[med-svn] [SCM] r-bioc-biobase branch, meta, updated. meta/2.12.1-1-3-g8e22365
Charles Plessy
plessy at debian.org
Wed Nov 2 05:37:27 UTC 2011
The following commit has been merged in the meta branch:
commit 8e223659d22a9c30da6269a8b27db97fb01c144a
Author: Charles Plessy <plessy at debian.org>
Date: Wed Nov 2 14:36:55 2011 +0900
Build logs for r-bioc-biobase_2.14.0-1_amd64.changes.
diff --git a/amd64.changes b/amd64.changes
index 4a0bd70..bb4621c 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
Format: 1.8
-Date: Thu, 04 Aug 2011 08:58:03 +0900
+Date: Wed, 02 Nov 2011 13:52:04 +0900
Source: r-bioc-biobase
Binary: r-bioc-biobase
Architecture: source amd64
-Version: 2.12.2-1
+Version: 2.14.0-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -14,39 +14,42 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
r-bioc-biobase - base functions for Bioconductor
Changes:
- r-bioc-biobase (2.12.2-1) unstable; urgency=low
+ r-bioc-biobase (2.14.0-1) unstable; urgency=low
.
- * New upstream release.
+ [cb6b786] Bioconductor release 2.9.
+ [d70e490] Build-Depend on R >= 2.10 according to DESCRIPTION.
+ [ae99e35] Include 7 digits of the commit id in the changelog entry.
+ [33b5d47] Compress binary package with xz.
Checksums-Sha1:
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- e4e05aeb8ca8959374106a799f2ce1a983778978 5417 r-bioc-biobase_2.12.2-1.diff.gz
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+ de6dd8f4eb63de38906027244d09a5865508b2c5 2311488 r-bioc-biobase_2.14.0-1_amd64.deb
Checksums-Sha256:
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- 34efe354d34268e12c335fae538af4507a13a24a62a08c066fda4319bf5fd97c 2221612 r-bioc-biobase_2.12.2.orig.tar.gz
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Files:
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- ab1f805e3261f9f2e8788a9630b85d3e 5417 gnu-r optional r-bioc-biobase_2.12.2-1.diff.gz
- fe3a5776523f7006aa0a1452479fec56 2667938 gnu-r optional r-bioc-biobase_2.12.2-1_amd64.deb
+ 64e0fdd6694e4578157f1d94bcfecfca 2004 gnu-r optional r-bioc-biobase_2.14.0-1.dsc
+ e62df79e3f94d0e0544214ba49dc7030 1926376 gnu-r optional r-bioc-biobase_2.14.0.orig.tar.gz
+ cdefbd9d3a2abe8f9e029be2b64f8d8d 5645 gnu-r optional r-bioc-biobase_2.14.0-1.diff.gz
+ e25a000722284b6876a4df237e9bb1f4 2311488 gnu-r optional r-bioc-biobase_2.14.0-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index 2ae2244..ce63812 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,28 +1,26 @@
-sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on aqwa.igloo
+sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on anx191
╔══════════════════════════════════════════════════════════════════════════════╗
-║ r-bioc-biobase 2.12.2-1 (amd64) 04 août 2011 09:09 ║
+║ r-bioc-biobase 2.14.0-1 (amd64) 02 Nov 2011 13:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-bioc-biobase
-Version: 2.12.2-1
-Source Version: 2.12.2-1
+Version: 2.14.0-1
+Source Version: 2.14.0-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/r-bioc-biobase-mh84sH/r-bioc-biobase-2.12.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/r-bioc-biobase-mh84sH' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-6916a6a9-d5b0-46c0-a15e-58ff0d3a31c8' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/r-bioc-biobase-sHkKd3/r-bioc-biobase-2.14.0' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/r-bioc-biobase-sHkKd3' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-7fbe1793-6843-40a0-baa6-6a3229218014' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Hit ftp://ftp.jaist.ac.jp sid InRelease
-Hit ftp://ftp.jaist.ac.jp sid/main Sources/DiffIndex
-Hit ftp://ftp.jaist.ac.jp sid/main amd64 Packages/DiffIndex
-Hit ftp://ftp.jaist.ac.jp sid/main TranslationIndex
-Hit ftp://ftp.jaist.ac.jp sid/main Translation-fr
+Hit http://ftp.jp.debian.org sid InRelease
+Hit http://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
+Hit http://ftp.jp.debian.org sid/main TranslationIndex
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -37,14 +35,14 @@ Reading state information...
Local sources
─────────────
-r-bioc-biobase_2.12.2-1.dsc exists in .; copying to chroot
+r-bioc-biobase_2.14.0-1.dsc exists in .; copying to chroot
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-2I4rqF/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-ta3ZMk/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -56,19 +54,11 @@ 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 0 not upgraded.
-Need to get 0 B/716 B of archives.
-After this operation, 0 B of additional disk space will be used.
-Selecting previously deselected package sbuild-build-depends-core-dummy.
-(Reading database ... 10847 files and directories currently installed.)
-Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), r-base-dev
-Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), r-base-dev
-dpkg-deb: building package `sbuild-build-depends-r-bioc-biobase-dummy' in `/«BUILDDIR»/resolver-d9HHHw/apt_archive/sbuild-build-depends-r-bioc-biobase-dummy.deb'.
+sbuild-build-depends-core-dummy is already the newest version.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), r-base-dev (>= 2.10)
+Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), r-base-dev (>= 2.10)
+dpkg-deb: building package `sbuild-build-depends-r-bioc-biobase-dummy' in `/«BUILDDIR»/resolver-3Rn59f/apt_archive/sbuild-build-depends-r-bioc-biobase-dummy.deb'.
OK
Reading package lists...
