2-21 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.18-2 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 init-system-helpers_1.18 initramfs-tools_0.115 initscripts_2.88dsf-53 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.1 libasan0_4.8.2-21 libasprintf0c2_0.18.3.2-1 libatomic1_4.9.0-4 libattr1_1:2.4.47-1 libaudit-common_1:2.3.6-1 libaudit1_1:2.3.6-1 libblas-dev_1.2.20110419-7 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.7 libbz2-1.0_1.0.6-5 libbz2-dev_1.0.6-5 libc-bin_2.18-5 libc-dev-bin_2.18-5 libc6_2.18-5 libc6-dev_2.18-5 libcairo2_1.12.16-2+rpi1 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcroco3_0.6.8-2 libdatrie1_0.2.8-1 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-3 libdpkg-perl_1.17.6+rpi1 libdrm2_2.4.54-1 libexpat1_2.1.0-5 libffi6_3.1~rc1+r3.0.13-12 libfontconfig1_2.11.0-5 libfreetype6_2.5.2-1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-21 libgcc1_1:4.9.0-4 libgdbm3_1.8.3-12 libgfortran-4.8-dev_4.8.2-21 libgfortran3_4.9.0-4 libgl1-mesa-glx_10.1.2-1 libglapi-mesa_10.1.2-1 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-2 libgomp1_4.9.0-4 libgraphite2-3_1.2.4-2 libharfbuzz0b_0.9.28-1 libice6_2:1.0.8-2 libisl10_0.12.2-1 libjbig0_2.0-2.1 libjpeg8_8d-2 libjpeg8-dev_8d-2 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblapack-dev_3.5.0-2 liblapack3_3.5.0-2 liblocale-gettext-perl_1.05-8 liblzma-dev_5.1.1alpha+20120614-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.18-1 libmount1_2.20.1-5.7 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncurses5-dev_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpango-1.0-0_1.36.3-1 libpangocairo-1.0-0_1.36.3-1 libpangoft2-1.0-0_1.36.3-1 libpaper-utils_1.1.24+nmu3 libpaper1_1.1.24+nmu3 libpcre3_1:8.31-5 libpcre3-dev_1:8.31-5 libpcrecpp0_1:8.31-5 libpipeline1_1.3.0-1 libpixman-1-0_0.32.4-1 libpng12-0_1.2.50-1 libpng12-dev_1.2.50-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libreadline-dev_6.3-6 libreadline6_6.3-6 libreadline6-dev_6.3-6 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libsm6_2:1.2.1-2 libss2_1.42.9-3 libstdc++-4.8-dev_4.8.2-21 libstdc++6_4.9.0-4 libtcl8.5_8.5.15-4 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.20-3 libthai0_0.1.20-3 libtiff5_4.0.3-8 libtimedate-perl_2.3000-2 libtinfo-dev_5.9+20140118-1 libtinfo5_5.9+20140118-1 libtk8.5_8.5.15-4 libudev1_204-8 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.7 libx11-6_2:1.6.2-2 libx11-data_2:1.6.2-2 libx11-xcb1_2:1.6.2-2 libxau6_1:1.0.8-1 libxcb-dri2-0_1.10-2 libxcb-dri3-0_1.10-2 libxcb-glx0_1.10-2 libxcb-present0_1.10-2 libxcb-render0_1.10-2 libxcb-shm0_1.10-2 libxcb-sync1_1.10-2 libxcb1_1.10-2 libxdamage1_1:1.1.4-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-1 libxft2_2.3.1-2 libxml2_2.9.1+dfsg1-3 libxrender1_1:0.9.8-1 libxshmfence1_1.1-2 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.13.10-1+rpi1 login_1:4.1.5.1-1.1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.7 multiarch-support_2.18-5 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.1.5.1-1.1 patch_2.7.1-5 perl_5.18.2-2+b1 perl-base_5.18.2-2+b1 perl-modules_5.18.2-2 plymouth_0.8.8-16 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 r-base-core_3.1.0-1 r-base-dev_3.1.0-1 r-cran-lattice_0.20-29-1 r-cran-nlme_3.1.117-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-cran-ape-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-53 sysvinit_2.88dsf-53 sysvinit-core_2.88dsf-53 sysvinit-utils_2.88dsf-53 tar_1.27.1-2 tzdata_2014b-1 ucf_3.0029 udev_204-8 unzip_6.0-12 util-linux_2.20.1-5.7 x11-common_1:7.7+7 xdg-utils_1.1.0~rc1+git20111210-7.1 xz-utils_5.1.1alpha+20120614-2 zip_3.0-8 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon May 12 19:43:29 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-cran-ape_3.1-1-1.dsc
dpkg-source: info: extracting r-cran-ape in r-cran-ape-3.1-1
dpkg-source: info: unpacking r-cran-ape_3.1-1.orig.tar.gz
dpkg-source: info: unpacking r-cran-ape_3.1-1-1.debian.tar.xz
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-72306588-63d4-4280-9ada-6a8a1f2bfef7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package r-cran-ape
dpkg-buildpackage: source version 3.1-1-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-cran-ape-3.1-1
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
debian/rules build-arch
test -x debian/rules
mkdir -p "."