@@ -81,286 +71,277 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils cdbs debhelper dpatch file fontconfig fontconfig-config gettext
- gettext-base gfortran gfortran-4.6 groff-base html2text intltool-debian
- libblas-dev libblas3gf libbz2-dev libcairo2 libcroco3 libdatrie1 libexpat1
- libfontconfig1 libfreetype6 libgfortran3 libglib2.0-0 libice6 libjpeg62
- libjpeg8 libjpeg8-dev liblapack-dev liblapack3gf libmagic1 libncurses5-dev
+ cdbs debhelper dpatch file fontconfig fontconfig-config gettext gettext-base
+ gfortran gfortran-4.6 groff-base html2text intltool-debian libblas-dev
+ libblas3gf libbz2-dev libcairo2 libcroco3 libdatrie1 libexpat1
+ libfontconfig1 libfreetype6 libgfortran3 libglib2.0-0 libice6 libjpeg8
+ libjpeg8-dev liblapack-dev liblapack3gf libmagic1 libncurses5-dev
libpango1.0-0 libpaper-utils libpaper1 libpcre3 libpcre3-dev libpcrecpp0
- libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libreadline-dev
- libreadline6-dev libsm6 libthai-data libthai0 libtiff4 libunistring0
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- libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 man-db po-debconf
- r-base-core r-base-dev tcl8.5 tk8.5 ttf-dejavu-core ucf unzip x11-common
- xdg-utils zip zlib1g-dev
+ libpipeline1 libpixman-1-0 libpng12-dev libreadline-dev libreadline6-dev
+ libsm6 libthai-data libthai0 libtiff4 libtinfo-dev libunistring0 libx11-6
+ libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
+ libxft2 libxml2 libxrender1 libxss1 libxt6 man-db po-debconf r-base-core
+ r-base-dev tcl8.5 tk8.5 ttf-dejavu-core ucf unzip x11-common xdg-utils zip
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make curl defoma gettext-doc
- gfortran-multilib gfortran-doc gfortran-4.6-multilib gfortran-4.6-doc
- libgfortran3-dbg groff ncurses-doc ttf-baekmuk ttf-arphic-gbsn00lp
- ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp less www-browser
- libmail-box-perl r-doc-info r-doc-pdf r-mathlib r-base-html tclreadline
- gvfs-bin
+ devscripts dh-make curl defoma gettext-doc gfortran-multilib gfortran-doc
+ gfortran-4.6-multilib gfortran-4.6-doc libgfortran3-dbg groff ncurses-doc
+ ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
+ ttf-arphic-bkai00mp less www-browser libmail-box-perl r-doc-info r-doc-pdf
+ r-mathlib r-base-html tclreadline gvfs-bin
Recommended packages:
autotools-dev patchutils autopoint libglib2.0-data shared-mime-info
x-ttcidfont-conf xml-core libmail-sendmail-perl r-recommended r-doc-html
xterm x-terminal-emulator libfile-mimeinfo-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper dpatch file fontconfig fontconfig-config gettext
- gettext-base gfortran gfortran-4.6 groff-base html2text intltool-debian
- libblas-dev libblas3gf libbz2-dev libcairo2 libcroco3 libdatrie1 libexpat1
- libfontconfig1 libfreetype6 libgfortran3 libglib2.0-0 libice6 libjpeg62
- libjpeg8 libjpeg8-dev liblapack-dev liblapack3gf libmagic1 libncurses5-dev
+ cdbs debhelper dpatch file fontconfig fontconfig-config gettext gettext-base
+ gfortran gfortran-4.6 groff-base html2text intltool-debian libblas-dev
+ libblas3gf libbz2-dev libcairo2 libcroco3 libdatrie1 libexpat1
+ libfontconfig1 libfreetype6 libgfortran3 libglib2.0-0 libice6 libjpeg8
+ libjpeg8-dev liblapack-dev liblapack3gf libmagic1 libncurses5-dev
libpango1.0-0 libpaper-utils libpaper1 libpcre3 libpcre3-dev libpcrecpp0
- libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libreadline-dev
- libreadline6-dev libsm6 libthai-data libthai0 libtiff4 libunistring0
- libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6
- libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 man-db po-debconf
- r-base-core r-base-dev sbuild-build-depends-r-bioc-biobase-dummy tcl8.5
- tk8.5 ttf-dejavu-core ucf unzip x11-common xdg-utils zip zlib1g-dev
+ libpipeline1 libpixman-1-0 libpng12-dev libreadline-dev libreadline6-dev
+ libsm6 libthai-data libthai0 libtiff4 libtinfo-dev libunistring0 libx11-6
+ libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
+ libxft2 libxml2 libxrender1 libxss1 libxt6 man-db po-debconf r-base-core
+ r-base-dev sbuild-build-depends-r-bioc-biobase-dummy tcl8.5 tk8.5
+ ttf-dejavu-core ucf unzip x11-common xdg-utils zip zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 77 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/53.4 MB of archives.
-After this operation, 132 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10847 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ...
-Selecting previously deselected package libdatrie1.
+0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/56.9 MB of archives.
+After this operation, 128 MB of additional disk space will be used.
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10887 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_amd64.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_amd64.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_amd64.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ...
+Selecting previously unselected package libdatrie1.
Unpacking libdatrie1 (from .../libdatrie1_0.2.4-3_amd64.deb) ...
-Selecting previously deselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7_amd64.deb) ...
-Selecting previously deselected package libfreetype6.
-Unpacking libfreetype6 (from .../libfreetype6_2.4.4-2_amd64.deb) ...
-Selecting previously deselected package ucf.
+Selecting previously unselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7.1_amd64.deb) ...
+Selecting previously unselected package libfreetype6.
+Unpacking libfreetype6 (from .../libfreetype6_2.4.7-2_amd64.deb) ...
+Selecting previously unselected package ucf.
Unpacking ucf (from .../ucf_3.0025+nmu2_all.deb) ...
Moving old data out of the way
-Selecting previously deselected package ttf-dejavu-core.
-Unpacking ttf-dejavu-core (from .../ttf-dejavu-core_2.33-1_all.deb) ...
-Selecting previously deselected package fontconfig-config.
+Selecting previously unselected package ttf-dejavu-core.
+Unpacking ttf-dejavu-core (from .../ttf-dejavu-core_2.33-2_all.deb) ...
+Selecting previously unselected package fontconfig-config.
Unpacking fontconfig-config (from .../fontconfig-config_2.8.0-3_all.deb) ...
-Selecting previously deselected package libfontconfig1.
+Selecting previously unselected package libfontconfig1.
Unpacking libfontconfig1 (from .../libfontconfig1_2.8.0-3_amd64.deb) ...
-Selecting previously deselected package libgfortran3.
-Unpacking libgfortran3 (from .../libgfortran3_4.6.1-5_amd64.deb) ...
-Selecting previously deselected package x11-common.
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+Unpacking libgfortran3 (from .../libgfortran3_4.6.2-3_amd64.deb) ...
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+Unpacking x11-common (from .../x11-common_1%3a7.6+9_all.deb) ...
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Unpacking libice6 (from .../libice6_2%3a1.0.7-2_amd64.deb) ...
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Unpacking libxau6 (from .../libxau6_1%3a1.0.6-3_amd64.deb) ...
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Unpacking libxdmcp6 (from .../libxdmcp6_1%3a1.1.0-3_amd64.deb) ...
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+Unpacking libx11-data (from .../libx11-data_2%3a1.4.4-2_all.deb) ...
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Unpacking libxcb-render0 (from .../libxcb-render0_1.7-3_amd64.deb) ...
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+Unpacking libpango1.0-0 (from .../libpango1.0-0_1.29.4-2_amd64.deb) ...
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Unpacking libsm6 (from .../libsm6_2%3a1.2.0-2_amd64.deb) ...
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Unpacking libxext6 (from .../libxext6_2%3a1.3.0-3_amd64.deb) ...
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Unpacking libxt6 (from .../libxt6_1%3a1.1.1-2_amd64.deb) ...
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+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ...
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Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
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Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
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+Unpacking dpatch (from .../archives/dpatch_2.0.33_all.deb) ...
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+Unpacking gfortran-4.6 (from .../gfortran-4.6_4.6.2-3_amd64.deb) ...
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+Unpacking gfortran (from .../gfortran_4%3a4.6.1-3_amd64.deb) ...
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+Unpacking libblas3gf (from .../libblas3gf_1.2.20110419-2_amd64.deb) ...
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+Unpacking libblas-dev (from .../libblas-dev_1.2.20110419-2_amd64.deb) ...
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+Unpacking libbz2-dev (from .../libbz2-dev_1.0.5-7_amd64.deb) ...
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Unpacking libjpeg8-dev (from .../libjpeg8-dev_8c-2_amd64.deb) ...
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+Unpacking liblapack3gf (from .../liblapack3gf_3.3.1-1_amd64.deb) ...
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+Unpacking liblapack-dev (from .../liblapack-dev_3.3.1-1_amd64.deb) ...
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Unpacking libpaper1 (from .../libpaper1_1.1.24+nmu1_amd64.deb) ...
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Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
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Unpacking libpng12-dev (from .../libpng12-dev_1.2.46-3_amd64.deb) ...
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+Unpacking libreadline6-dev (from .../libreadline6-dev_6.2-7_amd64.deb) ...
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+Unpacking libreadline-dev (from .../libreadline-dev_6.2-7_amd64.deb) ...
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Unpacking zip (from .../archives/zip_3.0-4_amd64.deb) ...
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Unpacking tk8.5 (from .../tk8.5_8.5.10-1_amd64.deb) ...
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+Selecting previously unselected package r-base-core.
+Unpacking r-base-core (from .../r-base-core_2.14.0-1_amd64.deb) ...
+Selecting previously unselected package r-base-dev.
+Unpacking r-base-dev (from .../r-base-dev_2.14.0-1_all.deb) ...
+Selecting previously unselected package sbuild-build-depends-r-bioc-biobase-dummy.
Unpacking sbuild-build-depends-r-bioc-biobase-dummy (from .../sbuild-build-depends-r-bioc-biobase-dummy.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpipeline1 (1.2.0-4) ...
+Setting up libpcre3 (8.12-4) ...
+Setting up libglib2.0-0 (2.28.8-1) ...
+No schema files found: doing nothing.
+Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libcroco3 (0.6.2-2) ...
Setting up libdatrie1 (0.2.4-3) ...
-Setting up libexpat1 (2.0.1-7) ...
-Setting up libfreetype6 (2.4.4-2) ...
+Setting up libexpat1 (2.0.1-7.1) ...
+Setting up libfreetype6 (2.4.7-2) ...
Setting up ucf (3.0025+nmu2) ...
-Setting up ttf-dejavu-core (2.33-1) ...
+Setting up ttf-dejavu-core (2.33-2) ...
Setting up fontconfig-config (2.8.0-3) ...
Setting up libfontconfig1 (2.8.0-3) ...
-Setting up libgfortran3 (4.6.1-5) ...
-Setting up x11-common (1:7.6+7) ...
+Setting up libgfortran3 (4.6.2-3) ...
+Setting up x11-common (1:7.6+9) ...
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6 (2:1.0.7-2) ...
-Setting up libpixman-1-0 (0.22.2-1) ...
-Setting up libpng12-0 (1.2.46-3) ...
+Setting up libpixman-1-0 (0.23.8-1) ...
Setting up libxau6 (1:1.0.6-3) ...
Setting up libxdmcp6 (1:1.1.0-3) ...
Setting up libxcb1 (1.7-3) ...
-Setting up libx11-data (2:1.4.4-1) ...
-Setting up libx11-6 (2:1.4.4-1) ...
+Setting up libx11-data (2:1.4.4-2) ...
+Setting up libx11-6 (2:1.4.4-2) ...