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
dh_installdirs usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.1.0-1)" >> debian/r-cran-ape.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-cran-ape/usr/lib/R/site-library --clean \
. ; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-cran-ape/usr/lib/R/site-library \
--clean . ;\
fi
* installing *source* package 'ape' ...
** package 'ape' successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory `/«PKGBUILDDIR»/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c BIONJ.c -o BIONJ.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c NNI.c -o NNI.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SPR.c -o SPR.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c TBR.c -o TBR.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c additive.c -o additive.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ape.c -o ape.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bNNI.c -o bNNI.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bionjs.c -o bionjs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bipartition.c -o bipartition.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bitsplits.c -o bitsplits.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c delta_plot.c -o delta_plot.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dist_dna.c -o dist_dna.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dist_nodes.c -o dist_nodes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ewLasso.c -o ewLasso.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c heap.c -o heap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mat_expo.c -o mat_expo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c me.c -o me.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c me_balanced.c -o me_balanced.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c me_ols.c -o me_ols.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mvr.c -o mvr.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mvrs.c -o mvrs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c nj.c -o nj.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c njs.c -o njs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pic.c -o pic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c plot_phylo.c -o plot_phylo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rTrait.c -o rTrait.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c read_dna.c -o read_dna.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c reorder_phylo.c -o reorder_phylo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c treePop.c -o treePop.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tree_build.c -o tree_build.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tree_phylo.c -o tree_phylo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c triangMtd.c -o triangMtd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c triangMtds.c -o triangMtds.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ultrametric.c -o ultrametric.o
gcc -std=gnu99 -shared -Wl,-z,relro -o ape.so BIONJ.o NNI.o SPR.o TBR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o rTrait.o read_dna.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -llapack -lblas -lgfortran -lm -L/usr/lib/R/lib -lR
make[1]: Leaving directory `/«PKGBUILDDIR»/src'
make[1]: Entering directory `/«PKGBUILDDIR»/src'
make[1]: Leaving directory `/«PKGBUILDDIR»/src'
installing to /«PKGBUILDDIR»/debian/r-cran-ape/usr/lib/R/site-library/ape/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ape)
rm -vf /«PKGBUILDDIR»/debian/r-cran-ape/usr/lib/R/site-library/R.css \
/«PKGBUILDDIR»/debian/r-cran-ape/usr/lib/R/site-library/ape/COPYING \
/«PKGBUILDDIR»/debian/r-cran-ape/usr/lib/R/site-library/ape/LICENSE.txt
if test -f debian/overrides; then \
install -d /«PKGBUILDDIR»/debian/r-cran-ape/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/«PKGBUILDDIR»/debian/r-cran-ape/usr/share/lintian/overrides/r-cran-ape; \
fi
Adding cdbs dependencies to debian/r-cran-ape.substvars
dh_installdirs -pr-cran-ape
dh_installdocs -pr-cran-ape ./NEWS
dh_installexamples -pr-cran-ape
dh_installman -pr-cran-ape
dh_installinfo -pr-cran-ape
dh_installmenu -pr-cran-ape
dh_installcron -pr-cran-ape
dh_installinit -pr-cran-ape
dh_installdebconf -pr-cran-ape
dh_installemacsen -pr-cran-ape
dh_installcatalogs -pr-cran-ape
dh_installpam -pr-cran-ape
dh_installlogrotate -pr-cran-ape
dh_installlogcheck -pr-cran-ape
dh_installchangelogs -pr-cran-ape
dh_installudev -pr-cran-ape
dh_lintian -pr-cran-ape
dh_bugfiles -pr-cran-ape
dh_install -pr-cran-ape
dh_link -pr-cran-ape
dh_installmime -pr-cran-ape
dh_installgsettings -pr-cran-ape
dh_strip -pr-cran-ape
dh_compress -pr-cran-ape
dh_fixperms -pr-cran-ape
dh_makeshlibs -pr-cran-ape
dh_installdeb -pr-cran-ape
dh_perl -pr-cran-ape
dh_shlibdeps -pr-cran-ape
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-cran-ape/usr/lib/R/site-library/ape/libs/ape.so was not linked against libgfortran.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-cran-ape/usr/lib/R/site-library/ape/libs/ape.so was not linked against libblas.so.3 (it uses none of the library's symbols)
dh_gencontrol -pr-cran-ape
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -pr-cran-ape
dh_builddeb -pr-cran-ape
dpkg-deb: building package `r-cran-ape' in `../r-cran-ape_3.1-1-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-cran-ape_3.1-1-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build r-cran-ape-3.1-1
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140531-0710
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-cran-ape_3.1-1-1_armhf.changes:
─────────────────────────────────
Format: 1.8
Date: Sun, 13 Apr 2014 17:00:00 +0200
Source: r-cran-ape
Binary: r-cran-ape
Architecture: armhf
Version: 3.1-1-1
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Dylan Aïssi <bob.dybian@gmail.com>
Description:
r-cran-ape - GNU R package for Analyses of Phylogenetics and Evolution
Closes: 746208
Changes:
r-cran-ape (3.1-1-1) unstable; urgency=low
.