Setting up libxcb-render0 (1.7-3) ...
Setting up libxcb-shm0 (1.7-3) ...
Setting up libxrender1 (1:0.9.6-2) ...
Setting up libcairo2 (1.10.2-6.1) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
Setting up libthai-data (0.1.15-2) ...
Setting up libthai0 (0.1.15-2) ...
Setting up libxft2 (2.2.0-3) ...
Setting up fontconfig (2.8.0-3) ...
Cleaning up old fontconfig caches... done.
Regenerating fonts cache... done.
-Setting up libpango1.0-0 (1.28.4-2) ...
+Setting up libpango1.0-0 (1.29.4-2) ...
+Setting up libpcrecpp0 (8.12-4) ...
Setting up libsm6 (2:1.2.0-2) ...
+Setting up libjpeg8 (8c-2) ...
+Setting up libtiff4 (3.9.5-2) ...
+Setting up libunistring0 (0.9.3-5) ...
Setting up libxext6 (2:1.3.0-3) ...
+Setting up libxss1 (1:1.2.1-2) ...
Setting up libxt6 (1:1.1.1-2) ...
-Setting up bsdmainutils (8.2.3) ...
-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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up libmagic1 (5.09-2) ...
+Setting up file (5.09-2) ...
+Setting up gettext-base (0.18.1.1-5) ...
+Setting up cdbs (0.4.99) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.3) ...
-Setting up cdbs (0.4.96) ...
-Setting up dpatch (2.0.31) ...
-Setting up gfortran-4.6 (4.6.1-5) ...
-Setting up gfortran (4:4.6.1-2) ...
+Setting up debhelper (8.9.8) ...
+Setting up dpatch (2.0.33) ...
+Setting up gfortran-4.6 (4.6.2-3) ...
+Setting up gfortran (4:4.6.1-3) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode.
-Setting up libblas3gf (1.2-8) ...
+Setting up libblas3gf (1.2.20110419-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3gf to provide /usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode.
-Setting up libblas-dev (1.2-8) ...
+Setting up libblas-dev (1.2.20110419-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode.
-Setting up libbz2-dev (1.0.5-6) ...
-Setting up libjpeg62 (6b1-2) ...
-Setting up libjpeg8 (8c-2) ...
+Setting up libbz2-dev (1.0.5-7) ...
Setting up libjpeg8-dev (8c-2) ...
-Setting up liblapack3gf (3.3.0-4) ...
+Setting up liblapack3gf (3.3.1-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode.
-Setting up liblapack-dev (3.3.0-4) ...
+Setting up liblapack-dev (3.3.1-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode.
-Setting up libncurses5-dev (5.9-1) ...
+Setting up libtinfo-dev (5.9-3) ...
+Setting up libncurses5-dev (5.9-3) ...
Setting up libpaper1 (1.1.24+nmu1) ...
Creating config file /etc/papersize with new version
Setting up libpaper-utils (1.1.24+nmu1) ...
-Setting up libpcrecpp0 (8.12-3) ...
-Setting up libpcre3-dev (8.12-3) ...
+Setting up libpcre3-dev (8.12-4) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up libpng12-dev (1.2.46-3) ...
-Setting up libreadline6-dev (6.2-2) ...
-Setting up libreadline-dev (6.2-2) ...
-Setting up libtiff4 (3.9.5-1) ...
-Setting up libxss1 (1:1.2.1-1) ...
+Setting up libreadline6-dev (6.2-7) ...
+Setting up libreadline-dev (6.2-7) ...
Setting up zip (3.0-4) ...
Setting up unzip (6.0-5) ...
Setting up xdg-utils (1.1.0~rc1-2) ...
@@ -368,20 +349,20 @@ Setting up tcl8.5 (8.5.10-1) ...
update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode.
Setting up tk8.5 (8.5.10-1) ...
update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode.
-Setting up r-base-core (2.13.1-1) ...
+Setting up r-base-core (2.14.0-1) ...
Setting R_PAPERSIZE_USER default to 'a4'
Creating config file /etc/R/Renviron with new version
-Setting up r-base-dev (2.13.1-1) ...
+Setting up r-base-dev (2.14.0-1) ...
Setting up sbuild-build-depends-r-bioc-biobase-dummy (0.invalid.0) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.53.20110729-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-5 gcc-4.6_4.6.1-5 libc6-dev_2.13-13 libstdc++6_4.6.1-5 libstdc++6-4.6-dev_4.6.1-5 linux-libc-dev_3.0.0-1
-Package versions: apt_0.8.15.5 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110729-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-5 dash_0.5.5.1-7.4 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.3 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffutils_1:3.0-1 dpatch_2.0.31 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-2 g++-4.6_4.6.1-5 gcc_4:4.6.1-2 gcc-4.6_4.6.1-5 gcc-4.6-base_4.6.1-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran_4:4.6.1-2 gfortran-4.6_4.6.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblas-dev_1.2-8 libblas3gf_1.2-8 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-6 libbz2-dev_1.0.5-6 libc-bin_2.13-13 libc-dev-bin_2.13-13 libc6_2.13-13 libc6-dev_2.13-13 libcairo2_1.10.2-6.1 libclass-isa-perl_0.36-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdatrie1_0.2.4-3 libdb4.7_4.7.25-20 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.4-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-5 libgdbm3_1.8.3-10 libgfortran3_4.6.1-5 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-5 libice6_2:1.0.7-2 libjpeg62_6b1-2 libjpeg8_8c-2 libjpeg8-dev_8c-2 liblapack-dev_3.3.0-4 liblapack3gf_3.3.0-4 liblocale-gettext-perl_1.05-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-5 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpango1.0-0_1.28.4-2 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_8.12-3 libpcre3-dev_8.12-3 libpcrecpp0_8.12-3 libpipeline1_1.2.0-3 libpixman-1-0_0.22.2-1 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpod-plainer-perl_1.03-1 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-5 libreadline-dev_6.2-2 libreadline6_6.2-2 libreadline6-dev_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libsm6_2:1.2.0-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-5 libstdc++6-4.6-dev_4.6.1-5 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.15-2 libthai0_0.1.15-2 libtiff4_3.9.5-1 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-18 libuuid1_2.19.1-5 libx11-6_2:1.4.4-1 libx11-data_2:1.4.4-1 libxau6_1:1.0.6-3 libxcb-render0_1.7-3 libxcb-shm0_1.7-3 libxcb1_1.7-3 libxdmcp6_1:1.1.0-3 libxext6_2:1.3.0-3 libxft2_2.2.0-3 libxml2_2.7.8.dfsg-4 libxrender1_1:0.9.6-2 libxss1_1:1.2.1-1 libxt6_1:1.1.1-2 linux-libc-dev_3.0.0-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-13 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-2 perl-base_5.12.4-2 perl-modules_5.12.4-2 po-debconf_1.0.16+nmu1 r-base-core_2.13.1-1 r-base-dev_2.13.1-1 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-biobase-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tcl8.5_8.5.10-1 tk8.5_8.5.10-1 ttf-dejavu-core_2.33-1 tzdata_2011h-3 ucf_3.0025+nmu2 unzip_6.0-5 util-linux_2.19.1-5 x11-common_1:7.6+7 xdg-utils_1.1.0~rc1-2 xz-utils_5.0.0-2 zip_3.0-4 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.39-bpo.2-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 libc6-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 linux-libc-dev_3.0.0-5
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpatch_2.0.33 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gfortran_4:4.6.1-3 gfortran-4.6_4.6.2-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblas-dev_1.2.20110419-2 libblas3gf_1.2.20110419-2 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libbz2-dev_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcairo2_1.10.2-6.1 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdatrie1_0.2.4-3 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.1 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libgfortran3_4.6.2-3 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 libgpm2_1.20.4-4 libice6_2:1.0.7-2 libjpeg8_8c-2 libjpeg8-dev_8c-2 liblapack-dev_3.3.1-1 liblapack3gf_3.3.1-1 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-3 libncurses5-dev_5.9-3 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpango1.0-0_1.29.4-2 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_8.12-4 libpcre3-dev_8.12-4 libpcrecpp0_8.12-4 libpipeline1_1.2.0-4 libpixman-1-0_0.23.8-1 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-3 libreadline-dev_6.2-7 libreadline6_6.2-7 libreadline6-dev_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsm6_2:1.2.0-2 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.15-2 libthai0_0.1.15-2 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-3 libtinfo5_5.9-3 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libxau6_1:1.0.6-3 libxcb-render0_1.7-3 libxcb-shm0_1.7-3 libxcb1_1.7-3 libxdmcp6_1:1.1.0-3 libxext6_2:1.3.0-3 libxft2_2.2.0-3 libxml2_2.7.8.dfsg-5 libxrender1_1:0.9.6-2 libxss1_1:1.2.1-2 libxt6_1:1.1.1-2 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-3 ncurses-bin_5.9-3 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 r-base-core_2.14.0-1 r-base-dev_2.14.0-1 readline-common_6.2-7 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-biobase-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tcl8.5_8.5.10-1 tk8.5_8.5.10-1 ttf-dejavu-core_2.33-2 tzdata_2011n-1 ucf_3.0025+nmu2 unzip_6.0-5 util-linux_2.19.1-5 x11-common_1:7.6+9 xdg-utils_1.1.0~rc1-2 xz-utils_5.1.1alpha+20110809-3 zip_3.0-4 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -391,10 +372,10 @@ Package versions: apt_0.8.15.5 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (r-bioc-biobase_2.12.2-1.dsc)
-dpkg-source: info: extracting r-bioc-biobase in r-bioc-biobase-2.12.2
-dpkg-source: info: unpacking r-bioc-biobase_2.12.2.orig.tar.gz
-dpkg-source: info: applying r-bioc-biobase_2.12.2-1.diff.gz
+dpkg-source: warning: extracting unsigned source package (r-bioc-biobase_2.14.0-1.dsc)
+dpkg-source: info: extracting r-bioc-biobase in r-bioc-biobase-2.14.0
+dpkg-source: info: unpacking r-bioc-biobase_2.14.0.orig.tar.gz
+dpkg-source: info: applying r-bioc-biobase_2.14.0-1.diff.gz
Check disc space
────────────────
@@ -411,8 +392,8 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-6916a6a9-d5b0-46c0-a15e-58ff0d3a31c8
-SCHROOT_UID=1000
+SCHROOT_SESSION_ID=sid-amd64-sbuild-7fbe1793-6843-40a0-baa6-6a3229218014
+SCHROOT_UID=31051
SCHROOT_USER=charles
SHELL=/bin/sh
TERM=xterm
@@ -422,15 +403,10 @@ USERNAME=charles
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package r-bioc-biobase
-dpkg-buildpackage: source version 2.12.2-1
+dpkg-buildpackage: source version 2.14.0-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build r-bioc-biobase-2.12.2
+ dpkg-source --before-build r-bioc-biobase-2.14.0
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
/usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead
@@ -456,16 +432,17 @@ if test -d src; then \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
- dpkg-source -b r-bioc-biobase-2.12.2
+ dpkg-source -b r-bioc-biobase-2.14.0
dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1)
dpkg-source: info: using source format `1.0'
-dpkg-source: info: building r-bioc-biobase using existing r-bioc-biobase_2.12.2.orig.tar.gz
-dpkg-source: info: building r-bioc-biobase in r-bioc-biobase_2.12.2-1.diff.gz
-dpkg-source: info: building r-bioc-biobase in r-bioc-biobase_2.12.2-1.dsc
+dpkg-source: info: building r-bioc-biobase using existing r-bioc-biobase_2.14.0.orig.tar.gz
+dpkg-source: info: building r-bioc-biobase in r-bioc-biobase_2.14.0-1.diff.gz
+dpkg-source: info: building r-bioc-biobase in r-bioc-biobase_2.14.0-1.dsc
debian/rules build
/usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
/usr/share/cdbs/1/rules/simple-patchsys.mk:31: WARNING: simple-patchsys.mk is deprecated - please use source format 3.0 (quilt) instead
make[1]: Entering directory `/«PKGBUILDDIR»'
@@ -488,6 +465,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
dh_installdirs usr/lib/R/site-library
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
@@ -500,13 +478,13 @@ if test -f /usr/bin/xvfb-run; then \
* installing *source* package 'Biobase' ...