* Initial Debian Release. (Closes: #746208)
Checksums-Sha1:
ce5ebdf6f80b4286df2bca70a818be1e8f40819f 1158868 r-cran-ape_3.1-1-1_armhf.deb
Checksums-Sha256:
98e504cf4cbae331a5b1132b913d7d78c17667ab4c0733ec31b3a397d5281b71 1158868 r-cran-ape_3.1-1-1_armhf.deb
Files:
3e3e9f64c8bd828833a732e97e5b4596 1158868 gnu-r optional r-cran-ape_3.1-1-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
r-cran-ape_3.1-1-1_armhf.deb
────────────────────────────
new debian package, version 2.0.
size 1158868 bytes: control archive=2520 bytes.
1402 bytes, 24 lines control
3682 bytes, 48 lines md5sums
Package: r-cran-ape
Version: 3.1-1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1358
Depends: libblas3 | libblas.so.3, libc6 (>= 2.4), libgfortran3 (>= 4.3), liblapack3 | liblapack.so.3, r-base-core (>= 3.1.0-1), r-cran-nlme, r-cran-lattice
Section: gnu-r
Priority: optional
Homepage: http://cran.r-project.org/web/packages/ape/index.html
Description: GNU R package for Analyses of Phylogenetics and Evolution
This package provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data in a
phylogenetic framework, ancestral character analyses, analyses of
diversification and macroevolution, computing distances from allelic
and nucleotide data, reading and writing nucleotide sequences, and
several tools such as Mantel's test, generalized skyline plots,
graphical exploration of phylogenetic data (alex, trex, kronoviz),
estimation of absolute evolutionary rates and clock-like trees using
mean path lengths and penalized likelihood. Phylogeny estimation can
be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and
several methods handling incomplete distance matrices (NJ*, BIONJ*,
MVR*, and the corresponding triangle method). Some functions call
external applications (PhyML, Clustal, T-Coffee, Muscle) whose
results are returned into R.
drwxr-xr-x root/root 0 2014-05-31 07:10 ./
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/
drwxr-xr-x root/root 0 2014-05-31 07:09 ./usr/lib/
drwxr-xr-x root/root 0 2014-05-31 07:09 ./usr/lib/R/
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/ape/
-rw-r--r-- root/root 3501 2014-05-31 07:09 ./usr/lib/R/site-library/ape/NAMESPACE
-rw-r--r-- root/root 89739 2014-05-31 07:09 ./usr/lib/R/site-library/ape/NEWS
-rw-r--r-- root/root 2809 2014-05-31 07:09 ./usr/lib/R/site-library/ape/DESCRIPTION
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/ape/Meta/
-rw-r--r-- root/root 1674 2014-05-31 07:09 ./usr/lib/R/site-library/ape/Meta/package.rds
-rw-r--r-- root/root 7178 2014-05-31 07:10 ./usr/lib/R/site-library/ape/Meta/Rd.rds
-rw-r--r-- root/root 6852 2014-05-31 07:10 ./usr/lib/R/site-library/ape/Meta/hsearch.rds
-rw-r--r-- root/root 3753 2014-05-31 07:10 ./usr/lib/R/site-library/ape/Meta/links.rds
-rw-r--r-- root/root 509 2014-05-31 07:10 ./usr/lib/R/site-library/ape/Meta/data.rds
-rw-r--r-- root/root 192 2014-05-31 07:10 ./usr/lib/R/site-library/ape/Meta/vignette.rds
-rw-r--r-- root/root 1106 2014-05-31 07:10 ./usr/lib/R/site-library/ape/Meta/nsInfo.rds
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/ape/libs/
-rw-r--r-- root/root 125744 2014-05-31 07:10 ./usr/lib/R/site-library/ape/libs/ape.so
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/ape/R/
-rw-r--r-- root/root 1056 2014-05-31 07:10 ./usr/lib/R/site-library/ape/R/ape
-rw-r--r-- root/root 210050 2014-05-31 07:10 ./usr/lib/R/site-library/ape/R/ape.rdb
-rw-r--r-- root/root 4495 2014-05-31 07:10 ./usr/lib/R/site-library/ape/R/ape.rdx
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/
-rw-r--r-- root/root 412 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/HP.links.rda
-rw-r--r-- root/root 2509 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/bird.families.rda