** libs
make[1]: Entering directory `/«PKGBUILDDIR»/src'
-gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c Rinit.c -o Rinit.o
-gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c anyMissing.c -o anyMissing.o
-gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c envir.c -o envir.o
-gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c matchpt.c -o matchpt.o
-gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c rowMedians.c -o rowMedians.o
-gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c sublist_extract.c -o sublist_extract.o
-gcc -shared -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib64/R/lib -lR
+gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c Rinit.c -o Rinit.o
+gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c anyMissing.c -o anyMissing.o
+gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c envir.c -o envir.o
+gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c matchpt.c -o matchpt.o
+gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c rowMedians.c -o rowMedians.o
+gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c sublist_extract.c -o sublist_extract.o
+gcc -std=gnu99 -shared -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory `/«PKGBUILDDIR»/src'
make[1]: Entering directory `/«PKGBUILDDIR»/src'
make[1]: Leaving directory `/«PKGBUILDDIR»/src'
@@ -518,6 +496,13 @@ installing to /«PKGBUILDDIR»/debian/r-bioc-biobase/usr/lib/R/site-library/Biob
** help
*** installing help indices
** building package indices ...
+*** tangling vignette sources ...
+ 'BiobaseDevelopment.Rnw'
+ 'Bioconductor.Rnw'
+ 'ExpressionSetIntroduction.Rnw'
+ 'HowTo.Rnw'
+ 'Qviews.Rnw'
+ 'esApply.Rnw'
** testing if installed package can be loaded
* DONE (Biobase)
@@ -531,7 +516,7 @@ if test -f debian/overrides; then \
fi
Adding cdbs dependencies to debian/r-bioc-biobase.substvars
dh_installdirs -pr-bioc-biobase
-echo "R:Depends=r-base-core (>= 2.13.1~)" >> debian/r-bioc-biobase.substvars
+echo "R:Depends=r-base-core (>= 2.14.0~)" >> debian/r-bioc-biobase.substvars
dh_installdocs -pr-bioc-biobase ./NEWS
dh_installexamples -pr-bioc-biobase
dh_installman -pr-bioc-biobase
@@ -562,14 +547,14 @@ dh_perl -pr-bioc-biobase
dh_shlibdeps -pr-bioc-biobase
dh_gencontrol -pr-bioc-biobase
dh_md5sums -pr-bioc-biobase
-dh_builddeb -pr-bioc-biobase
-dpkg-deb: building package `r-bioc-biobase' in `../r-bioc-biobase_2.12.2-1_amd64.deb'.
- dpkg-genchanges >../r-bioc-biobase_2.12.2-1_amd64.changes
+dh_builddeb -pr-bioc-biobase -- -Z xz
+dpkg-deb: building package `r-bioc-biobase' in `../r-bioc-biobase_2.14.0-1_amd64.deb'.
+ dpkg-genchanges >../r-bioc-biobase_2.14.0-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build r-bioc-biobase-2.12.2
+ dpkg-source --after-build r-bioc-biobase-2.14.0
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110804-0910
+Build finished at 20111102-1354
Finished
────────
@@ -581,15 +566,15 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-r-bioc-biobase_2.12.2-1_amd64.changes:
+r-bioc-biobase_2.14.0-1_amd64.changes:
──────────────────────────────────────
Format: 1.8
-Date: Thu, 04 Aug 2011 08:58:03 +0900
+Date: Wed, 02 Nov 2011 13:52:04 +0900
Source: r-bioc-biobase
Binary: r-bioc-biobase
Architecture: source amd64
-Version: 2.12.2-1
+Version: 2.14.0-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -597,43 +582,47 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
r-bioc-biobase - base functions for Bioconductor
Changes:
- r-bioc-biobase (2.12.2-1) unstable; urgency=low
+ r-bioc-biobase (2.14.0-1) unstable; urgency=low
.
- * New upstream release.
+ [cb6b786] Bioconductor release 2.9.
+ [d70e490] Build-Depend on R >= 2.10 according to DESCRIPTION.
+ [ae99e35] Include 7 digits of the commit id in the changelog entry.
+ [33b5d47] Compress binary package with xz.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-r-bioc-biobase_2.12.2-1_amd64.deb
+r-bioc-biobase_2.14.0-1_amd64.deb
─────────────────────────────────
new debian package, version 2.0.
- size 2667938 bytes: control archive= 4938 bytes.
- 1187 bytes, 25 lines control
+ size 2311488 bytes: control archive= 4959 bytes.
+ 1217 bytes, 26 lines control
13314 bytes, 141 lines md5sums
Package: r-bioc-biobase
- Version: 2.12.2-1
+ Version: 2.14.0-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3796
- Depends: libc6 (>= 2.3), r-base-core (>= 2.13.1~)
+ Installed-Size: 3068
+ Pre-Depends: dpkg (>= 1.15.6)
+ Depends: libc6 (>= 2.3), r-base-core (>= 2.14.0~)
Section: gnu-r
Priority: optional
Homepage: http://www.bioconductor.org
@@ -654,177 +643,177 @@ r-bioc-biobase_2.12.2-1_amd64.deb
unofficial auto-generated Bioconductor packages for Debian and Ubuntu systems,
that are prepared by members of the Debian Med team.
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--rw-r--r-- root/root 91 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/Code/R/get at PKGNAME@.R
--rw-r--r-- root/root 201 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/Code/DESCRIPTION
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--rw-r--r-- root/root 487 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/Code/man/@PKGNAME at .Rd
--rw-r--r-- root/root 350 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/Code/man/get at PKGNAME@.Rd
--rw-r--r-- root/root 3988 2011-08-04 09:09 ./usr/lib/R/site-library/Biobase/NEWS
--rw-r--r-- root/root 516 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/testClass.R
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--rw-r--r-- root/root 2008 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/scripts/makeExpressionSetPackage.R
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--rw-r--r-- root/root 109039 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/extdata/exprsData.txt
--rw-r--r-- root/root 715 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/extdata/pData.txt
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--rw-r--r-- root/root 363959 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/R/Biobase.rdb
--rw-r--r-- root/root 8701 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/R/Biobase.rdx
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--rw-r--r-- root/root 212 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/ExpressionSet/DESCRIPTION
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--rw-r--r-- root/root 180 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/ExpressionSet/man/@PKGNAME at .Rd
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--rw-r--r-- root/root 5637 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/Meta/Rd.rds
--rw-r--r-- root/root 1027 2011-08-04 09:09 ./usr/lib/R/site-library/Biobase/Meta/package.rds
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--rw-r--r-- root/root 1359 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/Meta/nsInfo.rds
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--rw-r--r-- root/root 22056 2011-08-04 09:10 ./usr/lib/R/site-library/Biobase/libs/Biobase.so
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+-rw-r--r-- root/root 76485 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/VersionedClass_data/devel/bbsym.rda
+-rw-r--r-- root/root 183 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/VersionedClass_data/devel/VersionedBiobase.Rda
+-rw-r--r-- root/root 25005 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/VersionedClass_data/devel/sample.eSet.rda
+-rw-r--r-- root/root 1235 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/VersionedClass_data/devel/SnpSet.Rda
+-rw-r--r-- root/root 2096 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/esApply_test.R
+-rw-r--r-- root/root 8167 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/UpdateObject_test.R
+-rw-r--r-- root/root 477 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/runalltests.R
+-rw-r--r-- root/root 318 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/Makefile
+-rw-r--r-- root/root 6194 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/ExpressionSet_test.R
+-rw-r--r-- root/root 403 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/copyEnv_test.R
+-rw-r--r-- root/root 5015 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/VersionedClass_test.R
+-rw-r--r-- root/root 1907 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/subListExtract_test.R
+-rwxr-xr-x root/root 39 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/runall.sh
+-rw-r--r-- root/root 1257 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/utilities.R
+-rw-r--r-- root/root 8317 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/NChannelSet_test.R
+-rw-r--r-- root/root 10497 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/AnnotatedDataFrame_test.R
+-rwxr-xr-x root/root 213 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/runfile.sh
+-rw-r--r-- root/root 1515 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/matrix_test.R
+-rw-r--r-- root/root 2035 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/AssayData_test.R
+-rw-r--r-- root/root 629 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/DataClasses_test.R
+-rw-r--r-- root/root 180 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/checkClass_test.R
+-rw-r--r-- root/root 2040 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/unsaveSetSlot_test.R
+-rw-r--r-- root/root 4598 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/data.frame_test.R
+-rw-r--r-- root/root 951 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/cache_test.R
+-rw-r--r-- root/root 580 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/SnpSet_test.R
+-rw-r--r-- root/root 20153 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/EsetSubclasses_test.R
+-rw-r--r-- root/root 2522 2011-11-02 13:54 ./usr/lib/R/site-library/Biobase/UnitTests/combine_test.R
+drwxr-xr-x root/root 0 2011-11-02 13:54 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-02 13:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-02 13:54 ./usr/share/doc/r-bioc-biobase/
+-rw-r--r-- root/root 1380 2011-11-01 08:32 ./usr/share/doc/r-bioc-biobase/NEWS.gz
+-rw-r--r-- root/root 10574 2011-11-02 13:54 ./usr/share/doc/r-bioc-biobase/copyright
+-rw-r--r-- root/root 380 2011-11-02 13:54 ./usr/share/doc/r-bioc-biobase/changelog.Debian.gz
+-rw-r--r-- root/root 392 2011-11-02 13:54 ./usr/share/doc/r-bioc-biobase/README.Debian
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -835,8 +824,8 @@ drwxr-xr-x root/root 0 2011-08-04 09:10 ./usr/share/doc/r-bioc-biobase/
lintian
───────
-W: r-bioc-biobase source: unused-build-dependency-on-cdbs
I: r-bioc-biobase source: missing-debian-source-format
+P: r-bioc-biobase source: unversioned-copyright-format-uri http://dep.debian.net/deps/dep5/
P: r-bioc-biobase: no-upstream-changelog
I: Lintian run was successful.