-rw-r--r-- root/root 567 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/bird.orders.rda
-rw-r--r-- root/root 3544 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/carnivora.csv.gz
-rw-r--r-- root/root 11971 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/chiroptera.rda
-rw-r--r-- root/root 721 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/cynipids.rda
-rw-r--r-- root/root 1255 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/gopher.D.rda
-rw-r--r-- root/root 2189 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/hivtree.newick.rda
-rw-r--r-- root/root 1031 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/hivtree.table.txt.gz
-rw-r--r-- root/root 574 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/landplants.newick.rda
-rw-r--r-- root/root 1544 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/lice.D.rda
-rw-r--r-- root/root 979 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/lmorigin.ex1.rda
-rw-r--r-- root/root 455 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/lmorigin.ex2.rda
-rw-r--r-- root/root 714 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/mat3.RData
-rw-r--r-- root/root 49717 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/mat5M3ID.RData
-rw-r--r-- root/root 49548 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/mat5Mrand.RData
-rw-r--r-- root/root 445 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/opsin.newick.rda
-rw-r--r-- root/root 1160 2014-05-31 07:10 ./usr/lib/R/site-library/ape/data/woodmouse.rda
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/ape/doc/
-rw-r--r-- root/root 2712 2014-05-31 07:10 ./usr/lib/R/site-library/ape/doc/MoranI.R
-rw-r--r-- root/root 12851 2014-05-31 07:10 ./usr/lib/R/site-library/ape/doc/MoranI.Rnw
-rw-r--r-- root/root 126448 2014-05-31 07:10 ./usr/lib/R/site-library/ape/doc/MoranI.pdf
-rw-r--r-- root/root 1097 2014-05-31 07:10 ./usr/lib/R/site-library/ape/doc/index.html
-rw-r--r-- root/root 613 2014-05-31 07:10 ./usr/lib/R/site-library/ape/CITATION
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/ape/help/
-rw-r--r-- root/root 1414 2014-05-31 07:10 ./usr/lib/R/site-library/ape/help/paths.rds
-rw-r--r-- root/root 560467 2014-05-31 07:10 ./usr/lib/R/site-library/ape/help/ape.rdb
-rw-r--r-- root/root 3602 2014-05-31 07:10 ./usr/lib/R/site-library/ape/help/ape.rdx
-rw-r--r-- root/root 8866 2014-05-31 07:10 ./usr/lib/R/site-library/ape/help/AnIndex
-rw-r--r-- root/root 3176 2014-05-31 07:10 ./usr/lib/R/site-library/ape/help/aliases.rds
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/lib/R/site-library/ape/html/
-rw-r--r-- root/root 40458 2014-05-31 07:10 ./usr/lib/R/site-library/ape/html/00Index.html
-rw-r--r-- root/root 1179 2014-05-31 07:10 ./usr/lib/R/site-library/ape/html/R.css
-rw-r--r-- root/root 10262 2014-05-31 07:10 ./usr/lib/R/site-library/ape/INDEX
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/share/
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-05-31 07:10 ./usr/share/doc/r-cran-ape/
-rw-r--r-- root/root 1512 2014-05-12 19:40 ./usr/share/doc/r-cran-ape/copyright
-rw-r--r-- root/root 26414 2014-03-05 20:55 ./usr/share/doc/r-cran-ape/NEWS.gz
-rw-r--r-- root/root 166 2014-05-12 19:40 ./usr/share/doc/r-cran-ape/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 4968
Build-Time: 128
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 378
Job: r-cran-ape_3.1-1-1
Machine Architecture: armhf
Package: r-cran-ape
Package-Time: 554
Source-Version: 3.1-1-1
Space: 4968
Status: successful
Version: 3.1-1-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140531-0710
Build needed 00:09:14, 4968k disc space