@@ -854,31 +843,26 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- bsdmainutils* cdbs* debhelper* dpatch* file* fontconfig* fontconfig-config*
- gettext* gettext-base* gfortran* gfortran-4.6* groff-base* html2text*
+ cdbs* debhelper* dpatch* file* fontconfig* fontconfig-config* gettext*
+ gettext-base* gfortran* gfortran-4.6* groff-base* html2text*
intltool-debian* libblas-dev* libblas3gf* libbz2-dev* libcairo2* libcroco3*
libdatrie1* libexpat1* libfontconfig1* libfreetype6* libgfortran3*
- libglib2.0-0* libice6* libjpeg62* libjpeg8* libjpeg8-dev* liblapack-dev*
- liblapack3gf* libmagic1* libncurses5-dev* libpango1.0-0* libpaper-utils*
- libpaper1* libpcre3* libpcre3-dev* libpcrecpp0* libpipeline1* libpixman-1-0*
- libpng12-0* libpng12-dev* libreadline-dev* libreadline6-dev* libsm6*
- libthai-data* libthai0* libtiff4* libunistring0* libx11-6* libx11-data*
+ libglib2.0-0* libice6* libjpeg8* libjpeg8-dev* liblapack-dev* liblapack3gf*
+ libmagic1* libncurses5-dev* libpango1.0-0* libpaper-utils* libpaper1*
+ libpcre3* libpcre3-dev* libpcrecpp0* libpipeline1* libpixman-1-0*
+ libpng12-dev* libreadline-dev* libreadline6-dev* libsm6* libthai-data*
+ libthai0* libtiff4* libtinfo-dev* libunistring0* libx11-6* libx11-data*
libxau6* libxcb-render0* libxcb-shm0* libxcb1* libxdmcp6* libxext6* libxft2*
libxml2* libxrender1* libxss1* libxt6* man-db* po-debconf* r-base-core*
- r-base-dev* sbuild-build-depends-core-dummy*
- sbuild-build-depends-r-bioc-biobase-dummy* tcl8.5* tk8.5* ttf-dejavu-core*
- ucf* unzip* x11-common* xdg-utils* zip* zlib1g-dev*
-0 upgraded, 0 newly installed, 78 to remove and 0 not upgraded.
-After this operation, 132 MB disk space will be freed.
-(Reading database ... 14802 files and directories currently installed.)
+ r-base-dev* sbuild-build-depends-r-bioc-biobase-dummy* tcl8.5* tk8.5*
+ ttf-dejavu-core* ucf* unzip* x11-common* xdg-utils* zip* zlib1g-dev*
+0 upgraded, 0 newly installed, 75 to remove and 0 not upgraded.
+After this operation, 128 MB disk space will be freed.
+(Reading database ... 14781 files and directories currently installed.)
Removing sbuild-build-depends-r-bioc-biobase-dummy ...
Removing r-base-dev ...
Removing cdbs ...
Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
Removing dpatch ...
Purging configuration files for dpatch ...
Removing file ...
@@ -904,6 +888,8 @@ Removing gettext ...
Removing gettext-base ...
Removing gfortran ...
Removing gfortran-4.6 ...
+Removing man-db ...
+Purging configuration files for man-db ...
Removing groff-base ...
Purging configuration files for groff-base ...
Removing html2text ...
@@ -937,13 +923,10 @@ Removing libice6 ...
Purging configuration files for libice6 ...
Removing libtiff4 ...
Purging configuration files for libtiff4 ...
-Removing libjpeg62 ...
Removing libjpeg8-dev ...
Removing libjpeg8 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
-Removing libreadline-dev ...
-Removing libreadline6-dev ...
Removing libncurses5-dev ...
Removing libpaper-utils ...
Removing libpaper1 ...
@@ -958,9 +941,10 @@ Purging configuration files for libpipeline1 ...
Removing libpixman-1-0 ...
Purging configuration files for libpixman-1-0 ...
Removing libpng12-dev ...
-Removing libpng12-0 ...
-Purging configuration files for libpng12-0 ...
+Removing libreadline-dev ...
+Removing libreadline6-dev ...
Removing libthai-data ...
+Removing libtinfo-dev ...
Removing libunistring0 ...
Purging configuration files for libunistring0 ...
Removing libxss1 ...
@@ -984,7 +968,6 @@ Removing libxdmcp6 ...
Purging configuration files for libxdmcp6 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
-Removing sbuild-build-depends-core-dummy ...
Removing tcl8.5 ...
Purging configuration files for tcl8.5 ...
Removing ttf-dejavu-core ...
@@ -1005,18 +988,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 12272
-Build-Time: 19
+Build-Space: 10888
+Build-Time: 11
Distribution: unstable
-Install-Time: 22
-Job: r-bioc-biobase_2.12.2-1.dsc
+Install-Time: 89
+Job: r-bioc-biobase_2.14.0-1.dsc
Lintian: pass
Package: r-bioc-biobase
-Package-Time: 44
-Source-Version: 2.12.2-1
-Space: 12272
+Package-Time: 104
+Source-Version: 2.14.0-1
+Space: 10888
Status: successful
-Version: 2.12.2-1
+Version: 2.14.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110804-0910
-Build needed 00:00:44, 12272k disc space
+Finished at 20111102-1354
+Build needed 00:01:44, 10888k disc space
diff --git a/dsc b/dsc
index 94cd2af..5f66f3e 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 1.0
Source: r-bioc-biobase
Binary: r-bioc-biobase
Architecture: any
-Version: 2.12.2-1
+Version: 2.14.0-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>
Dm-Upload-Allowed: yes
@@ -13,31 +13,33 @@ Homepage: http://www.bioconductor.org
Standards-Version: 3.9.2
Vcs-Browser: http://git.debian.org/?p=debian-med/r-bioc-biobase.git
Vcs-Git: git://git.debian.org/git/debian-med/r-bioc-biobase.git
-Build-Depends: cdbs, debhelper (>= 8), r-base-dev
+Build-Depends: cdbs, debhelper (>= 8), r-base-dev (>= 2.10)
+Package-List:
+ r-bioc-biobase deb gnu-r optional
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- e4e05aeb8ca8959374106a799f2ce1a983778978 5417 r-bioc-biobase_2.12.2-1.diff.gz
+ f05d4a790530a559b30ca2e932526ac65cdcdcdd 1926376 r-bioc-biobase_2.14.0.orig.tar.gz
+ e8fb421e517d96d48d08df80a1687a524601bd50 5645 r-bioc-biobase_2.14.0-1.diff.gz
Checksums-Sha256:
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- ab1f805e3261f9f2e8788a9630b85d3e 5417 r-bioc-biobase_2.12.2-1.diff.gz
+ e62df79e3f94d0e0544214ba49dc7030 1926376 r-bioc-biobase_2.14.0.orig.tar.gz
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--
base functions for Bioconductor
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